Mercurial > repos > charles_s_test > seqsero2
view logtest @ 3:38ad1130d077 draft
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
| author | charles_s_test |
|---|---|
| date | Mon, 27 Nov 2017 11:21:07 -0500 |
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| children |
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Last login: Sat Nov 18 08:47:03 on ttys003 CFM5081985:GalaxySeqsero charles.strittmatter$ pwd /Users/charles.strittmatter/galaxy/galaxy/tools/GalaxySeqsero CFM5081985:GalaxySeqsero charles.strittmatter$ cd / CFM5081985:/ charles.strittmatter$ ls Applications Users dev net tmp Library Volumes etc opt usr Network bin home private var System cores installer.failurerequests sbin CFM5081985:/ charles.strittmatter$ pwd / CFM5081985:/ charles.strittmatter$ mkdir galaxy mkdir: galaxy: Permission denied CFM5081985:/ charles.strittmatter$ mkdir -f galaxy mkdir: illegal option -- f usage: mkdir [-pv] [-m mode] directory ... CFM5081985:/ charles.strittmatter$ ls Applications Users dev installer.failurerequests sbin Library Volumes etc net tmp Network bin galaxy opt usr System cores home private var CFM5081985:/ charles.strittmatter$ pwd / CFM5081985:/ charles.strittmatter$ ls -la total 69 drwxr-xr-x 31 root wheel 1122 Nov 18 13:33 . drwxr-xr-x 31 root wheel 1122 Nov 18 13:33 .. -rw-rw-r-- 1 root admin 8196 Nov 18 13:33 .DS_Store d--x--x--x 9 root wheel 306 Nov 16 13:10 .DocumentRevisions-V100 drwx------ 5 root wheel 170 Oct 23 16:54 .Spotlight-V100 d-wx-wx-wt 2 root wheel 68 Oct 23 16:39 .Trashes ---------- 1 root admin 0 Feb 25 2016 .file drwx------ 19 root wheel 646 Nov 18 09:21 .fseventsd drwxr-xr-x@ 2 root wheel 68 Aug 1 2015 .vol drwxrwxr-x+ 54 root admin 1836 Nov 14 09:27 Applications drwxr-xr-x+ 65 root wheel 2210 Oct 26 12:32 Library drwxr-xr-x@ 2 root wheel 68 Feb 11 2016 Network drwxr-xr-x@ 4 root wheel 136 Nov 16 13:05 System drwxr-xr-x 8 root admin 272 Oct 25 14:44 Users drwxrwxrwt@ 3 root admin 102 Nov 17 16:51 Volumes drwxr-xr-x@ 39 root wheel 1326 Nov 16 13:05 bin drwxrwxr-t@ 2 root admin 68 Feb 11 2016 cores dr-xr-xr-x 3 root wheel 4214 Nov 16 13:10 dev lrwxr-xr-x@ 1 root wheel 11 Oct 23 16:48 etc -> private/etc drwxr-xr-x 2 charles.strittmatter wheel 68 Nov 18 13:33 galaxy dr-xr-xr-x 2 root wheel 1 Nov 16 13:10 home -rw-r--r--@ 1 root wheel 313 Aug 2 2015 installer.failurerequests dr-xr-xr-x 2 root wheel 1 Nov 16 13:10 net drwxr-xr-x 3 root wheel 102 Mar 12 2014 opt drwxr-xr-x@ 6 root wheel 204 Oct 23 16:50 private drwxr-xr-x@ 59 root wheel 2006 Nov 16 13:05 sbin lrwxr-xr-x@ 1 root wheel 11 Oct 23 16:48 tmp -> private/tmp drwxr-xr-x@ 13 root wheel 442 Oct 26 12:32 usr lrwxr-xr-x@ 1 root wheel 11 Oct 23 16:48 var -> private/var CFM5081985:/ charles.strittmatter$ cd / CFM5081985:/ charles.strittmatter$ ls Applications Users dev home private var Library Volumes etc installer.failurerequests sbin Network bin galaxy net tmp System cores gtmep opt usr CFM5081985:/ charles.strittmatter$ cd galaxy/ CFM5081985:galaxy charles.strittmatter$ ls CITATION SECURITY_POLICY.md display_applications manage_db.sh run_tests.sh test-data CODE_OF_CONDUCT.md client doc manage_tools.sh run_tool_shed.sh tool-data CONTRIBUTING.md config external_service_types openid scripts tool_list.py CONTRIBUTORS.md contrib extract_dataset_parts.sh requirements.txt setup.cfg tools LICENSE.txt create_db.sh integrated_tool_panel.xml rolling_restart.sh static tox.ini Makefile cron lib run.sh templates README.rst database locale run_reports.sh test CFM5081985:galaxy charles.strittmatter$ cd tools CFM5081985:tools charles.strittmatter$ pwd /galaxy/tools CFM5081985:tools charles.strittmatter$ ls data_source filters meme ngs_simulation solid_tools stats evolution genomespace metag_tools phenotype_association sr_assembly visualization extract maf next_gen_conversion plotting sr_mapping CFM5081985:tools charles.strittmatter$ pwd /galaxy/tools CFM5081985:tools charles.strittmatter$ pwd /galaxy/tools CFM5081985:tools charles.strittmatter$ ls -la total 0 drwxr-xr-x 21 charles.strittmatter wheel 714 Nov 18 14:21 . drwxr-xr-x 49 charles.strittmatter wheel 1666 Nov 18 14:27 .. drwxr-xr-x 27 charles.strittmatter wheel 918 Nov 18 14:21 GalaxySeqsero drwxr-xr-x 39 charles.strittmatter wheel 1326 Nov 18 14:01 data_source drwxr-xr-x 7 charles.strittmatter wheel 238 Nov 18 14:01 evolution drwxr-xr-x 6 charles.strittmatter wheel 204 Nov 18 14:01 extract drwxr-xr-x 79 charles.strittmatter wheel 2686 Nov 18 14:01 filters drwxr-xr-x 8 charles.strittmatter wheel 272 Nov 18 14:01 genomespace drwxr-xr-x 35 charles.strittmatter wheel 1190 Nov 18 14:01 maf drwxr-xr-x 5 charles.strittmatter wheel 170 Nov 18 14:01 meme drwxr-xr-x 8 charles.strittmatter wheel 272 Nov 18 14:01 metag_tools drwxr-xr-x 11 charles.strittmatter wheel 374 Nov 18 14:01 next_gen_conversion drwxr-xr-x 4 charles.strittmatter wheel 136 Nov 18 14:01 ngs_simulation drwxr-xr-x 27 charles.strittmatter wheel 918 Nov 18 14:01 phenotype_association drwxr-xr-x 5 charles.strittmatter wheel 170 Nov 18 14:01 plotting drwxr-xr-x 9 charles.strittmatter wheel 306 Nov 18 14:01 solid_tools drwxr-xr-x 6 charles.strittmatter wheel 204 Nov 18 14:01 sr_assembly drwxr-xr-x 9 charles.strittmatter wheel 306 Nov 18 14:01 sr_mapping drwxr-xr-x 12 charles.strittmatter wheel 408 Nov 18 14:01 stats drwxr-xr-x 10 charles.strittmatter wheel 340 Nov 18 14:20 testdep drwxr-xr-x 5 charles.strittmatter wheel 170 Nov 18 14:01 visualization CFM5081985:tools charles.strittmatter$ pwd /galaxy/tools CFM5081985:tools charles.strittmatter$ ls GalaxySeqsero extract maf next_gen_conversion plotting sr_mapping visualization data_source filters meme ngs_simulation solid_tools stats evolution genomespace metag_tools phenotype_association sr_assembly testdep CFM5081985:tools charles.strittmatter$ cd .. CFM5081985:galaxy charles.strittmatter$ ls CITATION SECURITY_POLICY.md display_applications manage_db.sh run_tests.sh test-data CODE_OF_CONDUCT.md client doc manage_tools.sh run_tool_shed.sh tool-data CONTRIBUTING.md config external_service_types openid scripts tool_list.py CONTRIBUTORS.md contrib extract_dataset_parts.sh requirements.txt setup.cfg tools LICENSE.txt create_db.sh integrated_tool_panel.xml rolling_restart.sh static tox.ini Makefile cron lib run.sh templates README.rst database locale run_reports.sh test CFM5081985:galaxy charles.strittmatter$ pwd /galaxy CFM5081985:galaxy charles.strittmatter$ cd .. CFM5081985:/ charles.strittmatter$ ls Applications Users dev home private var Library Volumes etc installer.failurerequests sbin Network bin galaxy net tmp System cores gtmep opt usr CFM5081985:/ charles.strittmatter$ pwd / CFM5081985:/ charles.strittmatter$ ls Applications Users dev home private var Library Volumes etc installer.failurerequests sbin Network bin galaxy net tmp System cores gtmep opt usr CFM5081985:/ charles.strittmatter$ pwd / CFM5081985:/ charles.strittmatter$ cd galaxy/ CFM5081985:galaxy charles.strittmatter$ ls CITATION SECURITY_POLICY.md display_applications manage_db.sh run_tests.sh test-data CODE_OF_CONDUCT.md client doc manage_tools.sh run_tool_shed.sh tool-data CONTRIBUTING.md config external_service_types openid scripts tool_list.py CONTRIBUTORS.md contrib extract_dataset_parts.sh requirements.txt setup.cfg tools LICENSE.txt create_db.sh integrated_tool_panel.xml rolling_restart.sh static tox.ini Makefile cron lib run.sh templates README.rst database locale run_reports.sh test CFM5081985:galaxy charles.strittmatter$ cd .. CFM5081985:/ charles.strittmatter$ ls Applications Users dev home private var Library Volumes etc installer.failurerequests sbin Network bin galaxy net tmp System cores gtmep opt usr CFM5081985:/ charles.strittmatter$ pwd / CFM5081985:/ charles.strittmatter$ ls Applications Users dev home private var Library Volumes etc installer.failurerequests sbin Network bin galaxy net tmp System cores gtmep opt usr CFM5081985:/ charles.strittmatter$ ls -la total 69 drwxr-xr-x 32 root wheel 1156 Nov 18 14:04 . drwxr-xr-x 32 root wheel 1156 Nov 18 14:04 .. -rw-rw-r-- 1 root admin 10244 Nov 18 14:12 .DS_Store d--x--x--x 9 root wheel 306 Nov 16 13:10 .DocumentRevisions-V100 drwx------ 5 root wheel 170 Oct 23 16:54 .Spotlight-V100 d-wx-wx-wt 2 root wheel 68 Oct 23 16:39 .Trashes ---------- 1 root admin 0 Feb 25 2016 .file drwx------ 56 root wheel 1904 Nov 18 14:11 .fseventsd drwxr-xr-x@ 2 root wheel 68 Aug 1 2015 .vol drwxrwxr-x+ 54 root admin 1836 Nov 14 09:27 Applications drwxr-xr-x+ 65 root wheel 2210 Oct 26 12:32 Library drwxr-xr-x@ 2 root wheel 68 Feb 11 2016 Network drwxr-xr-x@ 4 root wheel 136 Nov 16 13:05 System drwxr-xr-x 8 root admin 272 Oct 25 14:44 Users drwxrwxrwt@ 3 root admin 102 Nov 17 16:51 Volumes drwxr-xr-x@ 39 root wheel 1326 Nov 16 13:05 bin drwxrwxr-t@ 2 root admin 68 Feb 11 2016 cores dr-xr-xr-x 3 root wheel 4214 Nov 16 13:10 dev lrwxr-xr-x@ 1 root wheel 11 Oct 23 16:48 etc -> private/etc drwxr-xr-x 49 charles.strittmatter wheel 1666 Nov 18 14:27 galaxy drwxr-xr-x 3 charles.strittmatter wheel 102 Nov 18 14:04 gtmep dr-xr-xr-x 2 root wheel 1 Nov 16 13:10 home -rw-r--r--@ 1 root wheel 313 Aug 2 2015 installer.failurerequests dr-xr-xr-x 2 root wheel 1 Nov 16 13:10 net drwxr-xr-x 3 root wheel 102 Mar 12 2014 opt drwxr-xr-x@ 6 root wheel 204 Oct 23 16:50 private drwxr-xr-x@ 59 root wheel 2006 Nov 16 13:05 sbin lrwxr-xr-x@ 1 root wheel 11 Oct 23 16:48 tmp -> private/tmp drwxr-xr-x@ 13 root wheel 442 Oct 26 12:32 usr lrwxr-xr-x@ 1 root wheel 11 Oct 23 16:48 var -> private/var CFM5081985:/ charles.strittmatter$ rm -rf galaxy/ rm: galaxy/: Permission denied CFM5081985:/ charles.strittmatter$ ll -bash: ll: command not found CFM5081985:/ charles.strittmatter$ ls Applications Users dev home private var Library Volumes etc installer.failurerequests sbin Network bin galaxy net tmp System cores gtmep opt usr CFM5081985:/ charles.strittmatter$ pwd / CFM5081985:/ charles.strittmatter$ cd ls -bash: cd: ls: No such file or directory CFM5081985:/ charles.strittmatter$ ls Applications Users dev home private var Library Volumes etc installer.failurerequests sbin Network bin galaxy net tmp System cores gtmep opt usr CFM5081985:/ charles.strittmatter$ pwd / CFM5081985:/ charles.strittmatter$ cd galaxy/ CFM5081985:galaxy charles.strittmatter$ ls CFM5081985:galaxy charles.strittmatter$ pwd /galaxy CFM5081985:galaxy charles.strittmatter$ cd .. CFM5081985:/ charles.strittmatter$ ls Applications Users dev home private var Library Volumes etc installer.failurerequests sbin Network bin galaxy net tmp System cores gtmep opt usr CFM5081985:/ charles.strittmatter$ pwd / CFM5081985:/ charles.strittmatter$ ls -la total 69 drwxr-xr-x 32 root wheel 1156 Nov 18 14:04 . drwxr-xr-x 32 root wheel 1156 Nov 18 14:04 .. -rw-rw-r-- 1 root admin 10244 Nov 18 14:35 .DS_Store d--x--x--x 9 root wheel 306 Nov 16 13:10 .DocumentRevisions-V100 drwx------ 5 root wheel 170 Oct 23 16:54 .Spotlight-V100 d-wx-wx-wt 2 root wheel 68 Oct 23 16:39 .Trashes ---------- 1 root admin 0 Feb 25 2016 .file drwx------ 62 root wheel 2108 Nov 18 14:34 .fseventsd drwxr-xr-x@ 2 root wheel 68 Aug 1 2015 .vol drwxrwxr-x+ 54 root admin 1836 Nov 14 09:27 Applications drwxr-xr-x+ 65 root wheel 2210 Oct 26 12:32 Library drwxr-xr-x@ 2 root wheel 68 Feb 11 2016 Network drwxr-xr-x@ 4 root wheel 136 Nov 16 13:05 System drwxr-xr-x 8 root admin 272 Oct 25 14:44 Users drwxrwxrwt@ 3 root admin 102 Nov 17 16:51 Volumes drwxr-xr-x@ 39 root wheel 1326 Nov 16 13:05 bin drwxrwxr-t@ 2 root admin 68 Feb 11 2016 cores dr-xr-xr-x 3 root wheel 4214 Nov 16 13:10 dev lrwxr-xr-x@ 1 root wheel 11 Oct 23 16:48 etc -> private/etc drwxr-xr-x 2 charles.strittmatter wheel 68 Nov 18 14:34 galaxy drwxr-xr-x 3 charles.strittmatter wheel 102 Nov 18 14:04 gtmep dr-xr-xr-x 2 root wheel 1 Nov 16 13:10 home -rw-r--r--@ 1 root wheel 313 Aug 2 2015 installer.failurerequests dr-xr-xr-x 2 root wheel 1 Nov 16 13:10 net drwxr-xr-x 3 root wheel 102 Mar 12 2014 opt drwxr-xr-x@ 6 root wheel 204 Oct 23 16:50 private drwxr-xr-x@ 59 root wheel 2006 Nov 16 13:05 sbin lrwxr-xr-x@ 1 root wheel 11 Oct 23 16:48 tmp -> private/tmp drwxr-xr-x@ 13 root wheel 442 Oct 26 12:32 usr lrwxr-xr-x@ 1 root wheel 11 Oct 23 16:48 var -> private/var CFM5081985:/ charles.strittmatter$ cd galaxy/ CFM5081985:galaxy charles.strittmatter$ ls CFM5081985:galaxy charles.strittmatter$ git clone -b release_17.09 https://github.com/galaxyproject/galaxy.git Cloning into 'galaxy'... remote: Counting objects: 311967, done. remote: Compressing objects: 100% (15/15), done. remote: Total 311967 (delta 4), reused 6 (delta 3), pack-reused 311949 Receiving objects: 100% (311967/311967), 370.93 MiB | 6.25 MiB/s, done. Resolving deltas: 100% (249070/249070), done. Checking out files: 100% (4625/4625), done. CFM5081985:galaxy charles.strittmatter$ ls galaxy CFM5081985:galaxy charles.strittmatter$ pwd /galaxy CFM5081985:galaxy charles.strittmatter$ CFM5081985:galaxy charles.strittmatter$ ls galaxy CFM5081985:galaxy charles.strittmatter$ pwd /galaxy CFM5081985:galaxy charles.strittmatter$ cd .. CFM5081985:/ charles.strittmatter$ ls Applications Users dev installer.failurerequests sbin Library Volumes etc net tmp Network bin galaxydir opt usr System cores home private var CFM5081985:/ charles.strittmatter$ pwd / CFM5081985:/ charles.strittmatter$ cd galaxydir/ CFM5081985:galaxydir charles.strittmatter$ ls galaxy CFM5081985:galaxydir charles.strittmatter$ cd galaxy/ CFM5081985:galaxy charles.strittmatter$ ls CITATION SECURITY_POLICY.md display_applications manage_tools.sh run_tool_shed.sh tool-data CODE_OF_CONDUCT.md client doc openid scripts tool_list.py CONTRIBUTING.md config external_service_types requirements.txt setup.cfg tools CONTRIBUTORS.md contrib extract_dataset_parts.sh rolling_restart.sh static tox.ini LICENSE.txt create_db.sh lib run.sh templates Makefile cron locale run_reports.sh test README.rst database manage_db.sh run_tests.sh test-data CFM5081985:galaxy charles.strittmatter$ sh run.sh Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample Initializing static/welcome.html from welcome.html.sample Running virtualenv with interpreter /usr/bin/python2.7 New python executable in .venv/bin/python Installing setuptools, pip, wheel...done. Activating virtualenv at .venv Collecting pip>=8.1 Using cached pip-9.0.1-py2.py3-none-any.whl Installing collected packages: pip Found existing installation: pip 7.1.2 Uninstalling pip-7.1.2: Successfully uninstalled pip-7.1.2 Successfully installed pip-9.0.1 Collecting bx-python==0.7.3 (from -r requirements.txt (line 2)) Downloading https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27m-macosx_10_6_intel.whl (1.2MB) 100% |████████████████████████████████| 1.2MB 6.9MB/s Collecting MarkupSafe==0.23 (from -r requirements.txt (line 3)) Downloading https://wheels.galaxyproject.org/packages/MarkupSafe-0.23-cp27-cp27m-macosx_10_6_intel.whl Collecting PyYAML==3.11 (from -r requirements.txt (line 4)) Downloading https://wheels.galaxyproject.org/packages/PyYAML-3.11-cp27-cp27m-macosx_10_6_intel.whl (192kB) 100% |████████████████████████████████| 194kB 6.8MB/s Collecting SQLAlchemy==1.0.15 (from -r requirements.txt (line 5)) Downloading https://wheels.galaxyproject.org/packages/SQLAlchemy-1.0.15-cp27-cp27m-macosx_10_6_intel.whl (987kB) 100% |████████████████████████████████| 993kB 7.9MB/s Collecting mercurial==3.7.3 (from -r requirements.txt (line 6)) Downloading https://wheels.galaxyproject.org/packages/mercurial-3.7.3-cp27-cp27m-macosx_10_6_intel.whl (1.4MB) 100% |████████████████████████████████| 1.4MB 6.5MB/s Collecting numpy==1.9.2 (from -r requirements.txt (line 7)) Downloading https://wheels.galaxyproject.org/packages/numpy-1.9.2-cp27-cp27m-macosx_10_6_intel.whl (3.7MB) 100% |████████████████████████████████| 3.7MB 7.1MB/s Collecting pycrypto==2.6.1 (from -r requirements.txt (line 8)) Downloading https://wheels.galaxyproject.org/packages/pycrypto-2.6.1-cp27-cp27m-macosx_10_6_intel.whl (534kB) 100% |████████████████████████████████| 542kB 8.7MB/s Collecting uWSGI==2.0.15 (from -r requirements.txt (line 9)) Downloading https://wheels.galaxyproject.org/packages/uWSGI-2.0.15-cp27-cp27m-macosx_10_6_intel.whl (418kB) 100% |████████████████████████████████| 419kB 8.8MB/s Collecting bz2file==0.98 (from -r requirements.txt (line 16)) Downloading https://wheels.galaxyproject.org/packages/bz2file-0.98-py2-none-any.whl Collecting ipaddress==1.0.18 (from -r requirements.txt (line 17)) Downloading https://wheels.galaxyproject.org/packages/ipaddress-1.0.18-py2-none-any.whl Collecting Paste==2.0.2 (from -r requirements.txt (line 18)) Downloading https://wheels.galaxyproject.org/packages/Paste-2.0.2-py2-none-any.whl (610kB) 100% |████████████████████████████████| 614kB 7.8MB/s Collecting PasteDeploy==1.5.2 (from -r requirements.txt (line 19)) Downloading https://wheels.galaxyproject.org/packages/PasteDeploy-1.5.2-py2.py3-none-any.whl Collecting docutils==0.12 (from -r requirements.txt (line 20)) Downloading https://wheels.galaxyproject.org/packages/docutils-0.12-py2-none-any.whl (509kB) 100% |████████████████████████████████| 512kB 9.4MB/s Collecting wchartype==0.1 (from -r requirements.txt (line 21)) Downloading https://wheels.galaxyproject.org/packages/wchartype-0.1-py2-none-any.whl Collecting repoze.lru==0.6 (from -r requirements.txt (line 22)) Collecting Routes==2.4.1 (from -r requirements.txt (line 23)) Downloading https://wheels.galaxyproject.org/packages/Routes-2.4.1-py2.py3-none-any.whl (48kB) 100% |████████████████████████████████| 51kB 13.9MB/s Collecting WebOb==1.4.1 (from -r requirements.txt (line 24)) Downloading https://wheels.galaxyproject.org/packages/WebOb-1.4.1-py2.py3-none-any.whl (73kB) 100% |████████████████████████████████| 81kB 11.3MB/s Collecting WebHelpers==1.3 (from -r requirements.txt (line 25)) Downloading https://wheels.galaxyproject.org/packages/WebHelpers-1.3-py2-none-any.whl (149kB) 100% |████████████████████████████████| 153kB 10.6MB/s Collecting Mako==1.0.2 (from -r requirements.txt (line 26)) Downloading https://wheels.galaxyproject.org/packages/Mako-1.0.2-py2-none-any.whl (76kB) 100% |████████████████████████████████| 81kB 12.2MB/s Collecting pytz==2015.4 (from -r requirements.txt (line 27)) Downloading https://wheels.galaxyproject.org/packages/pytz-2015.4-py2-none-any.whl (475kB) 100% |████████████████████████████████| 481kB 9.2MB/s Collecting Babel==2.4.0 (from -r requirements.txt (line 28)) Downloading https://wheels.galaxyproject.org/packages/Babel-2.4.0-py2.py3-none-any.whl (6.8MB) 100% |████████████████████████████████| 6.8MB 5.8MB/s Collecting Beaker==1.7.0 (from -r requirements.txt (line 29)) Downloading https://wheels.galaxyproject.org/packages/Beaker-1.7.0-py2-none-any.whl (44kB) 100% |████████████████████████████████| 51kB 19.5MB/s Collecting dictobj==0.3.1 (from -r requirements.txt (line 30)) Downloading https://wheels.galaxyproject.org/packages/dictobj-0.3.1-py2-none-any.whl Collecting nose==1.3.7 (from -r requirements.txt (line 31)) Downloading https://wheels.galaxyproject.org/packages/nose-1.3.7-py2-none-any.whl (154kB) 100% |████████████████████████████████| 163kB 10.8MB/s Collecting Parsley==1.3 (from -r requirements.txt (line 32)) Downloading https://wheels.galaxyproject.org/packages/Parsley-1.3-py2-none-any.whl (88kB) 100% |████████████████████████████████| 92kB 10.7MB/s Collecting six==1.10.0 (from -r requirements.txt (line 33)) Downloading https://wheels.galaxyproject.org/packages/six-1.10.0-py2.py3-none-any.whl Collecting Whoosh==2.7.4 (from -r requirements.txt (line 34)) Downloading https://wheels.galaxyproject.org/packages/Whoosh-2.7.4-py2.py3-none-any.whl (468kB) 100% |████████████████████████████████| 471kB 8.9MB/s Collecting galaxy_sequence_utils==1.0.2 (from -r requirements.txt (line 35)) Downloading https://wheels.galaxyproject.org/packages/galaxy_sequence_utils-1.0.2-py2.py3-none-any.whl Collecting h5py==2.7.1 (from -r requirements.txt (line 36)) Using cached h5py-2.7.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Collecting pykwalify==1.5.1 (from -r requirements.txt (line 39)) Collecting python-dateutil==2.5.3 (from -r requirements.txt (line 40)) Using cached python_dateutil-2.5.3-py2.py3-none-any.whl Collecting docopt==0.6.2 (from -r requirements.txt (line 41)) Collecting Cheetah==2.4.4 (from -r requirements.txt (line 44)) Downloading https://wheels.galaxyproject.org/packages/Cheetah-2.4.4-cp27-cp27m-macosx_10_6_intel.whl (180kB) 100% |████████████████████████████████| 184kB 8.6MB/s Collecting Markdown==2.6.3 (from -r requirements.txt (line 45)) Downloading https://wheels.galaxyproject.org/packages/Markdown-2.6.3-py2-none-any.whl (158kB) 100% |████████████████████████████████| 163kB 8.5MB/s Collecting bioblend==0.7.0 (from -r requirements.txt (line 48)) Downloading https://wheels.galaxyproject.org/packages/bioblend-0.7.0-py2.py3-none-any.whl (82kB) 100% |████████████████████████████████| 92kB 10.9MB/s Collecting boto==2.38.0 (from -r requirements.txt (line 49)) Downloading https://wheels.galaxyproject.org/packages/boto-2.38.0-py2.py3-none-any.whl (1.3MB) 100% |████████████████████████████████| 1.3MB 9.0MB/s Collecting requests==2.10.0 (from -r requirements.txt (line 50)) Downloading https://wheels.galaxyproject.org/packages/requests-2.10.0-py2-none-any.whl (506kB) 100% |████████████████████████████████| 512kB 9.2MB/s Collecting requests-toolbelt==0.4.0 (from -r requirements.txt (line 51)) Downloading https://wheels.galaxyproject.org/packages/requests_toolbelt-0.4.0-py2.py3-none-any.whl Collecting kombu==3.0.30 (from -r requirements.txt (line 54)) Downloading https://wheels.galaxyproject.org/packages/kombu-3.0.30-py2.py3-none-any.whl (241kB) 100% |████████████████████████████████| 245kB 8.1MB/s Collecting amqp==1.4.8 (from -r requirements.txt (line 55)) Downloading https://wheels.galaxyproject.org/packages/amqp-1.4.8-py2.py3-none-any.whl (51kB) 100% |████████████████████████████████| 61kB 14.1MB/s Collecting anyjson==0.3.3 (from -r requirements.txt (line 56)) Downloading https://wheels.galaxyproject.org/packages/anyjson-0.3.3-py2-none-any.whl Collecting psutil==4.1.0 (from -r requirements.txt (line 59)) Downloading https://wheels.galaxyproject.org/packages/psutil-4.1.0-cp27-cp27m-macosx_10_6_intel.whl (175kB) 100% |████████████████████████████████| 184kB 9.1MB/s Collecting pulsar-galaxy-lib==0.8.0 (from -r requirements.txt (line 60)) Using cached pulsar_galaxy_lib-0.8.0-py2-none-any.whl Collecting sqlalchemy-migrate==0.10.0 (from -r requirements.txt (line 63)) Downloading https://wheels.galaxyproject.org/packages/sqlalchemy_migrate-0.10.0-py2-none-any.whl (108kB) 100% |████████████████████████████████| 112kB 9.2MB/s Collecting decorator==4.0.2 (from -r requirements.txt (line 64)) Downloading https://wheels.galaxyproject.org/packages/decorator-4.0.2-py2.py3-none-any.whl Collecting Tempita==0.5.3dev (from -r requirements.txt (line 65)) Downloading https://wheels.galaxyproject.org/packages/Tempita-0.5.3.dev0-py2-none-any.whl Collecting sqlparse==0.1.16 (from -r requirements.txt (line 66)) Downloading https://wheels.galaxyproject.org/packages/sqlparse-0.1.16-py2-none-any.whl Collecting pbr==1.8.0 (from -r requirements.txt (line 67)) Downloading https://wheels.galaxyproject.org/packages/pbr-1.8.0-py2.py3-none-any.whl (87kB) 100% |████████████████████████████████| 92kB 11.6MB/s Collecting svgwrite==1.1.6 (from -r requirements.txt (line 70)) Downloading https://wheels.galaxyproject.org/packages/svgwrite-1.1.6-py2-none-any.whl (62kB) 100% |████████████████████████████████| 71kB 11.8MB/s Collecting pyparsing==2.1.1 (from -r requirements.txt (line 71)) Downloading https://wheels.galaxyproject.org/packages/pyparsing-2.1.1-py2.py3-none-any.whl Collecting Fabric==1.13.2 (from -r requirements.txt (line 74)) Downloading https://wheels.galaxyproject.org/packages/Fabric-1.13.2-py2-none-any.whl (92kB) 100% |████████████████████████████████| 102kB 11.1MB/s Collecting paramiko==2.2.1 (from -r requirements.txt (line 75)) Downloading https://wheels.galaxyproject.org/packages/paramiko-2.2.1-py2.py3-none-any.whl (176kB) 100% |████████████████████████████████| 184kB 9.7MB/s Collecting ecdsa==0.13 (from -r requirements.txt (line 76)) Downloading https://wheels.galaxyproject.org/packages/ecdsa-0.13-py2.py3-none-any.whl (44kB) 100% |████████████████████████████████| 51kB 5.8MB/s Collecting pysam==0.8.4+gx5 (from -r requirements.txt (line 79)) Downloading https://wheels.galaxyproject.org/packages/pysam-0.8.4+gx5-cp27-cp27m-macosx_10_6_intel.whl (6.9MB) 100% |████████████████████████████████| 6.9MB 3.5MB/s Collecting python-genomespaceclient==0.1.8 (from -r requirements.txt (line 82)) Collecting PasteScript (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Using cached PasteScript-2.0.2-py2.py3-none-any.whl Collecting pynacl>=1.0.1 (from paramiko==2.2.1->-r requirements.txt (line 75)) Using cached PyNaCl-1.2.0-cp27-cp27m-macosx_10_6_intel.whl Collecting pyasn1>=0.1.7 (from paramiko==2.2.1->-r requirements.txt (line 75)) Using cached pyasn1-0.3.7-py2.py3-none-any.whl Collecting bcrypt>=3.1.3 (from paramiko==2.2.1->-r requirements.txt (line 75)) Using cached bcrypt-3.1.4-cp27-cp27m-macosx_10_6_intel.whl Collecting cryptography>=1.1 (from paramiko==2.2.1->-r requirements.txt (line 75)) Using cached cryptography-2.1.3-cp27-cp27m-macosx_10_6_intel.whl Collecting boto3 (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Using cached boto3-1.4.7-py2.py3-none-any.whl Collecting python-swiftclient (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Using cached python_swiftclient-3.4.0-py2.py3-none-any.whl Collecting cffi>=1.4.1 (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Using cached cffi-1.11.2-cp27-cp27m-macosx_10_6_intel.whl Collecting idna>=2.1 (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Downloading https://wheels.galaxyproject.org/packages/idna-2.6-py2.py3-none-any.whl (56kB) 100% |████████████████████████████████| 61kB 6.7MB/s Collecting enum34; python_version < "3" (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Using cached enum34-1.1.6-py2-none-any.whl Collecting asn1crypto>=0.21.0 (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Using cached asn1crypto-0.23.0-py2.py3-none-any.whl Collecting botocore<1.8.0,>=1.7.0 (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Using cached botocore-1.7.47-py2.py3-none-any.whl Collecting jmespath<1.0.0,>=0.7.1 (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Using cached jmespath-0.9.3-py2.py3-none-any.whl Collecting s3transfer<0.2.0,>=0.1.10 (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Using cached s3transfer-0.1.11-py2.py3-none-any.whl Collecting futures>=3.0; python_version == "2.7" or python_version == "2.6" (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Downloading https://wheels.galaxyproject.org/packages/futures-3.1.1-py2-none-any.whl Collecting pycparser (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Installing collected packages: bx-python, MarkupSafe, PyYAML, SQLAlchemy, mercurial, numpy, pycrypto, uWSGI, bz2file, ipaddress, six, Paste, PasteDeploy, docutils, wchartype, repoze.lru, Routes, WebOb, WebHelpers, Mako, pytz, Babel, Beaker, dictobj, nose, Parsley, Whoosh, galaxy-sequence-utils, h5py, docopt, python-dateutil, pykwalify, Markdown, Cheetah, requests, requests-toolbelt, boto, bioblend, amqp, anyjson, kombu, psutil, PasteScript, pulsar-galaxy-lib, sqlparse, pbr, decorator, Tempita, sqlalchemy-migrate, pyparsing, svgwrite, pycparser, cffi, pynacl, pyasn1, bcrypt, idna, enum34, asn1crypto, cryptography, paramiko, Fabric, ecdsa, pysam, jmespath, botocore, futures, s3transfer, boto3, python-swiftclient, python-genomespaceclient Successfully installed Babel-2.4.0 Beaker-1.7.0 Cheetah-2.4.4 Fabric-1.13.2 Mako-1.0.2 Markdown-2.6.3 MarkupSafe-0.23 Parsley-1.3 Paste-2.0.2 PasteDeploy-1.5.2 PasteScript-2.0.2 PyYAML-3.11 Routes-2.4.1 SQLAlchemy-1.0.15 Tempita-0.5.3.dev0 WebHelpers-1.3 WebOb-1.4.1 Whoosh-2.7.4 amqp-1.4.8 anyjson-0.3.3 asn1crypto-0.23.0 bcrypt-3.1.4 bioblend-0.7.0 boto-2.38.0 boto3-1.4.7 botocore-1.7.47 bx-python-0.7.3 bz2file-0.98 cffi-1.11.2 cryptography-2.1.3 decorator-4.0.2 dictobj-0.3.1 docopt-0.6.2 docutils-0.12 ecdsa-0.13 enum34-1.1.6 futures-3.1.1 galaxy-sequence-utils-1.0.2 h5py-2.7.1 idna-2.6 ipaddress-1.0.18 jmespath-0.9.3 kombu-3.0.30 mercurial-3.7.3 nose-1.3.7 numpy-1.9.2 paramiko-2.2.1 pbr-1.8.0 psutil-4.1.0 pulsar-galaxy-lib-0.8.0 pyasn1-0.3.7 pycparser-2.18 pycrypto-2.6.1 pykwalify-1.5.1 pynacl-1.2.0 pyparsing-2.1.1 pysam-0.8.4+gx5 python-dateutil-2.5.3 python-genomespaceclient-0.1.8 python-swiftclient-3.4.0 pytz-2015.4 repoze.lru-0.6 requests-2.10.0 requests-toolbelt-0.4.0 s3transfer-0.1.11 six-1.10.0 sqlalchemy-migrate-0.10.0 sqlparse-0.1.16 svgwrite-1.1.6 uWSGI-2.0.15 wchartype-0.1 Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv galaxy.tools.deps WARNING 2017-11-18 14:49:49,027 Path './database/dependencies' does not exist, ignoring galaxy.tools.deps WARNING 2017-11-18 14:49:49,027 Path './database/dependencies' is not directory, ignoring galaxy.tools.deps DEBUG 2017-11-18 14:49:49,045 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.deps.conda_util INFO 2017-11-18 14:49:49,049 Installing Conda, this may take several minutes. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 23.7M 100 23.7M 0 0 6758k 0 0:00:03 0:00:03 --:--:-- 6759k PREFIX=/galaxydir/galaxy/database/dependencies/_conda installing: python-3.5.2-0 ... installing: conda-env-2.6.0-0 ... installing: openssl-1.0.2j-0 ... installing: pycosat-0.6.1-py35_1 ... installing: readline-6.2-2 ... installing: requests-2.11.1-py35_0 ... installing: ruamel_yaml-0.11.14-py35_0 ... installing: sqlite-3.13.0-0 ... installing: tk-8.5.18-0 ... installing: xz-5.2.2-0 ... installing: yaml-0.1.6-0 ... installing: zlib-1.2.8-3 ... installing: conda-4.2.12-py35_0 ... installing: pycrypto-2.6.1-py35_4 ... installing: pip-8.1.2-py35_0 ... installing: wheel-0.29.0-py35_0 ... installing: setuptools-27.2.0-py35_0 ... Python 3.5.2 :: Continuum Analytics, Inc. creating default environment... installation finished. Fetching package metadata ....... Solving package specifications: .......... Package plan for installation in environment /galaxydir/galaxy/database/dependencies/_conda: The following packages will be downloaded: package | build ---------------------------|----------------- asn1crypto-0.22.0 | py35_0 149 KB idna-2.6 | py35_0 123 KB pycparser-2.18 | py35_0 168 KB pyparsing-2.2.0 | py35_0 96 KB requests-2.14.2 | py35_0 725 KB six-1.10.0 | py35_0 17 KB cffi-1.10.0 | py35_0 199 KB packaging-16.8 | py35_0 30 KB cryptography-1.8.1 | py35_0 479 KB pyopenssl-17.0.0 | py35_0 76 KB conda-4.3.24 | py35_0 516 KB ------------------------------------------------------------ Total: 2.5 MB The following NEW packages will be INSTALLED: asn1crypto: 0.22.0-py35_0 cffi: 1.10.0-py35_0 cryptography: 1.8.1-py35_0 idna: 2.6-py35_0 packaging: 16.8-py35_0 pycparser: 2.18-py35_0 pyopenssl: 17.0.0-py35_0 pyparsing: 2.2.0-py35_0 six: 1.10.0-py35_0 The following packages will be UPDATED: conda: 4.2.12-py35_0 --> 4.3.24-py35_0 requests: 2.11.1-py35_0 --> 2.14.2-py35_0 DEBUG:galaxy.app:python path is: /galaxydir/galaxy/scripts, /galaxydir/galaxy/lib, /galaxydir/galaxy/.venv/lib/python27.zip, /galaxydir/galaxy/.venv/lib/python2.7, /galaxydir/galaxy/.venv/lib/python2.7/plat-darwin, /galaxydir/galaxy/.venv/lib/python2.7/plat-mac, /galaxydir/galaxy/.venv/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/Extras/lib/python, /galaxydir/galaxy/.venv/lib/python2.7/lib-tk, /galaxydir/galaxy/.venv/lib/python2.7/lib-old, /galaxydir/galaxy/.venv/lib/python2.7/lib-dynload, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/lib/python2.7/site-packages DEBUG:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config INFO:galaxy.config:Logging at '10' level to 'stdout' galaxy.queue_worker INFO 2017-11-18 14:50:22,196 Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE tool_shed.tool_shed_registry DEBUG 2017-11-18 14:50:22,302 Loading references to tool sheds from ./config/tool_sheds_conf.xml.sample tool_shed.tool_shed_registry DEBUG 2017-11-18 14:50:22,302 Loaded reference to tool shed: Galaxy Main Tool Shed galaxy.app DEBUG 2017-11-18 14:50:22,317 Using "galaxy.ini" config file: /galaxydir/galaxy/config/galaxy.ini.sample migrate.versioning.repository DEBUG 2017-11-18 14:50:22,500 Loading repository lib/galaxy/model/migrate... migrate.versioning.script.base DEBUG 2017-11-18 14:50:22,504 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... migrate.versioning.script.base DEBUG 2017-11-18 14:50:22,504 Script 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LibraryDatasetDatasetAssociation.visible_children - consider using remote() annotations to mark the remote side. % self.prop /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/relationships.py:2408: SAWarning: Non-simple column elements in primary join condition for property HistoryDatasetAssociation.visible_children - consider using remote() annotations to mark the remote side. % self.prop /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. 'storage.' % (dialect.name, dialect.driver)) 0005_cleanup_datasets_fix DEBUG 2017-11-18 14:50:24,561 0 items affected, and restored. 0005_cleanup_datasets_fix DEBUG 2017-11-18 14:50:24,561 Time elapsed: 0.164078950882 0005_cleanup_datasets_fix DEBUG 2017-11-18 14:50:24,561 Fixing a discrepancy concerning cleaning up deleted history items shared before HDAs. 0005_cleanup_datasets_fix DEBUG 2017-11-18 14:50:24,567 0 items affected, and restored. 0005_cleanup_datasets_fix DEBUG 2017-11-18 14:50:24,567 Time elapsed: 0.00611186027527 galaxy.model.migrate.check INFO 2017-11-18 14:50:24,578 galaxy.model.migrate.check INFO 2017-11-18 14:50:24,578 Migrating 5 -> 6... galaxy.model.migrate.check INFO 2017-11-18 14:50:24,964 galaxy.model.migrate.check INFO 2017-11-18 14:50:24,964 This migration script changes certain values in the history_dataset_association.extension galaxy.model.migrate.check INFO 2017-11-18 14:50:24,964 column, specifically 'qual' is changed to be 'qual454'. galaxy.model.migrate.check INFO 2017-11-18 14:50:24,965 galaxy.model.migrate.check INFO 2017-11-18 14:50:24,965 galaxy.model.migrate.check INFO 2017-11-18 14:50:24,965 Migrating 6 -> 7... galaxy.model.migrate.check INFO 2017-11-18 14:50:25,356 galaxy.model.migrate.check INFO 2017-11-18 14:50:25,356 This migration script creates the new history_user_share_association table, and adds galaxy.model.migrate.check INFO 2017-11-18 14:50:25,357 a new boolean type column to the history table. This provides support for sharing galaxy.model.migrate.check INFO 2017-11-18 14:50:25,357 histories in the same way that workflows are shared. galaxy.model.migrate.check INFO 2017-11-18 14:50:25,357 galaxy.model.migrate.check INFO 2017-11-18 14:50:25,357 galaxy.model.migrate.check INFO 2017-11-18 14:50:25,357 Migrating 7 -> 8... galaxy.model.migrate.check INFO 2017-11-18 14:50:25,924 galaxy.model.migrate.check INFO 2017-11-18 14:50:25,925 This migration script adds the following new tables for supporting Galaxy forms: galaxy.model.migrate.check INFO 2017-11-18 14:50:25,925 1) form_definition_current galaxy.model.migrate.check INFO 2017-11-18 14:50:25,925 2) form_definition galaxy.model.migrate.check INFO 2017-11-18 14:50:25,925 3) form_values galaxy.model.migrate.check INFO 2017-11-18 14:50:25,925 4) request_type galaxy.model.migrate.check INFO 2017-11-18 14:50:25,925 5) request galaxy.model.migrate.check INFO 2017-11-18 14:50:25,925 6) sample galaxy.model.migrate.check INFO 2017-11-18 14:50:25,926 7) sample_state galaxy.model.migrate.check INFO 2017-11-18 14:50:25,926 8) sample_event galaxy.model.migrate.check INFO 2017-11-18 14:50:25,926 galaxy.model.migrate.check INFO 2017-11-18 14:50:25,926 galaxy.model.migrate.check INFO 2017-11-18 14:50:25,926 Migrating 8 -> 9... galaxy.model.migrate.check INFO 2017-11-18 14:50:26,386 galaxy.model.migrate.check INFO 2017-11-18 14:50:26,386 This migration script adds a new column to 2 tables: galaxy.model.migrate.check INFO 2017-11-18 14:50:26,386 1) a new boolean type column named 'submitted' to the 'request' table galaxy.model.migrate.check INFO 2017-11-18 14:50:26,386 2) a new string type column named 'bar_code' to the 'sample' table galaxy.model.migrate.check INFO 2017-11-18 14:50:26,386 galaxy.model.migrate.check INFO 2017-11-18 14:50:26,386 galaxy.model.migrate.check INFO 2017-11-18 14:50:26,386 Migrating 9 -> 10... galaxy.model.migrate.check INFO 2017-11-18 14:50:26,828 galaxy.model.migrate.check INFO 2017-11-18 14:50:26,828 This migration script adds the history_dataset_association_display_at_authorization table, galaxy.model.migrate.check INFO 2017-11-18 14:50:26,829 which allows 'private' datasets to be displayed at external sites without making them public. galaxy.model.migrate.check INFO 2017-11-18 14:50:26,829 galaxy.model.migrate.check INFO 2017-11-18 14:50:26,829 If using mysql, this script will display the following error, which is corrected in the next galaxy.model.migrate.check INFO 2017-11-18 14:50:26,829 migration script: galaxy.model.migrate.check INFO 2017-11-18 14:50:26,829 history_dataset_association_display_at_authorization table failed: (OperationalError) galaxy.model.migrate.check INFO 2017-11-18 14:50:26,829 (1059, "Identifier name 'ix_history_dataset_association_display_at_authorization_update_time' galaxy.model.migrate.check INFO 2017-11-18 14:50:26,829 is too long galaxy.model.migrate.check INFO 2017-11-18 14:50:26,829 galaxy.model.migrate.check INFO 2017-11-18 14:50:26,829 galaxy.model.migrate.check INFO 2017-11-18 14:50:26,830 Migrating 10 -> 11... galaxy.model.migrate.check INFO 2017-11-18 14:50:26,846 galaxy.model.migrate.check INFO 2017-11-18 14:50:26,846 This script fixes a problem introduced in the previous migration script galaxy.model.migrate.check INFO 2017-11-18 14:50:26,846 0010_hda_display_at_atuhz_table.py . MySQL has a name length limit and galaxy.model.migrate.check INFO 2017-11-18 14:50:26,846 thus the index "ix_hdadaa_history_dataset_association_id" has to be galaxy.model.migrate.check INFO 2017-11-18 14:50:26,846 manually created. galaxy.model.migrate.check INFO 2017-11-18 14:50:26,847 galaxy.model.migrate.check INFO 2017-11-18 14:50:26,847 galaxy.model.migrate.check INFO 2017-11-18 14:50:26,847 Migrating 11 -> 12... galaxy.model.migrate.check INFO 2017-11-18 14:50:27,503 galaxy.model.migrate.check INFO 2017-11-18 14:50:27,503 This script adds a new user_address table that is currently only used with sample requests, where galaxy.model.migrate.check INFO 2017-11-18 14:50:27,503 a user can select from a list of his addresses to associate with the request. This script also galaxy.model.migrate.check INFO 2017-11-18 14:50:27,503 drops the request.submitted column which was boolean and replaces it with a request.state column galaxy.model.migrate.check INFO 2017-11-18 14:50:27,503 which is a string, allowing for more flexibility with request states. galaxy.model.migrate.check INFO 2017-11-18 14:50:27,504 galaxy.model.migrate.check INFO 2017-11-18 14:50:27,504 galaxy.model.migrate.check INFO 2017-11-18 14:50:27,504 Migrating 12 -> 13... galaxy.model.migrate.check INFO 2017-11-18 14:50:28,083 galaxy.model.migrate.check INFO 2017-11-18 14:50:28,083 This migration script eliminates all of the tables that were used for the 1st version of the galaxy.model.migrate.check INFO 2017-11-18 14:50:28,083 library templates where template fields and contents were each stored as a separate table row galaxy.model.migrate.check INFO 2017-11-18 14:50:28,083 in various library item tables. All of these tables are dropped in this script, eliminating all galaxy.model.migrate.check INFO 2017-11-18 14:50:28,083 existing template data. A total of 14 existing tables are dropped. galaxy.model.migrate.check INFO 2017-11-18 14:50:28,083 galaxy.model.migrate.check INFO 2017-11-18 14:50:28,084 We're now basing library templates on forms, so field contents are galaxy.model.migrate.check INFO 2017-11-18 14:50:28,084 stored as a jsonified list in the form_values table. This script introduces the following 3 galaxy.model.migrate.check INFO 2017-11-18 14:50:28,084 new association tables: galaxy.model.migrate.check INFO 2017-11-18 14:50:28,084 1) library_info_association galaxy.model.migrate.check INFO 2017-11-18 14:50:28,084 2) library_folder_info_association galaxy.model.migrate.check INFO 2017-11-18 14:50:28,084 3) library_dataset_dataset_info_association galaxy.model.migrate.check INFO 2017-11-18 14:50:28,084 galaxy.model.migrate.check INFO 2017-11-18 14:50:28,084 If using mysql, this script will throw an (OperationalError) exception due to a long index name on galaxy.model.migrate.check INFO 2017-11-18 14:50:28,084 the library_dataset_dataset_info_association table, which is OK because the script creates an index galaxy.model.migrate.check INFO 2017-11-18 14:50:28,084 with a shortened name. galaxy.model.migrate.check INFO 2017-11-18 14:50:28,084 galaxy.model.migrate.check INFO 2017-11-18 14:50:28,084 galaxy.model.migrate.check INFO 2017-11-18 14:50:28,085 Migrating 13 -> 14... galaxy.model.migrate.check INFO 2017-11-18 14:50:28,501 galaxy.model.migrate.check INFO 2017-11-18 14:50:28,501 Migration script to add support for "Pages". galaxy.model.migrate.check INFO 2017-11-18 14:50:28,501 1) Creates Page and PageRevision tables galaxy.model.migrate.check INFO 2017-11-18 14:50:28,501 2) Adds username column to User table galaxy.model.migrate.check INFO 2017-11-18 14:50:28,502 galaxy.model.migrate.check INFO 2017-11-18 14:50:28,502 galaxy.model.migrate.check INFO 2017-11-18 14:50:28,502 Migrating 14 -> 15... galaxy.model.migrate.check INFO 2017-11-18 14:50:28,958 galaxy.model.migrate.check INFO 2017-11-18 14:50:28,958 This migration script adds the tables necessary to support tagging of histories, galaxy.model.migrate.check INFO 2017-11-18 14:50:28,958 datasets, and history-dataset associations (user views of datasets). galaxy.model.migrate.check INFO 2017-11-18 14:50:28,959 galaxy.model.migrate.check INFO 2017-11-18 14:50:28,959 If using mysql, this script will display the following error, which is corrected in the next galaxy.model.migrate.check INFO 2017-11-18 14:50:28,959 migration script: galaxy.model.migrate.check INFO 2017-11-18 14:50:28,959 history_dataset_association_tag_association table failed: (OperationalError) galaxy.model.migrate.check INFO 2017-11-18 14:50:28,959 (1059, "Identifier name 'ix_history_dataset_association_tag_association_history_dataset_association_id' galaxy.model.migrate.check INFO 2017-11-18 14:50:28,959 is too long) galaxy.model.migrate.check INFO 2017-11-18 14:50:28,959 galaxy.model.migrate.check INFO 2017-11-18 14:50:28,959 galaxy.model.migrate.check INFO 2017-11-18 14:50:28,959 Migrating 15 -> 16... galaxy.model.migrate.check INFO 2017-11-18 14:50:29,358 galaxy.model.migrate.check INFO 2017-11-18 14:50:29,358 This script fixes a problem introduced in 0015_tagging.py. MySQL has a name length galaxy.model.migrate.check INFO 2017-11-18 14:50:29,359 limit and thus the index "ix_hda_ta_history_dataset_association_id" has to be galaxy.model.migrate.check INFO 2017-11-18 14:50:29,359 manually created. galaxy.model.migrate.check INFO 2017-11-18 14:50:29,359 galaxy.model.migrate.check INFO 2017-11-18 14:50:29,359 galaxy.model.migrate.check INFO 2017-11-18 14:50:29,359 Migrating 16 -> 17... galaxy.model.migrate.check INFO 2017-11-18 14:50:29,778 galaxy.model.migrate.check INFO 2017-11-18 14:50:29,778 This script adds 3 indexes to table columns: library_folder.name, galaxy.model.migrate.check INFO 2017-11-18 14:50:29,778 library_dataset.name, library_dataset_dataset_association.name. galaxy.model.migrate.check INFO 2017-11-18 14:50:29,778 galaxy.model.migrate.check INFO 2017-11-18 14:50:29,778 galaxy.model.migrate.check INFO 2017-11-18 14:50:29,778 Migrating 17 -> 18... galaxy.model.migrate.check INFO 2017-11-18 14:50:30,303 galaxy.model.migrate.check INFO 2017-11-18 14:50:30,303 This migration script provides support for (a) ordering tags by recency and galaxy.model.migrate.check INFO 2017-11-18 14:50:30,303 (b) tagging pages. This script deletes all existing tags. galaxy.model.migrate.check INFO 2017-11-18 14:50:30,303 galaxy.model.migrate.check INFO 2017-11-18 14:50:30,303 galaxy.model.migrate.check INFO 2017-11-18 14:50:30,303 Migrating 18 -> 19... galaxy.model.migrate.check INFO 2017-11-18 14:50:30,759 galaxy.model.migrate.check INFO 2017-11-18 14:50:30,760 This script creates a request.folder_id column which is a foreign galaxy.model.migrate.check INFO 2017-11-18 14:50:30,760 key to the library_folder table. This also adds a 'type' and 'layout' column galaxy.model.migrate.check INFO 2017-11-18 14:50:30,760 to the form_definition table. galaxy.model.migrate.check INFO 2017-11-18 14:50:30,760 galaxy.model.migrate.check INFO 2017-11-18 14:50:30,760 galaxy.model.migrate.check INFO 2017-11-18 14:50:30,760 Migrating 19 -> 20... galaxy.model.migrate.check INFO 2017-11-18 14:50:31,417 galaxy.model.migrate.check INFO 2017-11-18 14:50:31,417 This script creates a job_to_output_library_dataset table for allowing library galaxy.model.migrate.check INFO 2017-11-18 14:50:31,417 uploads to run as regular jobs. To support this, a library_folder_id column is galaxy.model.migrate.check INFO 2017-11-18 14:50:31,417 added to the job table, and library_folder/output_library_datasets relations galaxy.model.migrate.check INFO 2017-11-18 14:50:31,417 are added to the Job object. An index is also added to the dataset.state galaxy.model.migrate.check INFO 2017-11-18 14:50:31,417 column. galaxy.model.migrate.check INFO 2017-11-18 14:50:31,418 galaxy.model.migrate.check INFO 2017-11-18 14:50:31,418 galaxy.model.migrate.check INFO 2017-11-18 14:50:31,418 Migrating 20 -> 21... galaxy.model.migrate.check INFO 2017-11-18 14:50:31,870 galaxy.model.migrate.check INFO 2017-11-18 14:50:31,870 This migration script adds a user preferences table to Galaxy. galaxy.model.migrate.check INFO 2017-11-18 14:50:31,871 galaxy.model.migrate.check INFO 2017-11-18 14:50:31,871 galaxy.model.migrate.check INFO 2017-11-18 14:50:31,871 Migrating 21 -> 22... galaxy.model.migrate.check INFO 2017-11-18 14:50:32,179 galaxy.model.migrate.check INFO 2017-11-18 14:50:32,179 Migration script to add support for storing visualizations. galaxy.model.migrate.check INFO 2017-11-18 14:50:32,179 1) Creates Visualization and VisualizationRevision tables galaxy.model.migrate.check INFO 2017-11-18 14:50:32,179 galaxy.model.migrate.check INFO 2017-11-18 14:50:32,179 galaxy.model.migrate.check INFO 2017-11-18 14:50:32,179 Migrating 22 -> 23... galaxy.model.migrate.check INFO 2017-11-18 14:50:32,475 galaxy.model.migrate.check INFO 2017-11-18 14:50:32,476 Migration script to add columns for tracking whether pages are deleted and galaxy.model.migrate.check INFO 2017-11-18 14:50:32,476 publicly accessible. galaxy.model.migrate.check INFO 2017-11-18 14:50:32,476 galaxy.model.migrate.check INFO 2017-11-18 14:50:32,476 galaxy.model.migrate.check INFO 2017-11-18 14:50:32,476 Migrating 23 -> 24... galaxy.model.migrate.check INFO 2017-11-18 14:50:32,755 galaxy.model.migrate.check INFO 2017-11-18 14:50:32,755 Remove unique constraint from page slugs to allow creating a page with galaxy.model.migrate.check INFO 2017-11-18 14:50:32,755 the same slug as a deleted page. galaxy.model.migrate.check INFO 2017-11-18 14:50:32,755 galaxy.model.migrate.check INFO 2017-11-18 14:50:32,755 galaxy.model.migrate.check INFO 2017-11-18 14:50:32,755 Migrating 24 -> 25... galaxy.model.migrate.check INFO 2017-11-18 14:50:33,040 galaxy.model.migrate.check INFO 2017-11-18 14:50:33,041 This script adds a foreign key to the form_values table in the galaxy_user table galaxy.model.migrate.check INFO 2017-11-18 14:50:33,041 galaxy.model.migrate.check INFO 2017-11-18 14:50:33,041 galaxy.model.migrate.check INFO 2017-11-18 14:50:33,041 Migrating 25 -> 26... galaxy.model.migrate.check INFO 2017-11-18 14:50:33,449 galaxy.model.migrate.check INFO 2017-11-18 14:50:33,449 This script adds tables needed for Galaxy cloud functionality. galaxy.model.migrate.check INFO 2017-11-18 14:50:33,449 galaxy.model.migrate.check INFO 2017-11-18 14:50:33,449 galaxy.model.migrate.check INFO 2017-11-18 14:50:33,449 Migrating 26 -> 27... galaxy.model.migrate.check INFO 2017-11-18 14:50:33,856 galaxy.model.migrate.check INFO 2017-11-18 14:50:33,856 This migration script adds the request_event table and galaxy.model.migrate.check INFO 2017-11-18 14:50:33,857 removes the state field in the request table galaxy.model.migrate.check INFO 2017-11-18 14:50:33,857 galaxy.model.migrate.check INFO 2017-11-18 14:50:33,857 galaxy.model.migrate.check INFO 2017-11-18 14:50:33,857 Migrating 27 -> 28... galaxy.model.migrate.check INFO 2017-11-18 14:50:34,612 galaxy.model.migrate.check INFO 2017-11-18 14:50:34,612 This script adds the filename_override_metadata column to the JobExternalOutputMetadata table, galaxy.model.migrate.check INFO 2017-11-18 14:50:34,612 allowing existing metadata files to be written when using external metadata and a cluster galaxy.model.migrate.check INFO 2017-11-18 14:50:34,612 set up with read-only access to database/files galaxy.model.migrate.check INFO 2017-11-18 14:50:34,612 galaxy.model.migrate.check INFO 2017-11-18 14:50:34,612 galaxy.model.migrate.check INFO 2017-11-18 14:50:34,612 Migrating 28 -> 29... galaxy.model.migrate.check INFO 2017-11-18 14:50:35,144 galaxy.model.migrate.check INFO 2017-11-18 14:50:35,144 This migration script adds a user actions table to Galaxy. galaxy.model.migrate.check INFO 2017-11-18 14:50:35,144 galaxy.model.migrate.check INFO 2017-11-18 14:50:35,144 galaxy.model.migrate.check INFO 2017-11-18 14:50:35,145 Migrating 29 -> 30... galaxy.model.migrate.check INFO 2017-11-18 14:50:35,671 galaxy.model.migrate.check INFO 2017-11-18 14:50:35,671 Migration script to add column for a history slug. galaxy.model.migrate.check INFO 2017-11-18 14:50:35,671 galaxy.model.migrate.check INFO 2017-11-18 14:50:35,671 galaxy.model.migrate.check INFO 2017-11-18 14:50:35,671 Migrating 30 -> 31... galaxy.model.migrate.check INFO 2017-11-18 14:50:36,284 galaxy.model.migrate.check INFO 2017-11-18 14:50:36,284 Migration script to (a) add and populate necessary columns for doing community tagging of histories, datasets, and pages and (b) add table for doing individual and community tagging of workflows. galaxy.model.migrate.check INFO 2017-11-18 14:50:36,284 galaxy.model.migrate.check INFO 2017-11-18 14:50:36,284 galaxy.model.migrate.check INFO 2017-11-18 14:50:36,285 Migrating 31 -> 32... galaxy.model.migrate.check INFO 2017-11-18 14:50:36,747 galaxy.model.migrate.check INFO 2017-11-18 14:50:36,747 Migration script to add slug column for stored workflow. galaxy.model.migrate.check INFO 2017-11-18 14:50:36,747 galaxy.model.migrate.check INFO 2017-11-18 14:50:36,747 galaxy.model.migrate.check INFO 2017-11-18 14:50:36,747 Migrating 32 -> 33... galaxy.model.migrate.check INFO 2017-11-18 14:50:37,091 galaxy.model.migrate.check INFO 2017-11-18 14:50:37,092 Migration script to add necessary columns for distinguishing between viewing/importing and publishing histories, workflows, and pages. Script adds published column to histories and workflows and importable column to pages. galaxy.model.migrate.check INFO 2017-11-18 14:50:37,092 galaxy.model.migrate.check INFO 2017-11-18 14:50:37,092 galaxy.model.migrate.check INFO 2017-11-18 14:50:37,092 Migrating 33 -> 34... galaxy.model.migrate.check INFO 2017-11-18 14:50:37,392 galaxy.model.migrate.check INFO 2017-11-18 14:50:37,392 Migration script to create a table for page-user share association. galaxy.model.migrate.check INFO 2017-11-18 14:50:37,392 galaxy.model.migrate.check INFO 2017-11-18 14:50:37,392 galaxy.model.migrate.check INFO 2017-11-18 14:50:37,392 Migrating 34 -> 35... galaxy.model.migrate.check INFO 2017-11-18 14:50:37,779 galaxy.model.migrate.check INFO 2017-11-18 14:50:37,779 Migration script to (a) create tables for annotating objects and (b) create tags for workflow steps. galaxy.model.migrate.check INFO 2017-11-18 14:50:37,780 galaxy.model.migrate.check INFO 2017-11-18 14:50:37,780 galaxy.model.migrate.check INFO 2017-11-18 14:50:37,780 Migrating 35 -> 36... galaxy.model.migrate.check INFO 2017-11-18 14:50:38,134 galaxy.model.migrate.check INFO 2017-11-18 14:50:38,134 Migration script to add a deleted column to the following tables: galaxy.model.migrate.check INFO 2017-11-18 14:50:38,134 library_info_association, library_folder_info_association, library_dataset_dataset_info_association. galaxy.model.migrate.check INFO 2017-11-18 14:50:38,134 galaxy.model.migrate.check INFO 2017-11-18 14:50:38,134 galaxy.model.migrate.check INFO 2017-11-18 14:50:38,134 Migrating 36 -> 37... galaxy.model.migrate.check INFO 2017-11-18 14:50:38,722 galaxy.model.migrate.check INFO 2017-11-18 14:50:38,722 This migration script removes the library_id & folder_id fields in the 'request' table and galaxy.model.migrate.check INFO 2017-11-18 14:50:38,722 adds the same to the 'sample' table. This also adds a 'datatx' column to request_type table galaxy.model.migrate.check INFO 2017-11-18 14:50:38,722 to store the sequencer login information. Finally, this adds a 'dataset_files' column to galaxy.model.migrate.check INFO 2017-11-18 14:50:38,722 the sample table. galaxy.model.migrate.check INFO 2017-11-18 14:50:38,722 galaxy.model.migrate.check INFO 2017-11-18 14:50:38,722 galaxy.model.migrate.check INFO 2017-11-18 14:50:38,723 Migrating 37 -> 38... galaxy.model.migrate.check INFO 2017-11-18 14:50:39,086 galaxy.model.migrate.check INFO 2017-11-18 14:50:39,086 Migration script to add an inheritable column to the following tables: galaxy.model.migrate.check INFO 2017-11-18 14:50:39,086 library_info_association, library_folder_info_association. galaxy.model.migrate.check INFO 2017-11-18 14:50:39,086 Also, in case of sqlite check if the previous migration script deleted the galaxy.model.migrate.check INFO 2017-11-18 14:50:39,086 request table and if so, restore the table. galaxy.model.migrate.check INFO 2017-11-18 14:50:39,087 galaxy.model.migrate.check INFO 2017-11-18 14:50:39,087 galaxy.model.migrate.check INFO 2017-11-18 14:50:39,087 Migrating 38 -> 39... galaxy.model.migrate.check INFO 2017-11-18 14:50:39,399 galaxy.model.migrate.check INFO 2017-11-18 14:50:39,399 Migration script to add a synopsis column to the library table. galaxy.model.migrate.check INFO 2017-11-18 14:50:39,399 galaxy.model.migrate.check INFO 2017-11-18 14:50:39,399 galaxy.model.migrate.check INFO 2017-11-18 14:50:39,399 Migrating 39 -> 40... galaxy.model.migrate.check INFO 2017-11-18 14:50:39,729 galaxy.model.migrate.check INFO 2017-11-18 14:50:39,729 Migration script to (a) create tables for annotating pages. galaxy.model.migrate.check INFO 2017-11-18 14:50:39,729 galaxy.model.migrate.check INFO 2017-11-18 14:50:39,729 galaxy.model.migrate.check INFO 2017-11-18 14:50:39,729 Migrating 40 -> 41... galaxy.model.migrate.check INFO 2017-11-18 14:50:40,069 galaxy.model.migrate.check INFO 2017-11-18 14:50:40,069 Migration script to create tables for tracking workflow invocations. galaxy.model.migrate.check INFO 2017-11-18 14:50:40,069 galaxy.model.migrate.check INFO 2017-11-18 14:50:40,069 galaxy.model.migrate.check INFO 2017-11-18 14:50:40,069 Migrating 41 -> 42... galaxy.model.migrate.check INFO 2017-11-18 14:50:40,420 galaxy.model.migrate.check INFO 2017-11-18 14:50:40,421 Drop and readd workflow invocation tables, allowing null jobs galaxy.model.migrate.check INFO 2017-11-18 14:50:40,421 galaxy.model.migrate.check INFO 2017-11-18 14:50:40,421 galaxy.model.migrate.check INFO 2017-11-18 14:50:40,421 Migrating 42 -> 43... galaxy.model.migrate.check INFO 2017-11-18 14:50:40,864 galaxy.model.migrate.check INFO 2017-11-18 14:50:40,864 Migration script to create tables and columns for sharing visualizations. galaxy.model.migrate.check INFO 2017-11-18 14:50:40,864 galaxy.model.migrate.check INFO 2017-11-18 14:50:40,864 galaxy.model.migrate.check INFO 2017-11-18 14:50:40,864 Migrating 43 -> 44... galaxy.model.migrate.check INFO 2017-11-18 14:50:41,212 galaxy.model.migrate.check INFO 2017-11-18 14:50:41,212 Migration script to add a notify column to the request table. galaxy.model.migrate.check INFO 2017-11-18 14:50:41,212 galaxy.model.migrate.check INFO 2017-11-18 14:50:41,212 galaxy.model.migrate.check INFO 2017-11-18 14:50:41,213 Migrating 44 -> 45... galaxy.model.migrate.check INFO 2017-11-18 14:50:41,588 galaxy.model.migrate.check INFO 2017-11-18 14:50:41,588 Migration script to add the request_type_permissions table. galaxy.model.migrate.check INFO 2017-11-18 14:50:41,588 galaxy.model.migrate.check INFO 2017-11-18 14:50:41,588 galaxy.model.migrate.check INFO 2017-11-18 14:50:41,588 Migrating 45 -> 46... galaxy.model.migrate.check INFO 2017-11-18 14:50:42,182 galaxy.model.migrate.check INFO 2017-11-18 14:50:42,182 Migration script to create tables for handling post-job actions. galaxy.model.migrate.check INFO 2017-11-18 14:50:42,182 galaxy.model.migrate.check INFO 2017-11-18 14:50:42,182 galaxy.model.migrate.check INFO 2017-11-18 14:50:42,182 Migrating 46 -> 47... galaxy.model.migrate.check INFO 2017-11-18 14:50:42,516 galaxy.model.migrate.check INFO 2017-11-18 14:50:42,516 Add a user_id column to the job table. galaxy.model.migrate.check INFO 2017-11-18 14:50:42,516 galaxy.model.migrate.check INFO 2017-11-18 14:50:42,516 Updating user_id column in job table for 0 rows... galaxy.model.migrate.check INFO 2017-11-18 14:50:42,516 galaxy.model.migrate.check INFO 2017-11-18 14:50:42,517 Updated the user_id column for 0 rows in the job table. galaxy.model.migrate.check INFO 2017-11-18 14:50:42,517 0 rows have no user_id since the value was NULL in the galaxy_session table. galaxy.model.migrate.check INFO 2017-11-18 14:50:42,517 galaxy.model.migrate.check INFO 2017-11-18 14:50:42,517 galaxy.model.migrate.check INFO 2017-11-18 14:50:42,517 Migrating 47 -> 48... galaxy.model.migrate.check INFO 2017-11-18 14:50:42,872 galaxy.model.migrate.check INFO 2017-11-18 14:50:42,872 Add a state column to the history_dataset_association and library_dataset_dataset_association table. galaxy.model.migrate.check INFO 2017-11-18 14:50:42,872 galaxy.model.migrate.check INFO 2017-11-18 14:50:42,872 galaxy.model.migrate.check INFO 2017-11-18 14:50:42,872 Migrating 48 -> 49... galaxy.model.migrate.check INFO 2017-11-18 14:50:43,219 galaxy.model.migrate.check INFO 2017-11-18 14:50:43,219 Migration script to add the api_keys table. galaxy.model.migrate.check INFO 2017-11-18 14:50:43,219 galaxy.model.migrate.check INFO 2017-11-18 14:50:43,219 galaxy.model.migrate.check INFO 2017-11-18 14:50:43,220 Migrating 49 -> 50... galaxy.model.migrate.check INFO 2017-11-18 14:50:43,617 galaxy.model.migrate.check INFO 2017-11-18 14:50:43,617 This script drops tables that were associated with the old Galaxy Cloud functionality. galaxy.model.migrate.check INFO 2017-11-18 14:50:43,617 galaxy.model.migrate.check INFO 2017-11-18 14:50:43,617 galaxy.model.migrate.check INFO 2017-11-18 14:50:43,618 Migrating 50 -> 51... galaxy.model.migrate.check INFO 2017-11-18 14:50:43,946 galaxy.model.migrate.check INFO 2017-11-18 14:50:43,946 Migration script to add imported column for jobs table. galaxy.model.migrate.check INFO 2017-11-18 14:50:43,946 galaxy.model.migrate.check INFO 2017-11-18 14:50:43,946 galaxy.model.migrate.check INFO 2017-11-18 14:50:43,947 Migrating 51 -> 52... galaxy.model.migrate.check INFO 2017-11-18 14:50:44,325 galaxy.model.migrate.check INFO 2017-11-18 14:50:44,325 Migration script to add the sample_dataset table and remove the 'dataset_files' column galaxy.model.migrate.check INFO 2017-11-18 14:50:44,326 from the 'sample' table galaxy.model.migrate.check INFO 2017-11-18 14:50:44,326 galaxy.model.migrate.check INFO 2017-11-18 14:50:44,326 galaxy.model.migrate.check INFO 2017-11-18 14:50:44,326 Migrating 52 -> 53... galaxy.model.migrate.check INFO 2017-11-18 14:50:44,699 galaxy.model.migrate.check INFO 2017-11-18 14:50:44,699 Migration script to create tables for rating histories, datasets, workflows, pages, and visualizations. galaxy.model.migrate.check INFO 2017-11-18 14:50:44,699 galaxy.model.migrate.check INFO 2017-11-18 14:50:44,700 galaxy.model.migrate.check INFO 2017-11-18 14:50:44,700 Migrating 53 -> 54... galaxy.model.migrate.check INFO 2017-11-18 14:50:45,051 galaxy.model.migrate.check INFO 2017-11-18 14:50:45,052 Migration script to add dbkey column for visualization. galaxy.model.migrate.check INFO 2017-11-18 14:50:45,052 galaxy.model.migrate.check INFO 2017-11-18 14:50:45,052 galaxy.model.migrate.check INFO 2017-11-18 14:50:45,052 Migrating 54 -> 55... galaxy.model.migrate.check INFO 2017-11-18 14:50:45,407 galaxy.model.migrate.check INFO 2017-11-18 14:50:45,407 Migration script to add the post_job_action_association table. galaxy.model.migrate.check INFO 2017-11-18 14:50:45,407 galaxy.model.migrate.check INFO 2017-11-18 14:50:45,407 galaxy.model.migrate.check INFO 2017-11-18 14:50:45,407 Migrating 55 -> 56... galaxy.model.migrate.check INFO 2017-11-18 14:50:45,772 galaxy.model.migrate.check INFO 2017-11-18 14:50:45,772 Migration script to create tables for adding explicit workflow outputs. galaxy.model.migrate.check INFO 2017-11-18 14:50:45,772 galaxy.model.migrate.check INFO 2017-11-18 14:50:45,772 galaxy.model.migrate.check INFO 2017-11-18 14:50:45,772 Migrating 56 -> 57... galaxy.model.migrate.check INFO 2017-11-18 14:50:46,107 galaxy.model.migrate.check INFO 2017-11-18 14:50:46,107 Migration script to modify the 'notify' field in the 'request' table from a boolean galaxy.model.migrate.check INFO 2017-11-18 14:50:46,107 to a JSONType galaxy.model.migrate.check INFO 2017-11-18 14:50:46,107 galaxy.model.migrate.check INFO 2017-11-18 14:50:46,108 galaxy.model.migrate.check INFO 2017-11-18 14:50:46,108 Migrating 57 -> 58... galaxy.model.migrate.check INFO 2017-11-18 14:50:46,762 galaxy.model.migrate.check INFO 2017-11-18 14:50:46,762 Migration script to create table for exporting histories to archives. galaxy.model.migrate.check INFO 2017-11-18 14:50:46,762 galaxy.model.migrate.check INFO 2017-11-18 14:50:46,763 galaxy.model.migrate.check INFO 2017-11-18 14:50:46,763 Migrating 58 -> 59... galaxy.model.migrate.check INFO 2017-11-18 14:50:47,131 galaxy.model.migrate.check INFO 2017-11-18 14:50:47,131 Migration script to modify the 'file_path' field type in 'sample_dataset' table galaxy.model.migrate.check INFO 2017-11-18 14:50:47,131 to 'TEXT' so that it can support large file paths exceeding 255 characters galaxy.model.migrate.check INFO 2017-11-18 14:50:47,131 galaxy.model.migrate.check INFO 2017-11-18 14:50:47,131 galaxy.model.migrate.check INFO 2017-11-18 14:50:47,132 Migrating 59 -> 60... galaxy.model.migrate.check INFO 2017-11-18 14:50:47,504 galaxy.model.migrate.check INFO 2017-11-18 14:50:47,505 Migration script to create column and table for importing histories from galaxy.model.migrate.check INFO 2017-11-18 14:50:47,505 file archives. galaxy.model.migrate.check INFO 2017-11-18 14:50:47,505 galaxy.model.migrate.check INFO 2017-11-18 14:50:47,505 galaxy.model.migrate.check INFO 2017-11-18 14:50:47,505 Migrating 60 -> 61... galaxy.model.migrate.check INFO 2017-11-18 14:50:47,852 galaxy.model.migrate.check INFO 2017-11-18 14:50:47,852 Migration script to create tables task management. galaxy.model.migrate.check INFO 2017-11-18 14:50:47,852 galaxy.model.migrate.check INFO 2017-11-18 14:50:47,852 galaxy.model.migrate.check INFO 2017-11-18 14:50:47,852 Migrating 61 -> 62... galaxy.model.migrate.check INFO 2017-11-18 14:50:48,217 galaxy.model.migrate.check INFO 2017-11-18 14:50:48,217 Migration script to create table for associating sessions and users with galaxy.model.migrate.check INFO 2017-11-18 14:50:48,217 OpenIDs. galaxy.model.migrate.check INFO 2017-11-18 14:50:48,217 galaxy.model.migrate.check INFO 2017-11-18 14:50:48,217 galaxy.model.migrate.check INFO 2017-11-18 14:50:48,217 Migrating 62 -> 63... galaxy.model.migrate.check INFO 2017-11-18 14:50:48,572 galaxy.model.migrate.check INFO 2017-11-18 14:50:48,572 Migration script to create a new 'sequencer' table galaxy.model.migrate.check INFO 2017-11-18 14:50:48,572 galaxy.model.migrate.check INFO 2017-11-18 14:50:48,572 galaxy.model.migrate.check INFO 2017-11-18 14:50:48,573 Migrating 63 -> 64... galaxy.model.migrate.check INFO 2017-11-18 14:50:48,972 galaxy.model.migrate.check INFO 2017-11-18 14:50:48,973 Migration script to add the run and sample_run_association tables. galaxy.model.migrate.check INFO 2017-11-18 14:50:48,973 galaxy.model.migrate.check INFO 2017-11-18 14:50:48,973 galaxy.model.migrate.check INFO 2017-11-18 14:50:48,973 Migrating 64 -> 65... galaxy.model.migrate.check INFO 2017-11-18 14:50:49,346 galaxy.model.migrate.check INFO 2017-11-18 14:50:49,346 Migration script to add 'name' attribute to the JSON dict which describes galaxy.model.migrate.check INFO 2017-11-18 14:50:49,346 a form definition field and the form values in the database. In the 'form_values' galaxy.model.migrate.check INFO 2017-11-18 14:50:49,347 table, the 'content' column is now a JSON dict instead of a list. galaxy.model.migrate.check INFO 2017-11-18 14:50:49,347 galaxy.model.migrate.check INFO 2017-11-18 14:50:49,347 galaxy.model.migrate.check INFO 2017-11-18 14:50:49,347 Migrating 65 -> 66... galaxy.model.migrate.check INFO 2017-11-18 14:50:49,766 galaxy.model.migrate.check INFO 2017-11-18 14:50:49,766 Migration script to create table for storing deferred job and managed transfer galaxy.model.migrate.check INFO 2017-11-18 14:50:49,766 information. galaxy.model.migrate.check INFO 2017-11-18 14:50:49,766 galaxy.model.migrate.check INFO 2017-11-18 14:50:49,766 galaxy.model.migrate.check INFO 2017-11-18 14:50:49,766 Migrating 66 -> 67... galaxy.model.migrate.check INFO 2017-11-18 14:50:50,246 galaxy.model.migrate.check INFO 2017-11-18 14:50:50,246 Migration script to populate the 'sequencer' table and it is populated using unique galaxy.model.migrate.check INFO 2017-11-18 14:50:50,246 entries in the 'datatx_info' column in the 'request_type' table. It also deletes the 'datatx_info' galaxy.model.migrate.check INFO 2017-11-18 14:50:50,246 column in the 'request_type' table and adds a foreign key to the 'sequencer' table. The galaxy.model.migrate.check INFO 2017-11-18 14:50:50,246 actual contents of the datatx_info column are stored as form_values. galaxy.model.migrate.check INFO 2017-11-18 14:50:50,246 galaxy.model.migrate.check INFO 2017-11-18 14:50:50,246 galaxy.model.migrate.check INFO 2017-11-18 14:50:50,246 Migrating 67 -> 68... galaxy.model.migrate.check INFO 2017-11-18 14:50:50,756 galaxy.model.migrate.check INFO 2017-11-18 14:50:50,756 This migration script renames the sequencer table to 'external_service' table and galaxy.model.migrate.check INFO 2017-11-18 14:50:50,756 creates a association table, 'request_type_external_service_association' and galaxy.model.migrate.check INFO 2017-11-18 14:50:50,756 populates it. The 'sequencer_id' foreign_key from the 'request_type' table is removed. galaxy.model.migrate.check INFO 2017-11-18 14:50:50,756 The 'sequencer_type_id' column is renamed to 'external_service_type_id' in the renamed galaxy.model.migrate.check INFO 2017-11-18 14:50:50,757 table 'external_service'. Finally, adds a foreign key to the external_service table in the galaxy.model.migrate.check INFO 2017-11-18 14:50:50,757 sample_dataset table and populates it. galaxy.model.migrate.check INFO 2017-11-18 14:50:50,757 galaxy.model.migrate.check INFO 2017-11-18 14:50:50,757 galaxy.model.migrate.check INFO 2017-11-18 14:50:50,757 Migrating 68 -> 69... galaxy.model.migrate.check INFO 2017-11-18 14:50:51,147 galaxy.model.migrate.check INFO 2017-11-18 14:50:51,147 Migration script to rename the sequencer information form type to external service information form galaxy.model.migrate.check INFO 2017-11-18 14:50:51,147 galaxy.model.migrate.check INFO 2017-11-18 14:50:51,148 galaxy.model.migrate.check INFO 2017-11-18 14:50:51,148 Migrating 69 -> 70... galaxy.model.migrate.check INFO 2017-11-18 14:50:51,517 galaxy.model.migrate.check INFO 2017-11-18 14:50:51,517 Migration script to add 'info' column to the transfer_job table. galaxy.model.migrate.check INFO 2017-11-18 14:50:51,517 galaxy.model.migrate.check INFO 2017-11-18 14:50:51,517 galaxy.model.migrate.check INFO 2017-11-18 14:50:51,518 Migrating 70 -> 71... galaxy.model.migrate.check INFO 2017-11-18 14:50:51,956 galaxy.model.migrate.check INFO 2017-11-18 14:50:51,956 Migration script to add 'workflow' and 'history' columns for a sample. galaxy.model.migrate.check INFO 2017-11-18 14:50:51,956 galaxy.model.migrate.check INFO 2017-11-18 14:50:51,956 galaxy.model.migrate.check INFO 2017-11-18 14:50:51,957 Migrating 71 -> 72... galaxy.model.migrate.check INFO 2017-11-18 14:50:52,750 galaxy.model.migrate.check INFO 2017-11-18 14:50:52,750 Migration script to add 'pid' and 'socket' columns to the transfer_job table. galaxy.model.migrate.check INFO 2017-11-18 14:50:52,750 galaxy.model.migrate.check INFO 2017-11-18 14:50:52,750 galaxy.model.migrate.check INFO 2017-11-18 14:50:52,750 Migrating 72 -> 73... galaxy.model.migrate.check INFO 2017-11-18 14:50:53,129 galaxy.model.migrate.check INFO 2017-11-18 14:50:53,129 Migration script to add 'ldda_parent_id' column to the implicitly_converted_dataset_association table. galaxy.model.migrate.check INFO 2017-11-18 14:50:53,129 galaxy.model.migrate.check INFO 2017-11-18 14:50:53,129 galaxy.model.migrate.check INFO 2017-11-18 14:50:53,130 Migrating 73 -> 74... galaxy.model.migrate.check INFO 2017-11-18 14:50:53,545 galaxy.model.migrate.check INFO 2017-11-18 14:50:53,545 Migration script to add 'purged' column to the library_dataset table. galaxy.model.migrate.check INFO 2017-11-18 14:50:53,545 galaxy.model.migrate.check INFO 2017-11-18 14:50:53,546 galaxy.model.migrate.check INFO 2017-11-18 14:50:53,546 Migrating 74 -> 75... galaxy.model.migrate.check INFO 2017-11-18 14:50:53,945 galaxy.model.migrate.check INFO 2017-11-18 14:50:53,946 Migration script to add a 'subindex' column to the run table. galaxy.model.migrate.check INFO 2017-11-18 14:50:53,946 galaxy.model.migrate.check INFO 2017-11-18 14:50:53,946 galaxy.model.migrate.check INFO 2017-11-18 14:50:53,946 Migrating 75 -> 76... galaxy.model.migrate.check INFO 2017-11-18 14:50:54,320 galaxy.model.migrate.check INFO 2017-11-18 14:50:54,320 This migration script fixes the data corruption caused in the form_values galaxy.model.migrate.check INFO 2017-11-18 14:50:54,320 table (content json field) by migrate script 65. galaxy.model.migrate.check INFO 2017-11-18 14:50:54,320 galaxy.model.migrate.check INFO 2017-11-18 14:50:54,320 No corrupted rows found. galaxy.model.migrate.check INFO 2017-11-18 14:50:54,320 galaxy.model.migrate.check INFO 2017-11-18 14:50:54,320 Migrating 76 -> 77... galaxy.model.migrate.check INFO 2017-11-18 14:50:54,716 galaxy.model.migrate.check INFO 2017-11-18 14:50:54,717 Migration script to create table for storing tool tag associations. galaxy.model.migrate.check INFO 2017-11-18 14:50:54,717 galaxy.model.migrate.check INFO 2017-11-18 14:50:54,717 galaxy.model.migrate.check INFO 2017-11-18 14:50:54,717 Migrating 77 -> 78... galaxy.model.migrate.check INFO 2017-11-18 14:50:55,159 galaxy.model.migrate.check INFO 2017-11-18 14:50:55,160 Migration script to add 'total_size' column to the dataset table, 'purged' galaxy.model.migrate.check INFO 2017-11-18 14:50:55,160 column to the HDA table, and 'disk_usage' column to the User and GalaxySession galaxy.model.migrate.check INFO 2017-11-18 14:50:55,160 tables. galaxy.model.migrate.check INFO 2017-11-18 14:50:55,160 galaxy.model.migrate.check INFO 2017-11-18 14:50:55,160 galaxy.model.migrate.check INFO 2017-11-18 14:50:55,160 Migrating 78 -> 79... galaxy.model.migrate.check INFO 2017-11-18 14:50:55,565 galaxy.model.migrate.check INFO 2017-11-18 14:50:55,566 Migration script to add the job_to_input_library_dataset table. galaxy.model.migrate.check INFO 2017-11-18 14:50:55,566 galaxy.model.migrate.check INFO 2017-11-18 14:50:55,566 galaxy.model.migrate.check INFO 2017-11-18 14:50:55,566 Migrating 79 -> 80... galaxy.model.migrate.check INFO 2017-11-18 14:50:56,020 galaxy.model.migrate.check INFO 2017-11-18 14:50:56,021 Migration script to create tables for disk quotas. galaxy.model.migrate.check INFO 2017-11-18 14:50:56,021 galaxy.model.migrate.check INFO 2017-11-18 14:50:56,021 galaxy.model.migrate.check INFO 2017-11-18 14:50:56,021 Migrating 80 -> 81... galaxy.model.migrate.check INFO 2017-11-18 14:50:56,428 galaxy.model.migrate.check INFO 2017-11-18 14:50:56,428 Migration script to add a 'tool_version' column to the hda/ldda tables. galaxy.model.migrate.check INFO 2017-11-18 14:50:56,428 galaxy.model.migrate.check INFO 2017-11-18 14:50:56,428 galaxy.model.migrate.check INFO 2017-11-18 14:50:56,428 Migrating 81 -> 82... galaxy.model.migrate.check INFO 2017-11-18 14:50:56,853 galaxy.model.migrate.check INFO 2017-11-18 14:50:56,853 Migration script to add the tool_shed_repository table. galaxy.model.migrate.check INFO 2017-11-18 14:50:56,853 galaxy.model.migrate.check INFO 2017-11-18 14:50:56,853 galaxy.model.migrate.check INFO 2017-11-18 14:50:56,853 Migrating 82 -> 83... galaxy.model.migrate.check INFO 2017-11-18 14:50:57,294 galaxy.model.migrate.check INFO 2017-11-18 14:50:57,294 Migration script to add 'prepare_input_files_cmd' column to the task table and to rename a column. galaxy.model.migrate.check INFO 2017-11-18 14:50:57,294 galaxy.model.migrate.check INFO 2017-11-18 14:50:57,295 galaxy.model.migrate.check INFO 2017-11-18 14:50:57,295 Migrating 83 -> 84... galaxy.model.migrate.check INFO 2017-11-18 14:50:57,728 galaxy.model.migrate.check INFO 2017-11-18 14:50:57,728 Migration script to add 'ldda_id' column to the implicitly_converted_dataset_association table. galaxy.model.migrate.check INFO 2017-11-18 14:50:57,728 galaxy.model.migrate.check INFO 2017-11-18 14:50:57,728 galaxy.model.migrate.check INFO 2017-11-18 14:50:57,728 Migrating 84 -> 85... galaxy.model.migrate.check INFO 2017-11-18 14:50:58,148 galaxy.model.migrate.check INFO 2017-11-18 14:50:58,148 Migration script to add 'info' column to the task table. galaxy.model.migrate.check INFO 2017-11-18 14:50:58,148 galaxy.model.migrate.check INFO 2017-11-18 14:50:58,148 galaxy.model.migrate.check INFO 2017-11-18 14:50:58,148 Migrating 85 -> 86... galaxy.model.migrate.check INFO 2017-11-18 14:50:58,592 galaxy.model.migrate.check INFO 2017-11-18 14:50:58,592 Migration script to add the metadata, update_available and includes_datatypes columns to the tool_shed_repository table. galaxy.model.migrate.check INFO 2017-11-18 14:50:58,592 galaxy.model.migrate.check INFO 2017-11-18 14:50:58,592 galaxy.model.migrate.check INFO 2017-11-18 14:50:58,592 Migrating 86 -> 87... galaxy.model.migrate.check INFO 2017-11-18 14:50:59,467 galaxy.model.migrate.check INFO 2017-11-18 14:50:59,467 Migration script to create the tool_id_guid_map table. galaxy.model.migrate.check INFO 2017-11-18 14:50:59,467 galaxy.model.migrate.check INFO 2017-11-18 14:50:59,467 galaxy.model.migrate.check INFO 2017-11-18 14:50:59,467 Migrating 87 -> 88... galaxy.model.migrate.check INFO 2017-11-18 14:50:59,889 galaxy.model.migrate.check INFO 2017-11-18 14:50:59,890 Migration script to add the installed_changeset_revision column to the tool_shed_repository table. galaxy.model.migrate.check INFO 2017-11-18 14:50:59,890 galaxy.model.migrate.check INFO 2017-11-18 14:50:59,890 Updated the installed_changeset_revision column for 0 rows in the tool_shed_repository table. galaxy.model.migrate.check INFO 2017-11-18 14:50:59,890 galaxy.model.migrate.check INFO 2017-11-18 14:50:59,890 Migrating 88 -> 89... galaxy.model.migrate.check INFO 2017-11-18 14:51:00,339 galaxy.model.migrate.check INFO 2017-11-18 14:51:00,339 Migration script to add 'object_store_id' column to various tables galaxy.model.migrate.check INFO 2017-11-18 14:51:00,339 galaxy.model.migrate.check INFO 2017-11-18 14:51:00,340 galaxy.model.migrate.check INFO 2017-11-18 14:51:00,340 Migrating 89 -> 90... galaxy.model.migrate.check INFO 2017-11-18 14:51:00,798 galaxy.model.migrate.check INFO 2017-11-18 14:51:00,799 Migration script to add the uninstalled and dist_to_shed columns to the tool_shed_repository table. galaxy.model.migrate.check INFO 2017-11-18 14:51:00,799 galaxy.model.migrate.check INFO 2017-11-18 14:51:00,799 galaxy.model.migrate.check INFO 2017-11-18 14:51:00,799 Migrating 90 -> 91... galaxy.model.migrate.check INFO 2017-11-18 14:51:01,229 galaxy.model.migrate.check INFO 2017-11-18 14:51:01,229 Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table. galaxy.model.migrate.check INFO 2017-11-18 14:51:01,230 galaxy.model.migrate.check INFO 2017-11-18 14:51:01,230 Added 0 rows to the new tool_version table. galaxy.model.migrate.check INFO 2017-11-18 14:51:01,230 galaxy.model.migrate.check INFO 2017-11-18 14:51:01,230 Migrating 91 -> 92... galaxy.model.migrate.check INFO 2017-11-18 14:51:01,663 galaxy.model.migrate.check INFO 2017-11-18 14:51:01,663 Migration script to create the migrate_tools table. galaxy.model.migrate.check INFO 2017-11-18 14:51:01,663 galaxy.model.migrate.check INFO 2017-11-18 14:51:01,663 galaxy.model.migrate.check INFO 2017-11-18 14:51:01,663 Migrating 92 -> 93... galaxy.model.migrate.check INFO 2017-11-18 14:51:02,088 galaxy.model.migrate.check INFO 2017-11-18 14:51:02,088 Migration script to add a 'params' column to the 'job' table. galaxy.model.migrate.check INFO 2017-11-18 14:51:02,088 galaxy.model.migrate.check INFO 2017-11-18 14:51:02,088 galaxy.model.migrate.check INFO 2017-11-18 14:51:02,088 Migrating 93 -> 94... galaxy.model.migrate.check INFO 2017-11-18 14:51:02,533 galaxy.model.migrate.check INFO 2017-11-18 14:51:02,533 Migration script to add a 'handler' column to the 'job' table. galaxy.model.migrate.check INFO 2017-11-18 14:51:02,533 galaxy.model.migrate.check INFO 2017-11-18 14:51:02,533 galaxy.model.migrate.check INFO 2017-11-18 14:51:02,533 Migrating 94 -> 95... galaxy.model.migrate.check INFO 2017-11-18 14:51:02,972 galaxy.model.migrate.check INFO 2017-11-18 14:51:02,973 Migration script to create table for tracking history_dataset_association subsets. galaxy.model.migrate.check INFO 2017-11-18 14:51:02,973 galaxy.model.migrate.check INFO 2017-11-18 14:51:02,973 galaxy.model.migrate.check INFO 2017-11-18 14:51:02,973 Migrating 95 -> 96... galaxy.model.migrate.check INFO 2017-11-18 14:51:03,422 galaxy.model.migrate.check INFO 2017-11-18 14:51:03,423 Migration script to add column to openid table for provider. galaxy.model.migrate.check INFO 2017-11-18 14:51:03,423 Remove any OpenID entries with nonunique GenomeSpace Identifier galaxy.model.migrate.check INFO 2017-11-18 14:51:03,423 galaxy.model.migrate.check INFO 2017-11-18 14:51:03,423 galaxy.model.migrate.check INFO 2017-11-18 14:51:03,423 Migrating 96 -> 97... galaxy.model.migrate.check INFO 2017-11-18 14:51:03,872 galaxy.model.migrate.check INFO 2017-11-18 14:51:03,872 Migration script to add the ctx_rev column to the tool_shed_repository table. galaxy.model.migrate.check INFO 2017-11-18 14:51:03,872 galaxy.model.migrate.check INFO 2017-11-18 14:51:03,872 galaxy.model.migrate.check INFO 2017-11-18 14:51:03,872 Migrating 97 -> 98... galaxy.model.migrate.check INFO 2017-11-18 14:51:04,332 galaxy.model.migrate.check INFO 2017-11-18 14:51:04,332 Migration script to create the genome_index_tool_data table. galaxy.model.migrate.check INFO 2017-11-18 14:51:04,332 galaxy.model.migrate.check INFO 2017-11-18 14:51:04,332 galaxy.model.migrate.check INFO 2017-11-18 14:51:04,332 Migrating 98 -> 99... galaxy.model.migrate.check INFO 2017-11-18 14:51:04,758 galaxy.model.migrate.check INFO 2017-11-18 14:51:04,758 Migration script to add the tool_dependency table. galaxy.model.migrate.check INFO 2017-11-18 14:51:04,758 galaxy.model.migrate.check INFO 2017-11-18 14:51:04,758 galaxy.model.migrate.check INFO 2017-11-18 14:51:04,759 Migrating 99 -> 100... galaxy.model.migrate.check INFO 2017-11-18 14:51:05,183 galaxy.model.migrate.check INFO 2017-11-18 14:51:05,183 Migration script to alter the type of the tool_dependency.version column from TrimmedString(40) to Text. galaxy.model.migrate.check INFO 2017-11-18 14:51:05,183 galaxy.model.migrate.check INFO 2017-11-18 14:51:05,183 galaxy.model.migrate.check INFO 2017-11-18 14:51:05,183 Migrating 100 -> 101... galaxy.model.migrate.check INFO 2017-11-18 14:51:05,628 galaxy.model.migrate.check INFO 2017-11-18 14:51:05,628 Migration script to drop the installed_changeset_revision column from the tool_dependency table. galaxy.model.migrate.check INFO 2017-11-18 14:51:05,628 galaxy.model.migrate.check INFO 2017-11-18 14:51:05,628 galaxy.model.migrate.check INFO 2017-11-18 14:51:05,628 Migrating 101 -> 102... galaxy.model.migrate.check INFO 2017-11-18 14:51:06,057 galaxy.model.migrate.check INFO 2017-11-18 14:51:06,057 Migration script to add status and error_message columns to the tool_dependency table and drop the uninstalled column from the tool_dependency table. galaxy.model.migrate.check INFO 2017-11-18 14:51:06,057 galaxy.model.migrate.check INFO 2017-11-18 14:51:06,057 galaxy.model.migrate.check INFO 2017-11-18 14:51:06,057 Migrating 102 -> 103... galaxy.model.migrate.check INFO 2017-11-18 14:51:06,492 Migration script to add status and error_message columns to the tool_shed_repository table. galaxy.model.migrate.check INFO 2017-11-18 14:51:06,492 galaxy.model.migrate.check INFO 2017-11-18 14:51:06,492 Migrating 103 -> 104... galaxy.model.migrate.check INFO 2017-11-18 14:51:06,520 galaxy.model.migrate.check INFO 2017-11-18 14:51:06,520 Migrating 104 -> 105... galaxy.model.migrate.check INFO 2017-11-18 14:51:07,642 galaxy.model.migrate.check INFO 2017-11-18 14:51:07,642 Migration script to add the cleanup_event* tables. galaxy.model.migrate.check INFO 2017-11-18 14:51:07,643 galaxy.model.migrate.check INFO 2017-11-18 14:51:07,643 galaxy.model.migrate.check INFO 2017-11-18 14:51:07,643 Migrating 105 -> 106... 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,099 Creating index 'ix_metadata_file_lda_id' on column 'lda_id' in table 'metadata_file' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,130 Creating index 'ix_history_importable' on column 'importable' in table 'history' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,176 Creating index 'ix_sample_bar_code' on column 'bar_code' in table 'sample' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,201 Creating index 'ix_request_type_deleted' on column 'deleted' in table 'request_type' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,221 Creating index 'ix_galaxy_user_username' on column 'username' in table 'galaxy_user' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,265 Creating index 'ix_form_definition_type' on column 'type' in table 'form_definition' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,283 Creating index 'ix_form_definition_layout' on column 'layout' in table 'form_definition' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,290 Creating index 'ix_job_library_folder_id' on column 'library_folder_id' in table 'job' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,333 Creating index 'ix_page_published' on column 'published' in table 'page' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,366 Creating index 'ix_page_deleted' on column 'deleted' in table 'page' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,367 Creating index 'ix_galaxy_user_form_values_id' on column 'form_values_id' in table 'galaxy_user' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,376 Creating index 'ix_lia_deleted' on column 'deleted' in table 'library_info_association' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,413 Creating index 'ix_lfia_deleted' on column 'deleted' in table 'library_folder_info_association' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,452 Creating index 'ix_lddia_deleted' on column 'deleted' in table 'library_dataset_dataset_info_association' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,479 Creating index 'ix_sample_library_id' on column 'library_id' in table 'sample' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,479 Creating index 'ix_sample_folder_id' on column 'folder_id' in table 'sample' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,486 Creating index 'ix_lia_inheritable' on column 'inheritable' in table 'library_info_association' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,496 Creating index 'ix_lfia_inheritable' on column 'inheritable' in table 'library_folder_info_association' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,503 Creating index 'ix_job_imported' on column 'imported' in table 'job' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,504 Creating index 'ix_request_notification' on column 'notification' in table 'request' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,536 Creating index 'ix_sd_external_service_id' on column 'external_service_id' in table 'sample_dataset' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,562 Creating index 'ix_icda_ldda_parent_id' on column 'ldda_parent_id' in table 'implicitly_converted_dataset_association' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,606 Creating index 'ix_library_dataset_purged' on column 'purged' in table 'library_dataset' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,634 Creating index 'ix_run_subindex' on column 'subindex' in table 'run' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,662 Creating index 'ix_history_dataset_association_purged' on column 'purged' in table 'history_dataset_association' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,691 Creating index 'ix_galaxy_user_disk_usage' on column 'disk_usage' in table 'galaxy_user' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,692 Creating index 'ix_galaxy_session_disk_usage' on column 'disk_usage' in table 'galaxy_session' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,711 Creating index 'ix_icda_ldda_id' on column 'ldda_id' in table 'implicitly_converted_dataset_association' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,718 Creating index 'ix_tsr_includes_datatypes' on column 'includes_datatypes' in table 'tool_shed_repository' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,760 Creating index 'ix_dataset_object_store_id' on column 'object_store_id' in table 'dataset' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,788 Creating index 'ix_job_object_store_id' on column 'object_store_id' in table 'job' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,788 Creating index 'ix_metadata_file_object_store_id' on column 'object_store_id' in table 'metadata_file' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,789 Creating index 'ix_job_handler' on column 'handler' in table 'job' 0106_add_missing_indexes DEBUG 2017-11-18 14:51:08,789 Creating index 'ix_galaxy_user_email' on column 'email' in table 'galaxy_user' galaxy.model.migrate.check INFO 2017-11-18 14:51:08,811 galaxy.model.migrate.check INFO 2017-11-18 14:51:08,811 Migration script to create missing indexes. Adding new columns to existing tables via SQLAlchemy does not create the index, even if the column definition includes index=True. galaxy.model.migrate.check INFO 2017-11-18 14:51:08,811 galaxy.model.migrate.check INFO 2017-11-18 14:51:08,811 galaxy.model.migrate.check INFO 2017-11-18 14:51:08,811 Migrating 106 -> 107... galaxy.model.migrate.check INFO 2017-11-18 14:51:09,287 galaxy.model.migrate.check INFO 2017-11-18 14:51:09,287 Add the exit_code column to the Job and Task tables. galaxy.model.migrate.check INFO 2017-11-18 14:51:09,287 galaxy.model.migrate.check INFO 2017-11-18 14:51:09,287 galaxy.model.migrate.check INFO 2017-11-18 14:51:09,288 Migrating 107 -> 108... galaxy.model.migrate.check INFO 2017-11-18 14:51:09,831 galaxy.model.migrate.check INFO 2017-11-18 14:51:09,832 Add the ExtendedMetadata and ExtendedMetadataIndex tables galaxy.model.migrate.check INFO 2017-11-18 14:51:09,832 galaxy.model.migrate.check INFO 2017-11-18 14:51:09,832 galaxy.model.migrate.check INFO 2017-11-18 14:51:09,832 Migrating 108 -> 109... galaxy.model.migrate.check INFO 2017-11-18 14:51:10,329 galaxy.model.migrate.check INFO 2017-11-18 14:51:10,329 Migration script to add the repository_dependency and repository_repository_dependency_association tables. galaxy.model.migrate.check INFO 2017-11-18 14:51:10,329 galaxy.model.migrate.check INFO 2017-11-18 14:51:10,329 galaxy.model.migrate.check INFO 2017-11-18 14:51:10,329 Migrating 109 -> 110... galaxy.model.migrate.check INFO 2017-11-18 14:51:10,796 galaxy.model.migrate.check INFO 2017-11-18 14:51:10,796 Add UUID column to dataset table galaxy.model.migrate.check INFO 2017-11-18 14:51:10,796 galaxy.model.migrate.check INFO 2017-11-18 14:51:10,796 galaxy.model.migrate.check INFO 2017-11-18 14:51:10,796 Migrating 110 -> 111... galaxy.model.migrate.check INFO 2017-11-18 14:51:11,294 galaxy.model.migrate.check INFO 2017-11-18 14:51:11,294 Add support for job destinations to the job table galaxy.model.migrate.check INFO 2017-11-18 14:51:11,294 galaxy.model.migrate.check INFO 2017-11-18 14:51:11,294 galaxy.model.migrate.check INFO 2017-11-18 14:51:11,294 Migrating 111 -> 112... 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2017-11-18 14:51:11,771 Created data_manager_history_association table 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2017-11-18 14:51:11,786 Created data_manager_job_association table galaxy.model.migrate.check INFO 2017-11-18 14:51:11,798 galaxy.model.migrate.check INFO 2017-11-18 14:51:11,798 Migration script to add the data_manager_history_association table and data_manager_job_association. galaxy.model.migrate.check INFO 2017-11-18 14:51:11,798 galaxy.model.migrate.check INFO 2017-11-18 14:51:11,798 galaxy.model.migrate.check INFO 2017-11-18 14:51:11,798 Migrating 112 -> 113... galaxy.model.migrate.check INFO 2017-11-18 14:51:11,823 galaxy.model.migrate.check INFO 2017-11-18 14:51:11,823 Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. galaxy.model.migrate.check INFO 2017-11-18 14:51:11,823 galaxy.model.migrate.check INFO 2017-11-18 14:51:11,823 galaxy.model.migrate.check INFO 2017-11-18 14:51:11,823 Migrating 113 -> 114... galaxy.model.migrate.check INFO 2017-11-18 14:51:11,848 galaxy.model.migrate.check INFO 2017-11-18 14:51:11,849 Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. galaxy.model.migrate.check INFO 2017-11-18 14:51:11,849 galaxy.model.migrate.check INFO 2017-11-18 14:51:11,849 galaxy.model.migrate.check INFO 2017-11-18 14:51:11,849 Migrating 114 -> 115... galaxy.model.migrate.check INFO 2017-11-18 14:51:11,988 galaxy.model.migrate.check INFO 2017-11-18 14:51:11,989 Migrating 115 -> 116... galaxy.model.migrate.check INFO 2017-11-18 14:51:12,468 galaxy.model.migrate.check INFO 2017-11-18 14:51:12,468 Migration script to drop the update_available Boolean column and replace it with the tool_shed_status JSONType column in the tool_shed_repository table. galaxy.model.migrate.check INFO 2017-11-18 14:51:12,468 galaxy.model.migrate.check INFO 2017-11-18 14:51:12,468 galaxy.model.migrate.check INFO 2017-11-18 14:51:12,468 Migrating 116 -> 117... galaxy.model.migrate.check INFO 2017-11-18 14:51:12,970 galaxy.model.migrate.check INFO 2017-11-18 14:51:12,970 Adds 'active' and 'activation_token' columns to the galaxy_user table. galaxy.model.migrate.check INFO 2017-11-18 14:51:12,970 galaxy.model.migrate.check INFO 2017-11-18 14:51:12,971 galaxy.model.migrate.check INFO 2017-11-18 14:51:12,971 Migrating 117 -> 118... galaxy.model.migrate.check INFO 2017-11-18 14:51:13,524 galaxy.model.migrate.check INFO 2017-11-18 14:51:13,525 Add link from history_dataset_association to the extended_metadata table galaxy.model.migrate.check INFO 2017-11-18 14:51:13,525 galaxy.model.migrate.check INFO 2017-11-18 14:51:13,525 galaxy.model.migrate.check INFO 2017-11-18 14:51:13,525 Migrating 118 -> 119... galaxy.model.migrate.check INFO 2017-11-18 14:51:14,039 galaxy.model.migrate.check INFO 2017-11-18 14:51:14,039 Migration script for job metric plugins. galaxy.model.migrate.check INFO 2017-11-18 14:51:14,039 galaxy.model.migrate.check INFO 2017-11-18 14:51:14,039 galaxy.model.migrate.check INFO 2017-11-18 14:51:14,039 Migrating 119 -> 120... galaxy.model.migrate.check INFO 2017-11-18 14:51:14,825 galaxy.model.migrate.check INFO 2017-11-18 14:51:14,825 Migration script for tables related to dataset collections. galaxy.model.migrate.check INFO 2017-11-18 14:51:14,825 galaxy.model.migrate.check INFO 2017-11-18 14:51:14,825 galaxy.model.migrate.check INFO 2017-11-18 14:51:14,826 Migrating 120 -> 121... galaxy.model.migrate.check INFO 2017-11-18 14:51:15,399 galaxy.model.migrate.check INFO 2017-11-18 14:51:15,400 Add UUIDs to workflows galaxy.model.migrate.check INFO 2017-11-18 14:51:15,400 galaxy.model.migrate.check INFO 2017-11-18 14:51:15,400 galaxy.model.migrate.check INFO 2017-11-18 14:51:15,400 Migrating 121 -> 122... galaxy.model.migrate.check INFO 2017-11-18 14:51:15,946 galaxy.model.migrate.check INFO 2017-11-18 14:51:15,946 Migration script to grow MySQL blobs. galaxy.model.migrate.check INFO 2017-11-18 14:51:15,946 galaxy.model.migrate.check INFO 2017-11-18 14:51:15,946 galaxy.model.migrate.check INFO 2017-11-18 14:51:15,946 Migrating 122 -> 123... galaxy.model.migrate.check INFO 2017-11-18 14:51:16,613 galaxy.model.migrate.check INFO 2017-11-18 14:51:16,614 Migration script for workflow request tables. galaxy.model.migrate.check INFO 2017-11-18 14:51:16,614 galaxy.model.migrate.check INFO 2017-11-18 14:51:16,614 galaxy.model.migrate.check INFO 2017-11-18 14:51:16,614 Migrating 123 -> 124... galaxy.model.migrate.check INFO 2017-11-18 14:51:17,179 galaxy.model.migrate.check INFO 2017-11-18 14:51:17,179 Migration script for the job state history table galaxy.model.migrate.check INFO 2017-11-18 14:51:17,180 galaxy.model.migrate.check INFO 2017-11-18 14:51:17,180 galaxy.model.migrate.check INFO 2017-11-18 14:51:17,180 Migrating 124 -> 125... galaxy.model.migrate.check INFO 2017-11-18 14:51:17,735 galaxy.model.migrate.check INFO 2017-11-18 14:51:17,735 Migration script to enhance workflow step usability by adding labels and UUIDs. galaxy.model.migrate.check INFO 2017-11-18 14:51:17,735 galaxy.model.migrate.check INFO 2017-11-18 14:51:17,736 galaxy.model.migrate.check INFO 2017-11-18 14:51:17,736 Migrating 125 -> 126... galaxy.model.migrate.check INFO 2017-11-18 14:51:18,312 galaxy.model.migrate.check INFO 2017-11-18 14:51:18,312 Migration script for the password reset table galaxy.model.migrate.check INFO 2017-11-18 14:51:18,312 galaxy.model.migrate.check INFO 2017-11-18 14:51:18,312 galaxy.model.migrate.check INFO 2017-11-18 14:51:18,312 Migrating 126 -> 127... galaxy.model.migrate.check INFO 2017-11-18 14:51:19,611 galaxy.model.migrate.check INFO 2017-11-18 14:51:19,611 Migration script updating collections tables for output collections. galaxy.model.migrate.check INFO 2017-11-18 14:51:19,611 galaxy.model.migrate.check INFO 2017-11-18 14:51:19,611 galaxy.model.migrate.check INFO 2017-11-18 14:51:19,611 Migrating 127 -> 128... galaxy.model.migrate.check INFO 2017-11-18 14:51:20,191 galaxy.model.migrate.check INFO 2017-11-18 14:51:20,191 Migration script to add session update time (used for timeouts) galaxy.model.migrate.check INFO 2017-11-18 14:51:20,191 galaxy.model.migrate.check INFO 2017-11-18 14:51:20,191 galaxy.model.migrate.check INFO 2017-11-18 14:51:20,191 Migrating 128 -> 129... galaxy.model.migrate.check INFO 2017-11-18 14:51:20,786 galaxy.model.migrate.check INFO 2017-11-18 14:51:20,787 Migration script to allow invalidation of job external output metadata temp files galaxy.model.migrate.check INFO 2017-11-18 14:51:20,787 galaxy.model.migrate.check INFO 2017-11-18 14:51:20,787 galaxy.model.migrate.check INFO 2017-11-18 14:51:20,787 Migrating 129 -> 130... galaxy.model.migrate.check INFO 2017-11-18 14:51:21,397 galaxy.model.migrate.check INFO 2017-11-18 14:51:21,398 Migration script to change the 'value' column of 'user_preference' table from varchar to text. galaxy.model.migrate.check INFO 2017-11-18 14:51:21,398 galaxy.model.migrate.check INFO 2017-11-18 14:51:21,398 galaxy.model.migrate.check INFO 2017-11-18 14:51:21,398 Migrating 130 -> 131... galaxy.model.migrate.check INFO 2017-11-18 14:51:22,036 galaxy.model.migrate.check INFO 2017-11-18 14:51:22,036 Migration script to support subworkflows and workflow request input parameters galaxy.model.migrate.check INFO 2017-11-18 14:51:22,036 galaxy.model.migrate.check INFO 2017-11-18 14:51:22,036 galaxy.model.migrate.check INFO 2017-11-18 14:51:22,036 Migrating 131 -> 132... galaxy.model.migrate.check INFO 2017-11-18 14:51:22,074 galaxy.model.migrate.check INFO 2017-11-18 14:51:22,074 Migrating 132 -> 133... galaxy.model.migrate.check INFO 2017-11-18 14:51:22,650 galaxy.model.migrate.check INFO 2017-11-18 14:51:22,650 Add dependencies column to jobs table galaxy.model.migrate.check INFO 2017-11-18 14:51:22,650 galaxy.model.migrate.check INFO 2017-11-18 14:51:22,650 galaxy.model.migrate.check INFO 2017-11-18 14:51:22,650 Migrating 133 -> 134... galaxy.model.migrate.check INFO 2017-11-18 14:51:22,672 galaxy.model.migrate.check INFO 2017-11-18 14:51:22,672 Migration script to set the 'deleted' column of the galaxy.model.migrate.check INFO 2017-11-18 14:51:22,672 'history_dataset_association' table to True if 'purged' is True. galaxy.model.migrate.check INFO 2017-11-18 14:51:22,672 galaxy.model.migrate.check INFO 2017-11-18 14:51:22,673 galaxy.model.migrate.check INFO 2017-11-18 14:51:22,673 Migrating 134 -> 135... galaxy.model.migrate.check INFO 2017-11-18 14:51:23,273 galaxy.model.migrate.check INFO 2017-11-18 14:51:23,273 This migration script adds support for storing tags in the context of a dataset in a library galaxy.model.migrate.check INFO 2017-11-18 14:51:23,273 galaxy.model.migrate.check INFO 2017-11-18 14:51:23,274 migrate.versioning.repository DEBUG 2017-11-18 14:51:23,281 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,282 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,282 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,282 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,283 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,283 Loading script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,283 Script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,283 Loading script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,283 Script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,283 Loading script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,283 Script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,284 Loading script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,284 Script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,284 Loading script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,284 Script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,284 Loading script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,284 Script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,284 Loading script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,284 Script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,285 Loading script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,285 Script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,285 Loading script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,285 Script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,285 Loading script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:51:23,285 Script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py loaded successfully migrate.versioning.repository DEBUG 2017-11-18 14:51:23,285 Repository lib/tool_shed/galaxy_install/migrate loaded successfully migrate.versioning.repository DEBUG 2017-11-18 14:51:23,285 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))]) tool_shed.galaxy_install.migrate.check DEBUG 2017-11-18 14:51:23,307 The main Galaxy tool shed is not currently available, so skipped tool migration 1 until next server startup galaxy.config INFO 2017-11-18 14:51:23,335 Install database targetting Galaxy's database configuration. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,485 Loading datatypes from ./config/datatypes_conf.xml.sample galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,485 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,492 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,492 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,492 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,493 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,493 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,493 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,493 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,493 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,494 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,494 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,494 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,494 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,494 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,497 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,497 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,498 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,498 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,498 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,498 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,499 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,499 Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,499 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,502 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,502 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,503 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,503 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,503 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,504 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,504 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,504 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,505 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,505 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,505 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,506 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,506 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,506 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,506 Retrieved datatype module galaxy.datatypes.sequence:FastqGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,507 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,507 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,507 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,507 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,507 Retrieved datatype module galaxy.datatypes.sequence:FastqBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,508 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,508 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,508 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,508 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,508 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,509 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,509 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,509 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,509 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,509 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,510 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,510 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,510 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,510 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,510 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,511 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,511 Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,511 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,511 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,512 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,512 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,512 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,513 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,513 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,513 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,513 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,514 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,514 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,514 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,514 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,515 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,515 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,515 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,515 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,516 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,516 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,516 Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,516 Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,517 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,517 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,517 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,517 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,517 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,517 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,518 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,518 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,518 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,518 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,518 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,518 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,519 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,519 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,519 Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,519 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,531 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,531 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,531 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,532 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,532 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,532 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,533 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,533 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,533 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,533 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,533 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,535 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,535 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,535 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,535 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,536 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,536 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,536 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,537 Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,537 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,537 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,537 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,537 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,538 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,538 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,538 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,538 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,539 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,539 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,539 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,539 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,540 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,540 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,540 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,540 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,541 Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,541 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,541 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,541 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,541 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,542 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,542 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,542 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,542 Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,543 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,543 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,543 Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,543 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,544 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,544 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,544 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,544 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,544 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,544 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,545 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,545 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,545 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,545 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,545 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,545 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,546 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,546 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,546 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,547 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,547 Roadmaps is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,547 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,547 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,548 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,548 Sequences is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,548 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,548 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,549 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,550 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,551 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,551 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,552 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,553 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,554 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,554 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,554 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,554 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,554 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,555 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,555 Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,555 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,555 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,555 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,555 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,556 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,556 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,556 Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,556 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,556 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,557 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,557 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,557 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,557 Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,558 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,558 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,558 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,572 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,572 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,572 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,572 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,573 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,573 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,573 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,573 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,573 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,574 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,574 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,574 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,574 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,574 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,575 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,575 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,575 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,575 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,575 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,575 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,584 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,584 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,591 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,591 Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,591 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,591 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,592 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,592 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,592 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,592 Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,593 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,593 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,593 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,594 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,594 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,594 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,595 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,595 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,595 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,596 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,596 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,596 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,596 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,597 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,597 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,597 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,598 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,599 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,600 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,601 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,603 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,603 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,604 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,604 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,604 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,604 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,605 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,605 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,605 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,605 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,606 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,606 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,606 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,606 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,606 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,607 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,607 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,607 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,607 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,608 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,608 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,608 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,608 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,609 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,609 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,609 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,609 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,610 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,610 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,610 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,610 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,610 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,611 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,611 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,611 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,612 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,612 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,612 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,612 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,612 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,613 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,613 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,613 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,613 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,614 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,614 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,615 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,615 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,615 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,616 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,616 Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,616 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,616 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,616 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,617 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,617 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,617 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,617 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,617 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,617 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,618 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,618 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,618 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,618 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,618 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,619 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,619 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,619 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,619 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,619 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,619 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,620 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,620 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,620 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,623 Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,623 Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,635 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,636 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,637 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,637 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,638 Retrieved datatype module galaxy.datatypes.binary:Cel from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,638 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,638 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,638 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,639 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,639 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,639 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,639 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,648 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,648 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,649 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,649 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,650 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,650 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,650 Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,650 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,672 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,672 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,672 Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,672 Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,673 Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,673 Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,673 Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,673 Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,673 Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,674 Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,674 Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,674 Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,674 Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,674 Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,688 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,689 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,689 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,689 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,690 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,690 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,690 Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,690 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,691 Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,691 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,691 Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,691 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,691 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,692 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,692 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,692 Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,692 Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,692 Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,693 Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,694 Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,694 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,694 Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,694 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,694 Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,695 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,695 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,695 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,695 Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,695 Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,696 Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,696 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,696 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,696 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,696 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,696 Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,697 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,697 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,702 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,703 Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,709 Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,709 Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,710 Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,710 Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,710 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,710 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,711 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,721 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,721 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,721 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,722 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,722 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,722 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,722 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,722 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrtho from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,723 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,723 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylip from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,723 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,723 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,723 Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,724 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,724 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,724 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,724 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,724 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,724 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,724 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,725 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,725 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,725 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,725 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,725 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,725 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,725 Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,726 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,726 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,726 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,726 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,726 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,726 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,726 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,727 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,727 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,727 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,727 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,727 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,727 Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,727 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,728 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,728 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,728 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,728 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,728 Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,728 Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,729 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,729 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,729 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,729 Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,729 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,729 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,729 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,730 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,730 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,730 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,730 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,730 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,731 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,731 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,731 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,731 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,732 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,732 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,732 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,732 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,733 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,733 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,733 Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,733 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,733 Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,733 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,734 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,734 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,734 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,734 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,734 Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,734 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,734 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,735 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,735 Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,735 Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,735 Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,735 Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,735 Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,735 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,736 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,736 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerGz' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,736 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerBz2' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,736 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,736 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqGz' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,736 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqBz2' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,737 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,737 Loaded sniffer for datatype 'galaxy.datatypes.text:Html' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,737 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,737 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,737 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,737 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,738 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,738 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,738 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,738 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,738 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,738 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,739 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,739 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,739 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,739 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,739 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,739 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,740 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,740 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,740 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,740 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,740 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,740 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,741 Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,741 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,741 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,741 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,741 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,741 Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,742 Loaded sniffer for datatype 'galaxy.datatypes.binary:Cel' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,742 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,742 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,742 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,742 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,742 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,742 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,743 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,743 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,743 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,743 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,743 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,743 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,744 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,744 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,744 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,744 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,744 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,744 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,744 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,745 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,745 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,745 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,745 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,745 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,757 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,757 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,758 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,758 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,758 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,758 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,759 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,759 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:23,759 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.tools.data INFO 2017-11-18 14:51:24,473 Could not find tool data tool-data/all_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:24,475 Loaded 0 lines from 'tool-data/all_fasta.loc.sample' for 'all_fasta' galaxy.tools.data DEBUG 2017-11-18 14:51:24,475 Loaded tool data table 'all_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:24,476 Could not find tool data tool-data/bfast_indexes.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:24,478 Loaded 0 lines from 'tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' galaxy.tools.data DEBUG 2017-11-18 14:51:24,478 Loaded tool data table 'bfast_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:24,479 Could not find tool data tool-data/blastdb.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:24,481 Loaded 0 lines from 'tool-data/blastdb.loc.sample' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 14:51:24,481 Loaded tool data table 'blastdb' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:24,482 Could not find tool data tool-data/blastdb_p.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:24,483 Loaded 0 lines from 'tool-data/blastdb_p.loc.sample' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 14:51:24,484 Loaded tool data table 'blastdb_p' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:24,484 Could not find tool data tool-data/blastdb_d.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:24,486 Loaded 0 lines from 'tool-data/blastdb_d.loc.sample' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 14:51:24,486 Loaded tool data table 'blastdb_d' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data WARNING 2017-11-18 14:51:24,487 Cannot find index file 'tool-data/bwa_index.loc' for tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 14:51:24,487 Loaded tool data table 'bwa_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data WARNING 2017-11-18 14:51:24,488 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 14:51:24,488 Loaded tool data table 'bwa_indexes_color' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:24,488 Could not find tool data tool-data/maf_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:24,490 Loaded 0 lines from 'tool-data/maf_index.loc.sample' for 'indexed_maf_files' galaxy.tools.data DEBUG 2017-11-18 14:51:24,491 Loaded tool data table 'indexed_maf_files' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:24,491 Could not find tool data tool-data/ngs_sim_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:24,493 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' galaxy.tools.data DEBUG 2017-11-18 14:51:24,493 Loaded tool data table 'ngs_sim_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:24,494 Could not find tool data tool-data/perm_base_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:24,495 Loaded 0 lines from 'tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' galaxy.tools.data DEBUG 2017-11-18 14:51:24,496 Loaded tool data table 'perm_base_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:24,496 Could not find tool data tool-data/perm_color_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:24,498 Loaded 0 lines from 'tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' galaxy.tools.data DEBUG 2017-11-18 14:51:24,498 Loaded tool data table 'perm_color_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:24,499 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:24,500 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'picard_indexes' galaxy.tools.data DEBUG 2017-11-18 14:51:24,501 Loaded tool data table 'picard_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:24,502 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:24,502 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'srma_indexes' galaxy.tools.data DEBUG 2017-11-18 14:51:24,502 Loaded tool data table 'srma_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:24,503 Could not find tool data tool-data/mosaik_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:24,504 Loaded 0 lines from 'tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' galaxy.tools.data DEBUG 2017-11-18 14:51:24,504 Loaded tool data table 'mosaik_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:24,505 Could not find tool data tool-data/twobit.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:24,507 Loaded 0 lines from 'tool-data/twobit.loc.sample' for 'twobit' galaxy.tools.data DEBUG 2017-11-18 14:51:24,507 Loaded tool data table 'twobit' from file './config/tool_data_table_conf.xml.sample' requests.packages.urllib3.connectionpool INFO 2017-11-18 14:51:24,551 Starting new HTTP connection (1): igv.broadinstitute.org requests.packages.urllib3.connectionpool DEBUG 2017-11-18 14:51:25,016 "GET /genomes/genomes.txt HTTP/1.1" 200 15681 galaxy.tools.data DEBUG 2017-11-18 14:51:25,021 Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-RPgysD". galaxy.tools.data WARNING 2017-11-18 14:51:25,021 Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields): <Server-Side Genome List> galaxy.tools.data DEBUG 2017-11-18 14:51:25,024 Loaded 156 lines from '/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-RPgysD' for 'igv_broad_genomes' galaxy.tools.data DEBUG 2017-11-18 14:51:25,026 Loaded tool data table 'igv_broad_genomes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:25,027 Could not find tool data tool-data/liftOver.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:25,028 Loaded 0 lines from 'tool-data/liftOver.loc.sample' for 'liftOver' galaxy.tools.data DEBUG 2017-11-18 14:51:25,028 Loaded tool data table 'liftOver' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:25,029 Could not find tool data tool-data/bam_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:25,031 Loaded 1 lines from 'tool-data/bam_iobio.loc.sample' for 'bam_iobio' galaxy.tools.data DEBUG 2017-11-18 14:51:25,031 Loaded tool data table 'bam_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:25,032 Could not find tool data tool-data/vcf_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:25,033 Loaded 1 lines from 'tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' galaxy.tools.data DEBUG 2017-11-18 14:51:25,033 Loaded tool data table 'vcf_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:51:25,034 Could not find tool data tool-data/biom_simple_display.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:51:25,036 Loaded 1 lines from 'tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' galaxy.tools.data DEBUG 2017-11-18 14:51:25,036 Loaded tool data table 'biom_simple_display' from file './config/tool_data_table_conf.xml.sample' galaxy.jobs WARNING 2017-11-18 14:51:25,223 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/galaxydir/galaxy/config/galaxy.ini.sample" instead galaxy.jobs DEBUG 2017-11-18 14:51:25,223 Loading job configuration from /galaxydir/galaxy/config/galaxy.ini.sample galaxy.jobs DEBUG 2017-11-18 14:51:25,223 Done loading job configuration beaker.container DEBUG 2017-11-18 14:51:25,482 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache galaxy.tools.toolbox.base INFO 2017-11-18 14:51:25,490 Parsing the tool configuration ./config/tool_conf.xml.sample galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,526 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,531 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,539 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,544 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,547 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,556 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,559 Loaded tool id: biomart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,563 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,566 Loaded tool id: gramenemart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,572 Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,575 Loaded tool id: flymine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,579 Loaded tool id: flymine_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,583 Loaded tool id: modmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,586 Loaded tool id: mousemine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,593 Loaded tool id: ratmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,596 Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,599 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,602 Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,605 Loaded tool id: wormbase, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,609 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,612 Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,617 Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,620 Loaded tool id: hbvar, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,976 Loaded tool id: genomespace_importer, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,979 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,983 Loaded tool id: genomespace_exporter, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,986 Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,989 Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,992 Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:25,996 Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,029 Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,034 Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,040 Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,045 Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base ERROR 2017-11-18 14:51:26,048 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,051 Loaded tool id: addValue, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,055 Loaded tool id: cat1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,063 Loaded tool id: Cut1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,069 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,073 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,078 Loaded tool id: createInterval, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,078 Loaded tool id: Cut1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,082 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,086 Loaded tool id: Paste1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,092 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,096 Loaded tool id: random_lines1, version: 2.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,100 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,104 Loaded tool id: Show tail1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,108 Loaded tool id: trimmer, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,113 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,117 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,123 Loaded tool id: Filter1, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,129 Loaded tool id: sort1, version: 1.0.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,133 Loaded tool id: Grep1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,138 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,142 Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,145 Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,150 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,157 Loaded tool id: join1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,160 Loaded tool id: comp1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,165 Loaded tool id: Grouping1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,171 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,178 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,185 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,189 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,195 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,200 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,208 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,212 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,217 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,221 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,228 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,234 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,238 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,242 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,245 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,251 Loaded tool id: Extract genomic DNA 1, version: 2.2.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,257 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,264 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,268 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,278 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,284 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,290 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,296 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,301 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,305 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,309 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,314 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,325 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,329 Loaded tool id: Summary_Statistics1, version: 1.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,333 Loaded tool id: Count1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,338 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,346 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,350 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base INFO 2017-11-18 14:51:26,351 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 14:51:26,351 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 14:51:26,351 Reading tools from config files finshed (861.913 ms) galaxy.tools.deps DEBUG 2017-11-18 14:51:26,364 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.search DEBUG 2017-11-18 14:51:26,398 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 14:51:27,754 Toolbox index finished (1355.932 ms) galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,759 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,765 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,822 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,824 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,826 Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,828 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,830 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,834 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,836 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,840 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,842 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,845 Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,887 Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,897 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,934 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,936 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,946 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,957 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:27,960 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,006 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,010 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,014 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,066 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,069 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,072 Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,074 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,123 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,125 Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,128 Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,134 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,134 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,134 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,134 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,134 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,134 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,135 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,135 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,142 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,142 Adding inherited display application 'igv_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,151 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,151 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,151 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,152 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,154 Adding inherited display application 'igv_fasta' to datatype 'sequences' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,154 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,154 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,154 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,154 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,156 Adding inherited display application 'igv_fasta' to datatype 'mothur.align' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,159 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,160 Adding inherited display application 'igv_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,168 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,168 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,168 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,168 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,170 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,170 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,170 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,171 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,173 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,173 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,173 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,173 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,180 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,184 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,187 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,190 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,193 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,195 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,199 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,202 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,204 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,208 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,210 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,217 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,220 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,222 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,226 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,229 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,232 Loaded converter: CONVERTER_fasta_to_fai galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,235 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,236 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,237 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,239 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,240 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,245 Loaded converter: CONVERTER_fastqgz_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,247 Loaded converter: CONVERTER_fastqsangergz_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,250 Loaded converter: CONVERTER_fastqsolexagz_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,253 Loaded converter: CONVERTER_fastqcssangergz_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,256 Loaded converter: CONVERTER_fastqilluminagz_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,258 Loaded converter: CONVERTER_fastqbz2_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,263 Loaded converter: CONVERTER_fastqsangerbz2_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,267 Loaded converter: CONVERTER_fastqsolexabz2_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,269 Loaded converter: CONVERTER_fastqcssangerbz2_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,272 Loaded converter: CONVERTER_fastqilluminabz2_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,275 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,278 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,279 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,283 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,285 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,287 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,289 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,293 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,298 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,301 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,303 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,304 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,307 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,310 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,312 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,315 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,318 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,321 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,323 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,324 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,326 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,330 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,332 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,335 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,339 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,342 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,351 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,352 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,355 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,358 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,362 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,368 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,370 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,373 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,377 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,383 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,386 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,388 Loaded converter: CONVERTER_biom1_to_biom2 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,391 Loaded converter: CONVERTER_biom2_to_biom1 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,394 Loaded converter: CONVERTER_SMILES_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,397 Loaded converter: CONVERTER_SMILES_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,400 Loaded converter: CONVERTER_SMILES_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,403 Loaded converter: CONVERTER_SMILES_to_MOL galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,406 Loaded converter: CONVERTER_SMILES_to_MOL2 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,409 Loaded converter: CONVERTER_smiles_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,414 Loaded converter: CONVERTER_sdf_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,416 Loaded converter: CONVERTER_sdf_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,419 Loaded converter: CONVERTER_sdf_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,422 Loaded converter: CONVERTER_sdf_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,425 Loaded converter: CONVERTER_inchi_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,430 Loaded converter: CONVERTER_inchi_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,434 Loaded converter: CONVERTER_inchi_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,437 Loaded converter: CONVERTER_inchi_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,440 Loaded converter: CONVERTER_inchi_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,443 Loaded converter: CONVERTER_mol_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,447 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,450 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,453 Loaded converter: CONVERTER_mol_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,458 Loaded converter: CONVERTER_mol2_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,462 Loaded converter: CONVERTER_mol2_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,464 Loaded converter: CONVERTER_mol2_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,468 Loaded converter: CONVERTER_mol2_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,471 Loaded converter: CONVERTER_mol2_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,475 Loaded converter: CONVERTER_cml_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,479 Loaded converter: CONVERTER_cml_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,484 Loaded converter: CONVERTER_cml_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,487 Loaded converter: CONVERTER_cml_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,490 Loaded converter: CONVERTER_ref_to_seq_taxomony galaxy.datatypes.registry DEBUG 2017-11-18 14:51:28,501 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 14:51:28,521 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 14:51:28,522 Loaded history export tool: __EXPORT_HISTORY__ galaxy.web.base.pluginframework INFO 2017-11-18 14:51:28,528 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:51:28,532 Visualizations plugin disabled: Circster. Skipping... galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:51:28,535 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 14:51:28,535 VisualizationsRegistry, loaded plugin: csg galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:51:28,539 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 14:51:28,539 VisualizationsRegistry, loaded plugin: graphviz galaxy.web.base.pluginframework INFO 2017-11-18 14:51:28,542 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2017-11-18 14:51:28,548 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:51:28,551 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2017-11-18 14:51:28,555 VisualizationsRegistry, loaded plugin: trackster galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:51:28,557 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 14:51:28,557 VisualizationsRegistry, loaded plugin: unipept galaxy.tours INFO 2017-11-18 14:51:28,610 Loaded tour 'core.galaxy_ui' galaxy.tours INFO 2017-11-18 14:51:28,644 Loaded tour 'core.history' galaxy.tours INFO 2017-11-18 14:51:28,664 Loaded tour 'core.scratchbook' galaxy.webhooks WARNING 2017-11-18 14:51:28,666 directory not found: /galaxydir/galaxy/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config galaxy.jobs.manager DEBUG 2017-11-18 14:51:28,704 Starting job handler galaxy.jobs INFO 2017-11-18 14:51:28,704 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2017-11-18 14:51:28,719 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2017-11-18 14:51:28,719 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2017-11-18 14:51:28,720 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs DEBUG 2017-11-18 14:51:28,720 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2017-11-18 14:51:28,720 Loaded job runners plugins: local galaxy.jobs.handler INFO 2017-11-18 14:51:28,721 job handler stop queue started galaxy.jobs.handler INFO 2017-11-18 14:51:28,744 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 14:51:28,760 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 14:51:28,769 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.workflow.scheduling_manager DEBUG 2017-11-18 14:51:28,792 Starting workflow schedulers galaxy.app INFO 2017-11-18 14:51:28,794 Galaxy app startup finished (66790.953 ms) galaxy.web.framework.base DEBUG 2017-11-18 14:51:28,854 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,348 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,348 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,354 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,356 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,361 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,381 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,384 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,425 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,428 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,443 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,463 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,465 Enabling 'interactive_environments' controller, class: InteractiveEnvironmentsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,512 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,518 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,518 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,536 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,543 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,545 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,557 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,557 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,570 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,575 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,580 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,600 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,602 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,621 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,646 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,653 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,653 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,653 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,655 Enabling 'authenticate' API controller, class: AuthenticationController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,657 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,659 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,667 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,673 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,676 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,676 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,687 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,691 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,693 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,695 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,700 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,704 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,709 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,717 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,731 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,733 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,733 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,733 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,738 Enabling 'job_files' API controller, class: JobFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,744 Enabling 'jobs' API controller, class: JobController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,755 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,761 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,775 Enabling 'library_datasets' API controller, class: LibraryDatasetsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,777 Enabling 'metrics' API controller, class: MetricsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,779 Enabling 'page_revisions' API controller, class: PageRevisionsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,785 Enabling 'pages' API controller, class: PagesController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,787 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,788 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,790 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,799 Enabling 'remote_files' API controller, class: RemoteFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,809 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,812 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,814 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,819 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,871 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,878 Enabling 'tool_data' API controller, class: ToolData galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,880 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,894 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,900 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,916 Enabling 'toolshed' API controller, class: ToolShedController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,917 Enabling 'tours' API controller, class: ToursController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,932 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,938 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,940 Enabling 'webhooks' API controller, class: WebhooksController galaxy.web.framework.base DEBUG 2017-11-18 14:51:29,950 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.webapps.util DEBUG 2017-11-18 14:51:30,330 Enabling 'paste.httpexceptions' middleware galaxy.webapps.util DEBUG 2017-11-18 14:51:30,334 Enabling 'RecursiveMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:51:30,355 Enabling 'ErrorMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:51:30,360 Enabling 'TransLogger' middleware galaxy.webapps.util DEBUG 2017-11-18 14:51:30,361 Enabling 'XForwardedHostMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:51:30,363 Enabling 'RequestIDMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:51:30,371 Enabling 'BatchMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:51:30,372 Enabling 'wrap_in_static' middleware galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,389 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,389 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,390 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,390 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,390 added url, path to static middleware: /plugins/visualizations/unipept/static, ./config/plugins/visualizations/unipept/static galaxy.queue_worker INFO 2017-11-18 14:51:30,390 Binding and starting galaxy control worker for main galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,391 Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 140735112855552)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,392 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145307660288)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,401 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-3, started daemon 123145328693248)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,402 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-1, started daemon 123145320280064)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,406 Prior to webapp return, Galaxy thread <Thread(JobHandlerQueue.monitor_thread, started daemon 123145341313024)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,406 Prior to webapp return, Galaxy thread <Thread(WorkflowRequestMonitor.monitor_thread, started daemon 123145345519616)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,406 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-4, started daemon 123145332899840)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,406 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145311866880)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,406 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-2, started daemon 123145324486656)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,407 Prior to webapp return, Galaxy thread <Thread(JobHandlerStopQueue.monitor_thread, started daemon 123145337106432)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,407 Prior to webapp return, Galaxy thread <GalaxyQueueWorker(Thread-1, started daemon 123145349726208)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:51:30,408 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-0, started daemon 123145316073472)> is alive. Starting server in PID 29857. serving on http://127.0.0.1:8080 c^Cgalaxy.jobs.handler INFO 2017-11-18 14:52:53,644 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 14:52:53,645 job handler queue stopped galaxy.jobs.runners INFO 2017-11-18 14:52:53,645 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2017-11-18 14:52:53,646 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 14:52:53,646 job handler stop queue stopped CFM5081985:galaxy charles.strittmatter$ sh run.sh Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv galaxy.tools.deps DEBUG 2017-11-18 14:53:56,547 Unable to find config file './dependency_resolvers_conf.xml' DEBUG:galaxy.app:python path is: /galaxydir/galaxy/scripts, /galaxydir/galaxy/lib, /galaxydir/galaxy/.venv/lib/python27.zip, /galaxydir/galaxy/.venv/lib/python2.7, /galaxydir/galaxy/.venv/lib/python2.7/plat-darwin, /galaxydir/galaxy/.venv/lib/python2.7/plat-mac, /galaxydir/galaxy/.venv/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/Extras/lib/python, /galaxydir/galaxy/.venv/lib/python2.7/lib-tk, /galaxydir/galaxy/.venv/lib/python2.7/lib-old, /galaxydir/galaxy/.venv/lib/python2.7/lib-dynload, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/lib/python2.7/site-packages DEBUG:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config INFO:galaxy.config:Logging at '10' level to 'stdout' 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14:53:59,502 Loading script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:53:59,502 Script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:53:59,502 Loading script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:53:59,502 Script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:53:59,502 Loading script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:53:59,503 Script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:53:59,503 Loading script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:53:59,503 Script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:53:59,503 Loading script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:53:59,503 Script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py loaded successfully migrate.versioning.repository DEBUG 2017-11-18 14:53:59,503 Repository lib/tool_shed/galaxy_install/migrate loaded successfully migrate.versioning.repository DEBUG 2017-11-18 14:53:59,504 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))]) galaxy.config INFO 2017-11-18 14:54:09,191 Install database targetting Galaxy's database configuration. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,295 Loading datatypes from ./config/datatypes_conf.xml.sample galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,296 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,299 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,299 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,300 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,300 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,301 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,301 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,301 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,302 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,302 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,302 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,303 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,303 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,303 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,306 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,306 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,307 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,307 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,308 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,308 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,308 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,309 Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,309 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,312 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,312 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,313 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,314 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,314 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,315 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,316 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,316 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,316 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,317 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,317 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,317 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,318 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,318 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,318 Retrieved datatype module galaxy.datatypes.sequence:FastqGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,319 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,319 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,319 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,320 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,320 Retrieved datatype module galaxy.datatypes.sequence:FastqBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,320 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,321 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,321 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,321 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,322 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,322 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,322 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,323 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,323 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,323 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,324 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,324 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,324 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,324 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,325 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,325 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,326 Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,326 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,326 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,326 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,327 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,327 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,328 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,328 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,329 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,329 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,329 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,329 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,330 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,330 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,330 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,331 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,331 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,331 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,331 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,332 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,332 Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,332 Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,332 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,332 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,333 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,333 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,333 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,333 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,333 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,333 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,334 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,334 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,334 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,334 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,334 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,334 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,335 Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,335 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,340 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,340 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,340 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,341 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,341 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,341 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,341 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,342 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,342 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,342 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,342 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,342 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,343 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,343 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,343 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,343 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,343 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,343 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,344 Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,344 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,344 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,344 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,344 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,344 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,344 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,345 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,345 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,345 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,345 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,345 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,345 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,345 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,346 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,346 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,346 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,346 Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,346 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,347 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,347 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,347 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,348 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,349 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,350 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,351 Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,351 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,353 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,353 Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,353 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,353 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,354 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,354 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,354 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,354 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,354 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,354 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,355 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,355 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,355 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,355 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,355 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,355 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,355 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,355 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,356 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,356 Roadmaps is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,356 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,356 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,356 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,356 Sequences is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,356 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,357 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,357 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,357 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,357 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,357 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,358 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,358 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,358 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,358 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,358 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,359 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,359 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,359 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,359 Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,359 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,359 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,360 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,360 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,360 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,360 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,360 Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,361 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,361 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,361 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,361 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,362 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,362 Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,362 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,362 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,362 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,368 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,368 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,368 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,368 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,369 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,369 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,369 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,370 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,370 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,370 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,370 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,370 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,371 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,371 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,371 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,371 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,371 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,372 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,372 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,372 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,472 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,473 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,475 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,475 Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,476 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,476 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,476 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,477 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,477 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,477 Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,477 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,477 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,478 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,478 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,478 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,478 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,479 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,479 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,479 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,480 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,480 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,480 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,480 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,480 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,481 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,481 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,481 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,481 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,482 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,482 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,482 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,482 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,482 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,483 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,483 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,483 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,483 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,484 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,484 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,484 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,484 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,485 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,485 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,485 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,485 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,486 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,486 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,486 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,486 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,487 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,487 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,487 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,487 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,488 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,488 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,488 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,488 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,489 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,489 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,489 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,489 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,489 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,490 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,490 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,490 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,490 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,491 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,491 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,491 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,491 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,491 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,492 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,492 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,492 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,492 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,493 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,493 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,493 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,493 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,494 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,494 Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,494 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,494 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,495 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,495 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,495 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,495 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,496 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,496 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,496 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,496 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,496 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,497 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,497 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,498 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,498 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,498 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,498 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,499 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,499 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,499 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,499 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,500 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,500 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,502 Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,502 Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,505 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,506 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,506 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,506 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,506 Retrieved datatype module galaxy.datatypes.binary:Cel from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,507 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,507 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,507 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,507 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,507 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,508 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,508 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,510 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,511 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,511 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,511 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,511 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,512 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,512 Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,513 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,520 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,520 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,520 Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,520 Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,521 Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,521 Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,521 Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,521 Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,521 Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,522 Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,522 Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,522 Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,522 Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,522 Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,528 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,528 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,529 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,529 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,529 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,529 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,530 Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,530 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,530 Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,531 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,532 Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,532 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,533 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,534 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,535 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,536 Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,536 Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,537 Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,537 Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,537 Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,537 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,538 Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,538 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,538 Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,538 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,538 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,539 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,540 Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,540 Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,540 Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,540 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,541 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,541 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,541 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,541 Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,542 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,542 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,544 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,545 Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,547 Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,547 Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,548 Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,548 Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,549 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,549 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,549 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,552 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,553 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,553 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,553 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,553 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,554 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,554 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,554 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrtho from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,554 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,554 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylip from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,555 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,555 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,555 Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,555 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,556 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,556 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,556 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,556 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,556 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,556 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,556 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,557 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,557 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,557 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,557 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,557 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,557 Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,557 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,557 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,558 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,558 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,558 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,558 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,558 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,558 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,558 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,559 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,559 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,559 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,559 Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,559 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,559 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,559 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,560 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,560 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,560 Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,560 Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,560 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,560 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,561 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,561 Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,561 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,561 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,561 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,561 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,561 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,561 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,562 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,562 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,562 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,562 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,562 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,562 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,562 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,562 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,563 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,563 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,563 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,563 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,563 Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,564 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,564 Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,564 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,564 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,565 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,565 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,565 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,565 Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,565 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,566 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,566 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,566 Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,566 Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,566 Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,566 Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,566 Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,567 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,567 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,567 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerGz' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,567 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerBz2' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,567 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,567 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqGz' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,568 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqBz2' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,568 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,568 Loaded sniffer for datatype 'galaxy.datatypes.text:Html' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,568 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,568 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,568 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,569 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,569 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,569 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,569 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,569 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,569 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,570 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,570 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,570 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,570 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,570 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,570 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,571 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,571 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,571 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,571 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,571 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,571 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,571 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,572 Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,572 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,572 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,572 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,572 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,572 Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,573 Loaded sniffer for datatype 'galaxy.datatypes.binary:Cel' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,573 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,573 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,573 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,573 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,573 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,574 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,574 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,574 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,574 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,574 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,574 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,575 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,575 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,575 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,575 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,575 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,575 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,576 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,576 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,576 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,576 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,576 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,576 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,577 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,588 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,589 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,589 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,589 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,589 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,589 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,590 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,590 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:09,590 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.tools.data INFO 2017-11-18 14:54:10,405 Could not find tool data tool-data/all_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,406 Loaded 0 lines from 'tool-data/all_fasta.loc.sample' for 'all_fasta' galaxy.tools.data DEBUG 2017-11-18 14:54:10,406 Loaded tool data table 'all_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,407 Could not find tool data tool-data/bfast_indexes.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,408 Loaded 0 lines from 'tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' galaxy.tools.data DEBUG 2017-11-18 14:54:10,408 Loaded tool data table 'bfast_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,409 Could not find tool data tool-data/blastdb.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,410 Loaded 0 lines from 'tool-data/blastdb.loc.sample' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 14:54:10,410 Loaded tool data table 'blastdb' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,411 Could not find tool data tool-data/blastdb_p.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,412 Loaded 0 lines from 'tool-data/blastdb_p.loc.sample' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 14:54:10,412 Loaded tool data table 'blastdb_p' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,413 Could not find tool data tool-data/blastdb_d.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,414 Loaded 0 lines from 'tool-data/blastdb_d.loc.sample' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 14:54:10,414 Loaded tool data table 'blastdb_d' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data WARNING 2017-11-18 14:54:10,415 Cannot find index file 'tool-data/bwa_index.loc' for tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 14:54:10,415 Loaded tool data table 'bwa_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data WARNING 2017-11-18 14:54:10,415 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 14:54:10,416 Loaded tool data table 'bwa_indexes_color' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,416 Could not find tool data tool-data/maf_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,418 Loaded 0 lines from 'tool-data/maf_index.loc.sample' for 'indexed_maf_files' galaxy.tools.data DEBUG 2017-11-18 14:54:10,418 Loaded tool data table 'indexed_maf_files' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,418 Could not find tool data tool-data/ngs_sim_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,420 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' galaxy.tools.data DEBUG 2017-11-18 14:54:10,420 Loaded tool data table 'ngs_sim_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,421 Could not find tool data tool-data/perm_base_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,422 Loaded 0 lines from 'tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' galaxy.tools.data DEBUG 2017-11-18 14:54:10,422 Loaded tool data table 'perm_base_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,423 Could not find tool data tool-data/perm_color_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,424 Loaded 0 lines from 'tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' galaxy.tools.data DEBUG 2017-11-18 14:54:10,424 Loaded tool data table 'perm_color_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,425 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,425 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'picard_indexes' galaxy.tools.data DEBUG 2017-11-18 14:54:10,426 Loaded tool data table 'picard_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,426 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,426 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'srma_indexes' galaxy.tools.data DEBUG 2017-11-18 14:54:10,426 Loaded tool data table 'srma_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,427 Could not find tool data tool-data/mosaik_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,428 Loaded 0 lines from 'tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' galaxy.tools.data DEBUG 2017-11-18 14:54:10,428 Loaded tool data table 'mosaik_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,429 Could not find tool data tool-data/twobit.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,430 Loaded 0 lines from 'tool-data/twobit.loc.sample' for 'twobit' galaxy.tools.data DEBUG 2017-11-18 14:54:10,431 Loaded tool data table 'twobit' from file './config/tool_data_table_conf.xml.sample' requests.packages.urllib3.connectionpool INFO 2017-11-18 14:54:10,439 Starting new HTTP connection (1): igv.broadinstitute.org requests.packages.urllib3.connectionpool DEBUG 2017-11-18 14:54:10,893 "GET /genomes/genomes.txt HTTP/1.1" 200 15681 galaxy.tools.data DEBUG 2017-11-18 14:54:10,905 Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-wisKXM". galaxy.tools.data WARNING 2017-11-18 14:54:10,906 Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields): <Server-Side Genome List> galaxy.tools.data DEBUG 2017-11-18 14:54:10,908 Loaded 156 lines from '/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-wisKXM' for 'igv_broad_genomes' galaxy.tools.data DEBUG 2017-11-18 14:54:10,910 Loaded tool data table 'igv_broad_genomes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,911 Could not find tool data tool-data/liftOver.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,913 Loaded 0 lines from 'tool-data/liftOver.loc.sample' for 'liftOver' galaxy.tools.data DEBUG 2017-11-18 14:54:10,913 Loaded tool data table 'liftOver' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,914 Could not find tool data tool-data/bam_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,915 Loaded 1 lines from 'tool-data/bam_iobio.loc.sample' for 'bam_iobio' galaxy.tools.data DEBUG 2017-11-18 14:54:10,915 Loaded tool data table 'bam_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,916 Could not find tool data tool-data/vcf_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,917 Loaded 1 lines from 'tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' galaxy.tools.data DEBUG 2017-11-18 14:54:10,918 Loaded tool data table 'vcf_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:54:10,919 Could not find tool data tool-data/biom_simple_display.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:54:10,920 Loaded 1 lines from 'tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' galaxy.tools.data DEBUG 2017-11-18 14:54:10,920 Loaded tool data table 'biom_simple_display' from file './config/tool_data_table_conf.xml.sample' galaxy.jobs WARNING 2017-11-18 14:54:11,038 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/galaxydir/galaxy/config/galaxy.ini.sample" instead galaxy.jobs DEBUG 2017-11-18 14:54:11,038 Loading job configuration from /galaxydir/galaxy/config/galaxy.ini.sample galaxy.jobs DEBUG 2017-11-18 14:54:11,038 Done loading job configuration beaker.container DEBUG 2017-11-18 14:54:11,280 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache galaxy.tools.toolbox.base INFO 2017-11-18 14:54:11,290 Parsing the tool configuration ./config/tool_conf.xml.sample galaxy.tools.toolbox.base ERROR 2017-11-18 14:54:11,763 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base INFO 2017-11-18 14:54:11,913 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 14:54:11,914 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,914 Reading tools from config files finshed (624.085 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,914 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,915 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,915 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,915 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,915 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,915 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,916 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,916 Loaded tool id: biomart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,916 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,916 Loaded tool id: gramenemart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,917 Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,917 Loaded tool id: flymine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,917 Loaded tool id: flymine_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,917 Loaded tool id: modmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,917 Loaded tool id: mousemine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,917 Loaded tool id: ratmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,918 Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,918 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,918 Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,918 Loaded tool id: wormbase, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,918 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,918 Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,919 Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,919 Loaded tool id: hbvar, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,919 Loaded tool id: genomespace_importer, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,919 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,920 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,920 Loaded tool id: genomespace_exporter, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,920 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,921 Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,921 Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,921 Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,921 Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,922 Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,922 Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,922 Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,922 Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,922 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,922 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,923 Loaded tool id: addValue, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,923 Loaded tool id: cat1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,923 Loaded tool id: Cut1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,923 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,924 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,924 Loaded tool id: createInterval, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,924 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,924 Loaded tool id: Paste1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,924 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,925 Loaded tool id: random_lines1, version: 2.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,925 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,925 Loaded tool id: Show tail1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,925 Loaded tool id: trimmer, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,925 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,925 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,926 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,926 Loaded tool id: Filter1, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,926 Loaded tool id: sort1, version: 1.0.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,926 Loaded tool id: Grep1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,926 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,927 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,927 Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,927 Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,927 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,927 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,927 Loaded tool id: join1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,928 Loaded tool id: comp1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,928 Loaded tool id: Grouping1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,928 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,928 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,928 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,929 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,929 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,929 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,929 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,929 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,929 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,930 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,930 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,930 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,930 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,930 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,931 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,931 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,931 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,931 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,931 Loaded tool id: Extract genomic DNA 1, version: 2.2.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,931 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,932 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,932 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,932 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,932 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,932 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,933 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,933 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,933 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,933 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,933 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,934 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,934 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,934 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,934 Loaded tool id: Summary_Statistics1, version: 1.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,935 Loaded tool id: Count1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,935 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,935 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,935 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,935 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:54:11,935 Loading tool panel finished (20.993 ms) galaxy.tools.deps DEBUG 2017-11-18 14:54:11,939 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.search DEBUG 2017-11-18 14:54:11,967 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 14:54:13,361 Toolbox index finished (1394.495 ms) galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,364 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,366 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,414 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,414 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,415 Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,416 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,416 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,418 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,419 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,422 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,422 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,424 Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,468 Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,473 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,512 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,513 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,520 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,533 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,534 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,572 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,574 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,578 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,634 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,635 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,636 Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,637 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,683 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,684 Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,685 Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,687 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,687 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,687 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,687 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,687 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,687 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,687 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,687 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,699 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,699 Adding inherited display application 'igv_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,710 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,710 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,710 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,711 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,714 Adding inherited display application 'igv_fasta' to datatype 'sequences' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,715 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,715 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,715 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,715 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,717 Adding inherited display application 'igv_fasta' to datatype 'mothur.align' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,720 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,721 Adding inherited display application 'igv_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,731 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,732 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,732 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,732 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,733 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,733 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,733 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,733 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,735 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,735 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,735 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,735 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,739 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,740 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,741 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,744 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,748 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,749 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,751 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,752 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,753 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,754 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,756 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,757 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,758 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,761 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,762 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,764 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,767 Loaded converter: CONVERTER_fasta_to_fai galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,768 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,770 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,771 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,773 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,775 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,777 Loaded converter: CONVERTER_fastqgz_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,778 Loaded converter: CONVERTER_fastqsangergz_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,779 Loaded converter: CONVERTER_fastqsolexagz_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,781 Loaded converter: CONVERTER_fastqcssangergz_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,782 Loaded converter: CONVERTER_fastqilluminagz_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,783 Loaded converter: CONVERTER_fastqbz2_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,785 Loaded converter: CONVERTER_fastqsangerbz2_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,786 Loaded converter: CONVERTER_fastqsolexabz2_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,787 Loaded converter: CONVERTER_fastqcssangerbz2_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,788 Loaded converter: CONVERTER_fastqilluminabz2_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,789 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,790 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,793 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,797 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,798 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,800 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,801 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,802 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,803 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,805 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,806 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,807 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,808 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,810 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,812 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,814 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,816 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,818 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,820 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,822 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,823 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,824 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,828 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,832 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,833 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,834 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,836 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,837 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,838 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,839 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,842 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,844 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,845 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,846 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,847 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,848 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,849 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,851 Loaded converter: CONVERTER_biom1_to_biom2 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,852 Loaded converter: CONVERTER_biom2_to_biom1 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,853 Loaded converter: CONVERTER_SMILES_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,856 Loaded converter: CONVERTER_SMILES_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,858 Loaded converter: CONVERTER_SMILES_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,861 Loaded converter: CONVERTER_SMILES_to_MOL galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,863 Loaded converter: CONVERTER_SMILES_to_MOL2 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,865 Loaded converter: CONVERTER_smiles_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,867 Loaded converter: CONVERTER_sdf_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,869 Loaded converter: CONVERTER_sdf_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,870 Loaded converter: CONVERTER_sdf_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,872 Loaded converter: CONVERTER_sdf_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,873 Loaded converter: CONVERTER_inchi_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,875 Loaded converter: CONVERTER_inchi_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,876 Loaded converter: CONVERTER_inchi_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,881 Loaded converter: CONVERTER_inchi_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,883 Loaded converter: CONVERTER_inchi_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,884 Loaded converter: CONVERTER_mol_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,885 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,887 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,888 Loaded converter: CONVERTER_mol_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,889 Loaded converter: CONVERTER_mol2_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,891 Loaded converter: CONVERTER_mol2_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,892 Loaded converter: CONVERTER_mol2_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,894 Loaded converter: CONVERTER_mol2_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,895 Loaded converter: CONVERTER_mol2_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,897 Loaded converter: CONVERTER_cml_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,898 Loaded converter: CONVERTER_cml_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,899 Loaded converter: CONVERTER_cml_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,901 Loaded converter: CONVERTER_cml_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,904 Loaded converter: CONVERTER_ref_to_seq_taxomony galaxy.datatypes.registry DEBUG 2017-11-18 14:54:13,906 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 14:54:13,909 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 14:54:13,910 Loaded history export tool: __EXPORT_HISTORY__ galaxy.web.base.pluginframework INFO 2017-11-18 14:54:13,911 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:54:13,912 Visualizations plugin disabled: Circster. Skipping... galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:54:13,915 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 14:54:13,915 VisualizationsRegistry, loaded plugin: csg galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:54:13,916 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 14:54:13,917 VisualizationsRegistry, loaded plugin: graphviz galaxy.web.base.pluginframework INFO 2017-11-18 14:54:13,918 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2017-11-18 14:54:13,918 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:54:13,919 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2017-11-18 14:54:13,920 VisualizationsRegistry, loaded plugin: trackster galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:54:13,921 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 14:54:13,921 VisualizationsRegistry, loaded plugin: unipept galaxy.tours INFO 2017-11-18 14:54:13,972 Loaded tour 'core.galaxy_ui' galaxy.tours INFO 2017-11-18 14:54:14,005 Loaded tour 'core.history' galaxy.tours INFO 2017-11-18 14:54:14,022 Loaded tour 'core.scratchbook' galaxy.webhooks WARNING 2017-11-18 14:54:14,023 directory not found: /galaxydir/galaxy/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config galaxy.jobs.manager DEBUG 2017-11-18 14:54:14,027 Starting job handler galaxy.jobs INFO 2017-11-18 14:54:14,027 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2017-11-18 14:54:14,032 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2017-11-18 14:54:14,032 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2017-11-18 14:54:14,033 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs DEBUG 2017-11-18 14:54:14,033 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2017-11-18 14:54:14,033 Loaded job runners plugins: local galaxy.jobs.handler INFO 2017-11-18 14:54:14,034 job handler stop queue started galaxy.jobs.handler INFO 2017-11-18 14:54:14,049 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 14:54:14,055 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 14:54:14,056 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.workflow.scheduling_manager DEBUG 2017-11-18 14:54:14,064 Starting workflow schedulers galaxy.app INFO 2017-11-18 14:54:14,065 Galaxy app startup finished (15079.207 ms) galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,074 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,212 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,212 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,213 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,214 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,214 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,215 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,216 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,218 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,219 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,220 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,222 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,222 Enabling 'interactive_environments' controller, class: InteractiveEnvironmentsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,229 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,229 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,230 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,233 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,234 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,235 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,236 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,236 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,237 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,238 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,238 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,239 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,240 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,241 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,243 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,245 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,245 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,245 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,246 Enabling 'authenticate' API controller, class: AuthenticationController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,247 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,248 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,249 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,249 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,250 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,250 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,251 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,251 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,252 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,252 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,252 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,253 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,253 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,254 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,256 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,256 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,257 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,257 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,257 Enabling 'job_files' API controller, class: JobFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,258 Enabling 'jobs' API controller, class: JobController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,258 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,260 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,262 Enabling 'library_datasets' API controller, class: LibraryDatasetsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,262 Enabling 'metrics' API controller, class: MetricsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,262 Enabling 'page_revisions' API controller, class: PageRevisionsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,263 Enabling 'pages' API controller, class: PagesController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,263 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,263 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,264 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,266 Enabling 'remote_files' API controller, class: RemoteFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,267 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,267 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,268 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,268 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,283 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,283 Enabling 'tool_data' API controller, class: ToolData galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,284 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,285 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,286 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,286 Enabling 'toolshed' API controller, class: ToolShedController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,287 Enabling 'tours' API controller, class: ToursController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,288 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,288 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,289 Enabling 'webhooks' API controller, class: WebhooksController galaxy.web.framework.base DEBUG 2017-11-18 14:54:14,290 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.webapps.util DEBUG 2017-11-18 14:54:14,793 Enabling 'paste.httpexceptions' middleware galaxy.webapps.util DEBUG 2017-11-18 14:54:14,794 Enabling 'RecursiveMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:54:14,798 Enabling 'ErrorMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:54:14,799 Enabling 'TransLogger' middleware galaxy.webapps.util DEBUG 2017-11-18 14:54:14,799 Enabling 'XForwardedHostMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:54:14,799 Enabling 'RequestIDMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:54:14,800 Enabling 'BatchMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:54:14,800 Enabling 'wrap_in_static' middleware galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,805 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,805 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,805 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,805 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,806 added url, path to static middleware: /plugins/visualizations/unipept/static, ./config/plugins/visualizations/unipept/static galaxy.queue_worker INFO 2017-11-18 14:54:14,806 Binding and starting galaxy control worker for main galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,806 Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 140735112855552)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,807 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145307123712)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,807 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-4, started daemon 123145332363264)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,817 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-0, started daemon 123145315536896)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,817 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145311330304)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,817 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-2, started daemon 123145323950080)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,818 Prior to webapp return, Galaxy thread <Thread(JobHandlerStopQueue.monitor_thread, started daemon 123145336569856)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,818 Prior to webapp return, Galaxy thread <GalaxyQueueWorker(Thread-1, started daemon 123145349189632)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,818 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-3, started daemon 123145328156672)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,819 Prior to webapp return, Galaxy thread <Thread(WorkflowRequestMonitor.monitor_thread, started daemon 123145344983040)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,819 Prior to webapp return, Galaxy thread <Thread(JobHandlerQueue.monitor_thread, started daemon 123145340776448)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:54:14,820 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-1, started daemon 123145319743488)> is alive. Starting server in PID 29910. serving on http://127.0.0.1:8080 /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. 'storage.' % (dialect.name, dialect.driver)) 127.0.0.1 - - [18/Nov/2017:14:55:30 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:31 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:31 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:31 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:31 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:31 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:31 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:31 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:31 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:31 -0400] "GET /api/histories/f2db41e1fa331b3e/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:31 -0400] "GET /api/histories/f2db41e1fa331b3e?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:33 -0400] "GET /api/histories/f2db41e1fa331b3e/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:36 -0400] "GET /user/create HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:36 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/user/create" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:36 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/user/create" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. 'strategies for improved performance.' % expr) 127.0.0.1 - - [18/Nov/2017:14:55:58 -0400] "POST /user/create?cntrller=user HTTP/1.1" 200 - "http://localhost:8080/user/create" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:59 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/user/create?cntrller=user" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:55:59 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/user/create?cntrller=user" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:56:02 -0400] "GET /user/login HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:56:02 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/user/login" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:56:02 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/user/login" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:56:03 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:56:03 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:56:03 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:56:03 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:56:03 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:56:03 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:56:03 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:56:03 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:56:03 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:56:03 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:14:56:05 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ^Cgalaxy.jobs.handler INFO 2017-11-18 14:56:21,655 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 14:56:21,655 job handler queue stopped galaxy.jobs.runners INFO 2017-11-18 14:56:21,655 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2017-11-18 14:56:21,656 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 14:56:21,656 job handler stop queue stopped CFM5081985:galaxy charles.strittmatter$ sh run.sh Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv galaxy.tools.deps DEBUG 2017-11-18 14:58:54,945 Unable to find config file './dependency_resolvers_conf.xml' DEBUG:galaxy.app:python path is: /galaxydir/galaxy/scripts, /galaxydir/galaxy/lib, /galaxydir/galaxy/.venv/lib/python27.zip, /galaxydir/galaxy/.venv/lib/python2.7, /galaxydir/galaxy/.venv/lib/python2.7/plat-darwin, /galaxydir/galaxy/.venv/lib/python2.7/plat-mac, /galaxydir/galaxy/.venv/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/Extras/lib/python, /galaxydir/galaxy/.venv/lib/python2.7/lib-tk, /galaxydir/galaxy/.venv/lib/python2.7/lib-old, /galaxydir/galaxy/.venv/lib/python2.7/lib-dynload, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/lib/python2.7/site-packages DEBUG:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config INFO:galaxy.config:Logging at '10' level to 'stdout' galaxy.queue_worker INFO 2017-11-18 14:58:57,258 Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE tool_shed.tool_shed_registry DEBUG 2017-11-18 14:58:57,290 Loading references to tool sheds from ./config/tool_sheds_conf.xml.sample tool_shed.tool_shed_registry DEBUG 2017-11-18 14:58:57,291 Loaded reference to tool shed: Galaxy Main Tool Shed galaxy.app DEBUG 2017-11-18 14:58:57,292 Using "galaxy.ini" config file: /galaxydir/galaxy/config/galaxy.ini migrate.versioning.repository DEBUG 2017-11-18 14:58:57,343 Loading repository lib/galaxy/model/migrate... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,344 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,344 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,345 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,345 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,345 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,345 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,345 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,345 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,346 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,346 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,346 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,346 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,346 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,346 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,346 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,346 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,347 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,347 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,347 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,347 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,347 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,347 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,347 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,347 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,348 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,348 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,348 Loading script lib/galaxy/model/migrate/versions/0014_pages.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,348 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,348 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,348 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,348 Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,348 Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,349 Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,349 Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,349 Loading script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,349 Script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,349 Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,349 Script lib/galaxy/model/migrate/versions/0019_request_library_folder.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,349 Loading script lib/galaxy/model/migrate/versions/0020_library_upload_job.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,349 Script lib/galaxy/model/migrate/versions/0020_library_upload_job.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,350 Loading script lib/galaxy/model/migrate/versions/0021_user_prefs.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,350 Script lib/galaxy/model/migrate/versions/0021_user_prefs.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,350 Loading script lib/galaxy/model/migrate/versions/0022_visualization_tables.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,350 Script 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14:58:57,374 Loading script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,374 Script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,374 Loading script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,374 Script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,374 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,374 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,374 Loading script 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lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,477 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,477 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,477 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,477 Loading script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,477 Script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,477 Loading script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,478 Script 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14:58:57,478 Loading script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,479 Script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,479 Loading script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,479 Script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,479 Loading script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,479 Script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,479 Loading script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,479 Script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,479 Loading script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 14:58:57,480 Script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py loaded successfully migrate.versioning.repository DEBUG 2017-11-18 14:58:57,480 Repository lib/tool_shed/galaxy_install/migrate loaded successfully migrate.versioning.repository DEBUG 2017-11-18 14:58:57,480 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))]) tool_shed.galaxy_install.migrate.check INFO 2017-11-18 14:58:57,499 At migrate_tools version 12 galaxy.config INFO 2017-11-18 14:58:57,522 Install database targetting Galaxy's database configuration. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,580 Loading datatypes from ./config/datatypes_conf.xml.sample galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,582 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,584 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,584 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,584 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,584 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,585 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,585 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,585 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,585 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,585 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,586 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,586 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,586 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,586 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,586 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,587 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,587 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,587 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,587 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,588 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,588 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,588 Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,588 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,590 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,590 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,591 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,591 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,591 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,591 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,592 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,592 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,592 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,592 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,592 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,593 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,593 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,593 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,593 Retrieved datatype module galaxy.datatypes.sequence:FastqGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,593 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,594 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,594 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,594 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,594 Retrieved datatype module galaxy.datatypes.sequence:FastqBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,594 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,595 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,595 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,595 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,595 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,596 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,596 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,596 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,596 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,596 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,597 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,597 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,597 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,597 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,597 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,598 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,598 Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,598 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,598 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,599 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,599 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,599 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,599 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,600 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,600 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,600 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,600 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,601 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,601 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,601 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,601 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,602 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,602 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,602 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,602 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,603 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,603 Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,603 Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,603 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,603 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,603 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,604 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,604 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,604 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,604 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,604 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,604 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,604 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,605 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,605 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,605 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,605 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,605 Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,605 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,608 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,608 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,608 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,609 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,609 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,609 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,609 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,610 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,610 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,610 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,610 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,610 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,611 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,611 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,611 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,611 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,611 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,611 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,612 Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,612 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,612 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,612 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,612 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,613 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,613 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,613 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,613 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,613 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,614 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,614 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,614 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,614 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,614 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,615 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,615 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,615 Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,615 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,615 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,616 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,616 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,616 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,617 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,617 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,617 Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,618 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,618 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,618 Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,618 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,618 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,619 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,619 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,619 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,619 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,619 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,619 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,620 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,620 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,620 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,620 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,620 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,620 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,621 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,621 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,621 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,621 Roadmaps is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,621 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,621 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,622 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,622 Sequences is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,622 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,622 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,622 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,622 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,623 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,623 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,624 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,624 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,624 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,625 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,625 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,625 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,625 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,625 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,626 Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,626 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,626 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,626 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,626 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,627 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,627 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,627 Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,627 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,628 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,628 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,628 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,629 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,629 Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,630 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,631 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,631 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,636 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,636 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,637 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,637 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,637 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,637 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,637 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,638 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,638 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,638 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,638 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,639 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,639 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,639 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,639 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,639 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,639 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,640 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,640 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,640 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,641 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,641 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,642 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,642 Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,643 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,643 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,643 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,643 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,644 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,644 Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,644 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,644 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,645 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,645 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,645 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,645 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,646 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,646 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,646 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,646 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,646 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,647 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,647 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,647 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,647 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,648 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,648 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,648 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,648 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,649 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,649 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,649 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,649 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,649 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,650 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,650 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,650 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,650 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,651 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,651 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,651 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,651 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,651 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,653 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,653 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,653 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,654 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,654 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,654 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,654 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,654 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,655 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,655 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,655 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,655 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,656 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,656 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,746 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,747 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,747 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,747 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,747 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,748 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,748 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,748 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,748 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,749 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,749 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,749 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,749 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,750 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,750 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,750 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,750 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,751 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,751 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,751 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,751 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,751 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,752 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,752 Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,752 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,752 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,753 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,753 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,753 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,753 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,753 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,754 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,754 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,754 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,754 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,755 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,755 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,755 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,755 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,756 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,756 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,756 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,756 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,756 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,757 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,757 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,757 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,758 Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,758 Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,759 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,759 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,759 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,760 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,760 Retrieved datatype module galaxy.datatypes.binary:Cel from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,760 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,760 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,760 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,761 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,761 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,761 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,761 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,762 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,763 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,763 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,763 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,763 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,763 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,764 Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,764 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,766 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,766 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,766 Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,767 Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,767 Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,767 Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,767 Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,767 Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,768 Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,768 Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,768 Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,768 Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,768 Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,768 Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,771 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,771 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,772 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,772 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,772 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,772 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,773 Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,773 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,773 Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,773 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,773 Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,773 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,774 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,774 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,774 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,774 Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,774 Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,775 Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,775 Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,775 Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,775 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,775 Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,776 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,776 Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,776 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,776 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,777 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,777 Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,777 Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,777 Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,778 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,778 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,779 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,779 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,779 Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,780 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,780 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,781 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,781 Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,783 Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,783 Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,783 Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,783 Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,784 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,784 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,784 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,787 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,787 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,787 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,787 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,788 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,788 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,788 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,788 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrtho from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,788 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,788 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylip from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,788 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,789 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,789 Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,789 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,789 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,789 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,790 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,790 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,790 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,790 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,790 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,790 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,790 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,790 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,791 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,791 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,792 Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,792 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,793 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,793 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,793 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,794 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,794 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,794 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,794 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,794 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,795 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,795 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,795 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,796 Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,796 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,796 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,797 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,797 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,797 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,797 Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,797 Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,798 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,798 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,799 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,800 Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,800 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,800 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,800 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,801 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,801 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,801 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,801 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,801 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,801 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,801 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,802 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,802 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,802 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,802 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,802 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,802 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,803 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,803 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,803 Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,803 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,803 Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,803 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,803 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,804 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,804 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,804 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,804 Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,804 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,804 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,805 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,805 Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,805 Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,805 Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,805 Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,805 Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,805 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,806 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,806 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerGz' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,806 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerBz2' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,806 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,806 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqGz' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,806 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqBz2' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,807 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,807 Loaded sniffer for datatype 'galaxy.datatypes.text:Html' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,807 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,807 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,807 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,807 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,808 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,808 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,808 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,808 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,808 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,808 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,809 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,809 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,809 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,809 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,809 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,809 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,809 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,810 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,810 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,810 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,810 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,810 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,811 Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,811 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,811 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,811 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,811 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,811 Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,812 Loaded sniffer for datatype 'galaxy.datatypes.binary:Cel' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,812 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,812 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,812 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,812 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,812 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,813 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,813 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,813 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,813 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,813 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,814 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,814 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,814 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,814 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,814 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,814 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,815 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,815 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,815 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,815 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,815 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,815 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,816 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,816 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,822 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,822 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,822 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,822 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,822 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,823 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,823 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,823 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 14:58:57,823 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.tools.data INFO 2017-11-18 14:58:58,616 Could not find tool data tool-data/all_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:58,617 Loaded 0 lines from 'tool-data/all_fasta.loc.sample' for 'all_fasta' galaxy.tools.data DEBUG 2017-11-18 14:58:58,617 Loaded tool data table 'all_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:58,618 Could not find tool data tool-data/bfast_indexes.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:58,618 Loaded 0 lines from 'tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' galaxy.tools.data DEBUG 2017-11-18 14:58:58,618 Loaded tool data table 'bfast_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:58,618 Could not find tool data tool-data/blastdb.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:58,619 Loaded 0 lines from 'tool-data/blastdb.loc.sample' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 14:58:58,619 Loaded tool data table 'blastdb' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:58,619 Could not find tool data tool-data/blastdb_p.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:58,620 Loaded 0 lines from 'tool-data/blastdb_p.loc.sample' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 14:58:58,620 Loaded tool data table 'blastdb_p' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:58,620 Could not find tool data tool-data/blastdb_d.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:58,621 Loaded 0 lines from 'tool-data/blastdb_d.loc.sample' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 14:58:58,621 Loaded tool data table 'blastdb_d' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data WARNING 2017-11-18 14:58:58,621 Cannot find index file 'tool-data/bwa_index.loc' for tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 14:58:58,621 Loaded tool data table 'bwa_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data WARNING 2017-11-18 14:58:58,622 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 14:58:58,622 Loaded tool data table 'bwa_indexes_color' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:58,622 Could not find tool data tool-data/maf_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:58,623 Loaded 0 lines from 'tool-data/maf_index.loc.sample' for 'indexed_maf_files' galaxy.tools.data DEBUG 2017-11-18 14:58:58,623 Loaded tool data table 'indexed_maf_files' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:58,623 Could not find tool data tool-data/ngs_sim_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:58,623 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' galaxy.tools.data DEBUG 2017-11-18 14:58:58,623 Loaded tool data table 'ngs_sim_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:58,624 Could not find tool data tool-data/perm_base_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:58,624 Loaded 0 lines from 'tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' galaxy.tools.data DEBUG 2017-11-18 14:58:58,624 Loaded tool data table 'perm_base_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:58,624 Could not find tool data tool-data/perm_color_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:58,624 Loaded 0 lines from 'tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' galaxy.tools.data DEBUG 2017-11-18 14:58:58,625 Loaded tool data table 'perm_color_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:58,625 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:58,625 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'picard_indexes' galaxy.tools.data DEBUG 2017-11-18 14:58:58,625 Loaded tool data table 'picard_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:58,625 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:58,626 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'srma_indexes' galaxy.tools.data DEBUG 2017-11-18 14:58:58,626 Loaded tool data table 'srma_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:58,626 Could not find tool data tool-data/mosaik_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:58,626 Loaded 0 lines from 'tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' galaxy.tools.data DEBUG 2017-11-18 14:58:58,626 Loaded tool data table 'mosaik_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:58,627 Could not find tool data tool-data/twobit.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:58,627 Loaded 0 lines from 'tool-data/twobit.loc.sample' for 'twobit' galaxy.tools.data DEBUG 2017-11-18 14:58:58,627 Loaded tool data table 'twobit' from file './config/tool_data_table_conf.xml.sample' requests.packages.urllib3.connectionpool INFO 2017-11-18 14:58:58,637 Starting new HTTP connection (1): igv.broadinstitute.org requests.packages.urllib3.connectionpool DEBUG 2017-11-18 14:58:59,084 "GET /genomes/genomes.txt HTTP/1.1" 200 15681 galaxy.tools.data DEBUG 2017-11-18 14:58:59,090 Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-gmpw79". galaxy.tools.data WARNING 2017-11-18 14:58:59,091 Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields): <Server-Side Genome List> galaxy.tools.data DEBUG 2017-11-18 14:58:59,093 Loaded 156 lines from '/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-gmpw79' for 'igv_broad_genomes' galaxy.tools.data DEBUG 2017-11-18 14:58:59,096 Loaded tool data table 'igv_broad_genomes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:59,096 Could not find tool data tool-data/liftOver.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:59,097 Loaded 0 lines from 'tool-data/liftOver.loc.sample' for 'liftOver' galaxy.tools.data DEBUG 2017-11-18 14:58:59,097 Loaded tool data table 'liftOver' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:59,097 Could not find tool data tool-data/bam_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:59,098 Loaded 1 lines from 'tool-data/bam_iobio.loc.sample' for 'bam_iobio' galaxy.tools.data DEBUG 2017-11-18 14:58:59,098 Loaded tool data table 'bam_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:59,099 Could not find tool data tool-data/vcf_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:59,099 Loaded 1 lines from 'tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' galaxy.tools.data DEBUG 2017-11-18 14:58:59,099 Loaded tool data table 'vcf_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 14:58:59,100 Could not find tool data tool-data/biom_simple_display.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 14:58:59,100 Loaded 1 lines from 'tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' galaxy.tools.data DEBUG 2017-11-18 14:58:59,101 Loaded tool data table 'biom_simple_display' from file './config/tool_data_table_conf.xml.sample' galaxy.jobs WARNING 2017-11-18 14:58:59,160 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/galaxydir/galaxy/config/galaxy.ini" instead galaxy.jobs DEBUG 2017-11-18 14:58:59,160 Loading job configuration from /galaxydir/galaxy/config/galaxy.ini galaxy.jobs DEBUG 2017-11-18 14:58:59,160 Done loading job configuration beaker.container DEBUG 2017-11-18 14:58:59,250 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache galaxy.tools.toolbox.base INFO 2017-11-18 14:58:59,254 Parsing the tool configuration ./config/tool_conf.xml.sample galaxy.tools.toolbox.base ERROR 2017-11-18 14:58:59,428 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base INFO 2017-11-18 14:58:59,585 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 14:58:59,585 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,585 Reading tools from config files finshed (332.120 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,586 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,586 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,586 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,587 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,587 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,587 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,587 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,587 Loaded tool id: biomart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,588 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,588 Loaded tool id: gramenemart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,588 Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,588 Loaded tool id: flymine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,588 Loaded tool id: flymine_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,589 Loaded tool id: modmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,589 Loaded tool id: mousemine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,589 Loaded tool id: ratmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,589 Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,589 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,589 Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,590 Loaded tool id: wormbase, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,590 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,590 Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,590 Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,590 Loaded tool id: hbvar, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,590 Loaded tool id: genomespace_importer, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,591 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,591 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,591 Loaded tool id: genomespace_exporter, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,591 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,591 Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,591 Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,592 Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,592 Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,592 Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,592 Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,592 Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,593 Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,593 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,593 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,593 Loaded tool id: addValue, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,593 Loaded tool id: cat1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,593 Loaded tool id: Cut1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,593 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,594 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,594 Loaded tool id: createInterval, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,594 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,594 Loaded tool id: Paste1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,594 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,595 Loaded tool id: random_lines1, version: 2.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,595 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,595 Loaded tool id: Show tail1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,595 Loaded tool id: trimmer, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,595 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,595 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,595 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,596 Loaded tool id: Filter1, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,596 Loaded tool id: sort1, version: 1.0.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,596 Loaded tool id: Grep1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,596 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,596 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,597 Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,597 Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,597 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,597 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,597 Loaded tool id: join1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,597 Loaded tool id: comp1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,598 Loaded tool id: Grouping1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,598 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,598 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,598 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,598 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,598 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,599 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,599 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,599 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,599 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,600 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,600 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,600 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,600 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,600 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,600 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,601 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,601 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,601 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,601 Loaded tool id: Extract genomic DNA 1, version: 2.2.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,601 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,602 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,602 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,602 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,602 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,602 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,602 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,603 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,603 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,603 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,603 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,603 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,604 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,604 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,604 Loaded tool id: Summary_Statistics1, version: 1.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,604 Loaded tool id: Count1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,604 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,604 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,605 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,605 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 14:58:59,605 Loading tool panel finished (19.032 ms) galaxy.tools.deps DEBUG 2017-11-18 14:58:59,608 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.search DEBUG 2017-11-18 14:58:59,631 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 14:59:00,941 Toolbox index finished (1310.028 ms) galaxy.datatypes.registry DEBUG 2017-11-18 14:59:00,944 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:00,946 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,112 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,113 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,114 Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,114 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,115 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,116 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,117 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,119 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,120 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,122 Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,163 Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,168 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,210 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,211 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,216 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,229 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,230 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,283 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,285 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,289 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,361 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,363 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,364 Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,365 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,413 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,414 Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,415 Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,417 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,417 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,417 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,417 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,417 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,418 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,418 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,418 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,429 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,429 Adding inherited display application 'igv_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,439 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,439 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,439 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,439 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,441 Adding inherited display application 'igv_fasta' to datatype 'sequences' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,442 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,442 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,442 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,442 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,444 Adding inherited display application 'igv_fasta' to datatype 'mothur.align' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,445 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,445 Adding inherited display application 'igv_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,456 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,456 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,456 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,457 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,458 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,458 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,458 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,458 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,461 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,461 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,461 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,461 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,465 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,466 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,467 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,468 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,470 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,471 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,474 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,477 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,479 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,480 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,481 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,483 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,484 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,486 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,487 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,488 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,490 Loaded converter: CONVERTER_fasta_to_fai galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,491 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,493 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,495 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,498 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,500 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,502 Loaded converter: CONVERTER_fastqgz_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,504 Loaded converter: CONVERTER_fastqsangergz_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,507 Loaded converter: CONVERTER_fastqsolexagz_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,508 Loaded converter: CONVERTER_fastqcssangergz_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,510 Loaded converter: CONVERTER_fastqilluminagz_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,511 Loaded converter: CONVERTER_fastqbz2_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,513 Loaded converter: CONVERTER_fastqsangerbz2_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,514 Loaded converter: CONVERTER_fastqsolexabz2_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,515 Loaded converter: CONVERTER_fastqcssangerbz2_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,516 Loaded converter: CONVERTER_fastqilluminabz2_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,517 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,519 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,520 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,521 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,526 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,528 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,529 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,530 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,533 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,535 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,536 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,537 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,539 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,540 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,541 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,542 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,544 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,547 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,548 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,550 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,552 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,553 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,555 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,558 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,561 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,562 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,563 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,565 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,566 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,567 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,568 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,569 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,571 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,572 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,578 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,579 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,581 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,582 Loaded converter: CONVERTER_biom1_to_biom2 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,583 Loaded converter: CONVERTER_biom2_to_biom1 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,585 Loaded converter: CONVERTER_SMILES_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,586 Loaded converter: CONVERTER_SMILES_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,588 Loaded converter: CONVERTER_SMILES_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,590 Loaded converter: CONVERTER_SMILES_to_MOL galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,591 Loaded converter: CONVERTER_SMILES_to_MOL2 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,595 Loaded converter: CONVERTER_smiles_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,597 Loaded converter: CONVERTER_sdf_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,599 Loaded converter: CONVERTER_sdf_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,601 Loaded converter: CONVERTER_sdf_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,604 Loaded converter: CONVERTER_sdf_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,608 Loaded converter: CONVERTER_inchi_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,611 Loaded converter: CONVERTER_inchi_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,613 Loaded converter: CONVERTER_inchi_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,614 Loaded converter: CONVERTER_inchi_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,617 Loaded converter: CONVERTER_inchi_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,619 Loaded converter: CONVERTER_mol_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,620 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,622 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,624 Loaded converter: CONVERTER_mol_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,626 Loaded converter: CONVERTER_mol2_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,628 Loaded converter: CONVERTER_mol2_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,629 Loaded converter: CONVERTER_mol2_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,630 Loaded converter: CONVERTER_mol2_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,632 Loaded converter: CONVERTER_mol2_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,634 Loaded converter: CONVERTER_cml_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,635 Loaded converter: CONVERTER_cml_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,637 Loaded converter: CONVERTER_cml_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,640 Loaded converter: CONVERTER_cml_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,642 Loaded converter: CONVERTER_ref_to_seq_taxomony galaxy.datatypes.registry DEBUG 2017-11-18 14:59:01,644 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 14:59:01,648 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 14:59:01,652 Loaded history export tool: __EXPORT_HISTORY__ galaxy.web.base.pluginframework INFO 2017-11-18 14:59:01,653 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:59:01,654 Visualizations plugin disabled: Circster. Skipping... galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:59:01,654 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 14:59:01,655 VisualizationsRegistry, loaded plugin: csg galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:59:01,656 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 14:59:01,657 VisualizationsRegistry, loaded plugin: graphviz galaxy.web.base.pluginframework INFO 2017-11-18 14:59:01,660 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2017-11-18 14:59:01,663 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:59:01,663 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2017-11-18 14:59:01,665 VisualizationsRegistry, loaded plugin: trackster galaxy.visualization.plugins.config_parser INFO 2017-11-18 14:59:01,665 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 14:59:01,666 VisualizationsRegistry, loaded plugin: unipept galaxy.tours INFO 2017-11-18 14:59:01,713 Loaded tour 'core.galaxy_ui' galaxy.tours INFO 2017-11-18 14:59:01,739 Loaded tour 'core.history' galaxy.tours INFO 2017-11-18 14:59:01,756 Loaded tour 'core.scratchbook' galaxy.webhooks WARNING 2017-11-18 14:59:01,757 directory not found: /galaxydir/galaxy/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config galaxy.jobs.manager DEBUG 2017-11-18 14:59:01,762 Starting job handler galaxy.jobs INFO 2017-11-18 14:59:01,762 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2017-11-18 14:59:01,763 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2017-11-18 14:59:01,763 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2017-11-18 14:59:01,765 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs DEBUG 2017-11-18 14:59:01,765 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2017-11-18 14:59:01,765 Loaded job runners plugins: local galaxy.jobs.handler INFO 2017-11-18 14:59:01,765 job handler stop queue started galaxy.jobs.handler INFO 2017-11-18 14:59:01,782 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 14:59:01,793 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 14:59:01,795 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.workflow.scheduling_manager DEBUG 2017-11-18 14:59:01,799 Starting workflow schedulers galaxy.app INFO 2017-11-18 14:59:01,801 Galaxy app startup finished (4648.404 ms) galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,818 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,953 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,953 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,954 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,954 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,955 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,957 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,957 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,959 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,959 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,960 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,962 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,963 Enabling 'interactive_environments' controller, class: InteractiveEnvironmentsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,968 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,971 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,971 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,973 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,974 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,975 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,976 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,976 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,977 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,978 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,978 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,979 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,980 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,981 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,983 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,985 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,985 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,985 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,985 Enabling 'authenticate' API controller, class: AuthenticationController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,986 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,986 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,989 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,989 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,990 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,990 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,991 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,991 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,992 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,992 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,993 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,993 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,993 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,994 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,996 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,997 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,997 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,997 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:01,998 Enabling 'job_files' API controller, class: JobFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,001 Enabling 'jobs' API controller, class: JobController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,002 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,002 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,005 Enabling 'library_datasets' API controller, class: LibraryDatasetsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,005 Enabling 'metrics' API controller, class: MetricsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,006 Enabling 'page_revisions' API controller, class: PageRevisionsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,006 Enabling 'pages' API controller, class: PagesController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,007 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,007 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,008 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,013 Enabling 'remote_files' API controller, class: RemoteFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,014 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,015 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,015 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,015 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,026 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,026 Enabling 'tool_data' API controller, class: ToolData galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,027 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,028 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,028 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,029 Enabling 'toolshed' API controller, class: ToolShedController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,030 Enabling 'tours' API controller, class: ToursController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,031 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,031 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,032 Enabling 'webhooks' API controller, class: WebhooksController galaxy.web.framework.base DEBUG 2017-11-18 14:59:02,033 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.webapps.util DEBUG 2017-11-18 14:59:02,586 Enabling 'paste.httpexceptions' middleware galaxy.webapps.util DEBUG 2017-11-18 14:59:02,588 Enabling 'RecursiveMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:59:02,594 Enabling 'ErrorMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:59:02,595 Enabling 'TransLogger' middleware galaxy.webapps.util DEBUG 2017-11-18 14:59:02,595 Enabling 'XForwardedHostMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:59:02,595 Enabling 'RequestIDMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:59:02,596 Enabling 'BatchMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 14:59:02,596 Enabling 'wrap_in_static' middleware galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,602 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,602 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,602 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,603 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,603 added url, path to static middleware: /plugins/visualizations/unipept/static, ./config/plugins/visualizations/unipept/static galaxy.queue_worker INFO 2017-11-18 14:59:02,603 Binding and starting galaxy control worker for main galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,604 Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 140735112855552)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,604 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145308196864)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,614 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-2, started daemon 123145325023232)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,618 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-0, started daemon 123145316610048)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,618 Prior to webapp return, Galaxy thread <Thread(JobHandlerStopQueue.monitor_thread, started daemon 123145337643008)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,619 Prior to webapp return, Galaxy thread <Thread(WorkflowRequestMonitor.monitor_thread, started daemon 123145346056192)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,619 Prior to webapp return, Galaxy thread <GalaxyQueueWorker(Thread-1, started daemon 123145350262784)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,620 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-3, started daemon 123145329229824)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,620 Prior to webapp return, Galaxy thread <Thread(JobHandlerQueue.monitor_thread, started daemon 123145341849600)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,621 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-1, started daemon 123145320816640)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,621 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-4, started daemon 123145333436416)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 14:59:02,621 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145312403456)> is alive. Starting server in PID 30006. serving on http://127.0.0.1:8080 /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. 'storage.' % (dialect.name, dialect.driver)) /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. 'strategies for improved performance.' % expr) 127.0.0.1 - - [18/Nov/2017:15:00:10 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:10 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:10 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:10 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:10 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:10 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:10 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:11 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:11 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:11 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:11 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:12 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:12 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:12 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:13 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:13 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:14 -0400] "GET /admin_toolshed/browse_tool_sheds HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:14 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:15 -0400] "GET /admin_toolshed/browse_tool_shed?tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:45 -0400] "GET /admin_toolshed/prepare_for_install?changeset_revisions=ec2595e4d313&repository_ids=18e81ffc1cf9369e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:47 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=ec2595e4d313&repository_ids=18e81ffc1cf9369e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 15:00:48,892 Creating repository dependency objects... tool_shed.util.repository_util DEBUG 2017-11-18 15:00:49,413 Adding new row for repository 'package_bwa_0_5_9' in the tool_shed_repository table, status set to 'New'. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 15:00:49,426 Building repository dependency relationships... 127.0.0.1 - - [18/Nov/2017:15:00:48 -0400] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=ec2595e4d313&repository_ids=18e81ffc1cf9369e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:49 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.tool_dependency_util DEBUG 2017-11-18 15:00:52,232 Creating a new record for version 0.5.9 of tool dependency bwa for revision ec2595e4d313 of repository package_bwa_0_5_9. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 15:00:52,283 Updating an existing record for version 0.5.9 of tool dependency bwa for revision ec2595e4d313 of repository package_bwa_0_5_9 by updating the status from Never installed to Installing. tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 15:00:52,297 Attempting to download via url: http://depot.galaxyproject.org/package/darwin/x86_64/bwa/bwa-0.5.9-Darwin-x86_64.tgz 127.0.0.1 - - [18/Nov/2017:15:00:52 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 15:00:53,106 Successfully downloaded from url: http://depot.galaxyproject.org/package/darwin/x86_64/bwa/bwa-0.5.9-Darwin-x86_64.tgz tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 15:00:53,113 Changing status for tool dependency bwa from Installing to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 15:00:53,114 Updating an existing record for version 0.5.9 of tool dependency bwa for revision ec2595e4d313 of repository package_bwa_0_5_9 by updating the status from Installing to Installed. 127.0.0.1 - - [18/Nov/2017:15:00:49 -0400] "POST /admin_toolshed/manage_repositories HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:53 -0400] "GET /admin_toolshed/monitor_repository_installation?tool_shed_repository_ids=f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:00:55 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:07:25 -0400] "GET /admin_toolshed/browse_tool_sheds HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:07:25 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:07:26 -0400] "GET /admin_toolshed/browse_tool_shed?tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.deps DEBUG 2017-11-18 15:07:45,613 Dependency blast not found. galaxy.tools.deps DEBUG 2017-11-18 15:07:45,614 Dependency blast not found. galaxy.tools.deps DEBUG 2017-11-18 15:07:45,615 Dependency blast not found. galaxy.tools.deps DEBUG 2017-11-18 15:07:45,616 Dependency blast not found. galaxy.tools.deps DEBUG 2017-11-18 15:07:45,617 Dependency blast not found. galaxy.tools.deps DEBUG 2017-11-18 15:07:45,618 Dependency blast not found. galaxy.tools.deps DEBUG 2017-11-18 15:07:45,619 Dependency blast not found. galaxy.tools.deps DEBUG 2017-11-18 15:07:45,620 Dependency blast not found. galaxy.tools.deps DEBUG 2017-11-18 15:07:45,620 Dependency blast not found. galaxy.tools.deps DEBUG 2017-11-18 15:07:45,621 Dependency blast not found. galaxy.tools.deps DEBUG 2017-11-18 15:07:45,622 Dependency blast not found. galaxy.tools.deps DEBUG 2017-11-18 15:07:45,623 Dependency blast not found. galaxy.tools.deps DEBUG 2017-11-18 15:07:45,623 Dependency blast not found. galaxy.tools.deps DEBUG 2017-11-18 15:07:45,624 Dependency blast not found. 127.0.0.1 - - [18/Nov/2017:15:07:44 -0400] "GET /admin_toolshed/prepare_for_install?changeset_revisions=6f386c5dc4fb&repository_ids=1d92ebdf7e8d466c&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:07:47 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=6f386c5dc4fb&repository_ids=1d92ebdf7e8d466c&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 15:07:58,393 Creating repository dependency objects... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:07:59,887 Appending to tool panel section: Fetch Sequences tool_shed.util.repository_util DEBUG 2017-11-18 15:07:59,898 Adding new row for repository 'ncbi_blast_plus' in the tool_shed_repository table, status set to 'New'. galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:00,086 Appending to tool panel section: Fetch Sequences tool_shed.util.repository_util DEBUG 2017-11-18 15:08:00,101 Adding new row for repository 'blast_datatypes' in the tool_shed_repository table, status set to 'New'. galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:00,302 Appending to tool panel section: Fetch Sequences tool_shed.util.repository_util DEBUG 2017-11-18 15:08:00,313 Adding new row for repository 'package_blast_plus_2_5_0' in the tool_shed_repository table, status set to 'New'. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 15:08:00,322 Building repository dependency relationships... tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 15:08:00,348 Creating new repository_dependency record for installed revision 01b38f20197e of repository: blast_datatypes owned by devteam. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 15:08:00,419 Creating new repository_dependency record for installed revision 5dd2b68c7d04 of repository: package_blast_plus_2_5_0 owned by iuc. galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:00,452 Appending to tool panel section: Fetch Sequences 127.0.0.1 - - [18/Nov/2017:15:07:58 -0400] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=6f386c5dc4fb&repository_ids=1d92ebdf7e8d466c&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:00 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:00,689 Appending to tool panel section: Fetch Sequences /galaxydir/galaxy/lib/galaxy/datatypes/registry.py:98: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if root_dir and config: galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,323 Ignoring conflicting datatype with extension 'blastxml' from <Element 'datatypes' at 0x10b0f4d90>. galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,323 Ignoring conflicting datatype with extension 'blastdbn' from <Element 'datatypes' at 0x10b0f4d90>. galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,324 Ignoring conflicting datatype with extension 'blastdbp' from <Element 'datatypes' at 0x10b0f4d90>. galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,324 Ignoring conflicting datatype with extension 'blastdbd' from <Element 'datatypes' at 0x10b0f4d90>. galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,324 Ignoring conflicting datatype with extension 'maskinfo-asn1' from <Element 'datatypes' at 0x10b0f4d90>. galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,324 Ignoring conflicting datatype with extension 'maskinfo-asn1-binary' from <Element 'datatypes' at 0x10b0f4d90>. galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,324 Ignoring conflicting datatype with extension 'pssm-asn1' from <Element 'datatypes' at 0x10b0f4d90>. galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,331 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,331 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,331 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,331 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,331 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,332 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,332 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,332 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 15:08:03,332 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample 127.0.0.1 - - [18/Nov/2017:15:08:03 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:04,386 Appending to tool panel section: Fetch Sequences 127.0.0.1 - - [18/Nov/2017:15:08:07 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.data DEBUG 2017-11-18 15:08:07,770 Loaded 0 lines from './database/tmp/tmp-toolshed-gmfcrk6Pdf3/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:07,770 Loading another instance of data table 'blastdb' from file '../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 15:08:07,771 Loaded 0 lines from './database/tmp/tmp-toolshed-gmfcrk6Pdf3/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:07,771 Loading another instance of data table 'blastdb_p' from file '../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 15:08:07,771 Loaded 0 lines from './database/tmp/tmp-toolshed-gmfcrk6Pdf3/blastdb_d.loc' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:07,771 Loading another instance of data table 'blastdb_d' from file '../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,841 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb.loc' for tool data table 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:07,841 Loading another instance of data table 'blastdb' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,842 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_p.loc' for tool data table 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:07,842 Loading another instance of data table 'blastdb_p' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,842 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_d.loc' for tool data table 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:07,842 Loading another instance of data table 'blastdb_d' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,846 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb.loc' for tool data table 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:07,846 Loading another instance of data table 'blastdb' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,846 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_p.loc' for tool data table 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:07,846 Loading another instance of data table 'blastdb_p' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,847 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_d.loc' for tool data table 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:07,847 Loading another instance of data table 'blastdb_d' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,871 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb.loc' for tool data table 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:07,871 Loading another instance of data table 'blastdb' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,871 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_p.loc' for tool data table 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:07,871 Loading another instance of data table 'blastdb_p' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,871 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_d.loc' for tool data table 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:07,872 Loading another instance of data table 'blastdb_d' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,875 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb.loc' for tool data table 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:07,876 Loading another instance of data table 'blastdb' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,876 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_p.loc' for tool data table 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:07,876 Loading another instance of data table 'blastdb_p' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,876 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_d.loc' for tool data table 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:07,876 Loading another instance of data table 'blastdb_d' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,929 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb.loc' for tool data table 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:07,929 Loading another instance of data table 'blastdb' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,929 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_p.loc' for tool data table 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:07,929 Loading another instance of data table 'blastdb_p' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,930 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_d.loc' for tool data table 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:07,930 Loading another instance of data table 'blastdb_d' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,987 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb.loc' for tool data table 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:07,987 Loading another instance of data table 'blastdb' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,987 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_p.loc' for tool data table 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:07,987 Loading another instance of data table 'blastdb_p' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:07,988 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_d.loc' for tool data table 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:07,988 Loading another instance of data table 'blastdb_d' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,040 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb.loc' for tool data table 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:08,040 Loading another instance of data table 'blastdb' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,040 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_p.loc' for tool data table 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:08,041 Loading another instance of data table 'blastdb_p' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,041 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_d.loc' for tool data table 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:08,041 Loading another instance of data table 'blastdb_d' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,086 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb.loc' for tool data table 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:08,087 Loading another instance of data table 'blastdb' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,087 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_p.loc' for tool data table 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:08,087 Loading another instance of data table 'blastdb_p' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,087 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_d.loc' for tool data table 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:08,087 Loading another instance of data table 'blastdb_d' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,184 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb.loc' for tool data table 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:08,184 Loading another instance of data table 'blastdb' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,185 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_p.loc' for tool data table 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:08,185 Loading another instance of data table 'blastdb_p' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,185 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_d.loc' for tool data table 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:08,185 Loading another instance of data table 'blastdb_d' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,231 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb.loc' for tool data table 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:08,231 Loading another instance of data table 'blastdb' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,231 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_p.loc' for tool data table 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:08,231 Loading another instance of data table 'blastdb_p' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,232 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_d.loc' for tool data table 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:08,232 Loading another instance of data table 'blastdb_d' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,267 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb.loc' for tool data table 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:08,267 Loading another instance of data table 'blastdb' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,267 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_p.loc' for tool data table 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:08,267 Loading another instance of data table 'blastdb_p' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,268 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_d.loc' for tool data table 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:08,268 Loading another instance of data table 'blastdb_d' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,329 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb.loc' for tool data table 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:08,329 Loading another instance of data table 'blastdb' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,329 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_p.loc' for tool data table 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:08,329 Loading another instance of data table 'blastdb_p' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,330 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_d.loc' for tool data table 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:08,330 Loading another instance of data table 'blastdb_d' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,392 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb.loc' for tool data table 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:08,393 Loading another instance of data table 'blastdb' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,394 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_p.loc' for tool data table 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:08,394 Loading another instance of data table 'blastdb_p' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 15:08:08,394 Cannot find index file '/galaxydir/galaxy/tool-data/blastdb_d.loc' for tool data table 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:08,395 Loading another instance of data table 'blastdb_d' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/ncbi_blast_plus/tool-data/tool_data_table_conf.xml.sample', attempting to merge content. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 15:08:08,852 Creating a new record for version 2.5.0 of tool dependency blast for revision 6f386c5dc4fb of repository ncbi_blast_plus. The status is being set to Never installed. galaxy.tools.data DEBUG 2017-11-18 15:08:08,875 Could not parse existing tool data table config, assume no existing elements: [Errno 2] No such file or directory: u'/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/tool_data_table_conf.xml' galaxy.tools.data DEBUG 2017-11-18 15:08:08,878 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 15:08:08,878 Loading another instance of data table 'blastdb' from file '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 15:08:08,879 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 15:08:08,879 Loading another instance of data table 'blastdb_p' from file '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 15:08:08,879 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb_d.loc' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 15:08:08,879 Loading another instance of data table 'blastdb_d' from file '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/tool_data_table_conf.xml', attempting to merge content. 127.0.0.1 - - [18/Nov/2017:15:08:10 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:13 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:16 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:19 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:22 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:25 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:25,991 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,011 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,028 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,043 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_convert2blastmask_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,058 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,105 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,153 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,171 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,191 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_segmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,210 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,257 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,275 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,322 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,372 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,414 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.watcher DEBUG 2017-11-18 15:08:26,921 The file './config/shed_tool_conf.xml' has changes. galaxy.queue_worker DEBUG 2017-11-18 15:08:26,922 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 15:08:26,946 Parsing the tool configuration ./config/tool_conf.xml.sample galaxy.tools.toolbox.base ERROR 2017-11-18 15:08:26,952 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base INFO 2017-11-18 15:08:26,955 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 15:08:26,959 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,959 Reading tools from config files finshed (13.322 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,960 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,962 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,962 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,962 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,963 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,963 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,964 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,965 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,965 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,966 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,967 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,967 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,967 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,967 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,968 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,968 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_convert2blastmask_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,968 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,968 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,969 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,969 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,969 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_segmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,969 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,970 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,970 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,971 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,971 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,972 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,972 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,973 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,973 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 15:08:26,974 Loading tool panel finished (14.147 ms) galaxy.tools.deps DEBUG 2017-11-18 15:08:26,976 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 15:08:26,999 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:26,999 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:26,999 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:26,999 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:26,999 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,000 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,000 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,000 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,000 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,000 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,001 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,001 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,001 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,001 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,001 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,002 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,002 Loaded converter: CONVERTER_fasta_to_fai galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,002 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,002 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,002 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,003 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,003 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,003 Loaded converter: CONVERTER_fastqgz_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,003 Loaded converter: CONVERTER_fastqsangergz_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,003 Loaded converter: CONVERTER_fastqsolexagz_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,004 Loaded converter: CONVERTER_fastqcssangergz_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,004 Loaded converter: CONVERTER_fastqilluminagz_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,004 Loaded converter: CONVERTER_fastqbz2_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,004 Loaded converter: CONVERTER_fastqsangerbz2_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,004 Loaded converter: CONVERTER_fastqsolexabz2_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,004 Loaded converter: CONVERTER_fastqcssangerbz2_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,004 Loaded converter: CONVERTER_fastqilluminabz2_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,005 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,005 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,005 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,005 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,005 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,005 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,006 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,006 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,006 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,006 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,006 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,006 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,006 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,007 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,007 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,007 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,007 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,007 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,007 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,007 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,008 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,008 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,008 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,008 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,008 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,008 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,008 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,009 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,009 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,009 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,009 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,009 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,009 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,009 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,009 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,010 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,010 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,010 Loaded converter: CONVERTER_biom1_to_biom2 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,010 Loaded converter: CONVERTER_biom2_to_biom1 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,010 Loaded converter: CONVERTER_SMILES_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,010 Loaded converter: CONVERTER_SMILES_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,010 Loaded converter: CONVERTER_SMILES_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,010 Loaded converter: CONVERTER_SMILES_to_MOL galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,011 Loaded converter: CONVERTER_SMILES_to_MOL2 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,011 Loaded converter: CONVERTER_smiles_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,011 Loaded converter: CONVERTER_sdf_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,011 Loaded converter: CONVERTER_sdf_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,011 Loaded converter: CONVERTER_sdf_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,011 Loaded converter: CONVERTER_sdf_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,011 Loaded converter: CONVERTER_inchi_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,011 Loaded converter: CONVERTER_inchi_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,011 Loaded converter: CONVERTER_inchi_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,012 Loaded converter: CONVERTER_inchi_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,012 Loaded converter: CONVERTER_inchi_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,012 Loaded converter: CONVERTER_mol_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,012 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,012 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,012 Loaded converter: CONVERTER_mol_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,012 Loaded converter: CONVERTER_mol2_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,012 Loaded converter: CONVERTER_mol2_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,013 Loaded converter: CONVERTER_mol2_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,013 Loaded converter: CONVERTER_mol2_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,013 Loaded converter: CONVERTER_mol2_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,013 Loaded converter: CONVERTER_cml_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,013 Loaded converter: CONVERTER_cml_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,013 Loaded converter: CONVERTER_cml_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,013 Loaded converter: CONVERTER_cml_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,013 Loaded converter: CONVERTER_ref_to_seq_taxomony galaxy.datatypes.registry DEBUG 2017-11-18 15:08:27,015 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 15:08:27,016 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 15:08:27,018 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 15:08:27,018 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 15:08:27,048 Toolbox reload (126.719 ms) galaxy.tools.deps.conda_util DEBUG 2017-11-18 15:08:27,063 Executing command: /galaxydir/galaxy/database/dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --channel r --name __blast@2.5.0 blast=2.5.0 galaxy.queue_worker INFO 2017-11-18 15:08:27,874 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 15:08:27,875 Starting to build toolbox index. 127.0.0.1 - - [18/Nov/2017:15:08:28 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" Fetching package metadata .....galaxy.tools.search DEBUG 2017-11-18 15:08:30,090 Toolbox index finished (2215.090 ms) 127.0.0.1 - - [18/Nov/2017:15:08:32 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ..127.0.0.1 - - [18/Nov/2017:15:08:35 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:38 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:41 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ..127.0.0.1 - - [18/Nov/2017:15:08:44 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:46 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:46 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:47 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:47 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:47 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ......127.0.0.1 - - [18/Nov/2017:15:08:48 -0400] "GET /admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:48 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" .. Solving package specifications: . Package plan for installation in environment /galaxydir/galaxy/database/dependencies/_conda/envs/__blast@2.5.0: The following NEW packages will be INSTALLED: blast: 2.5.0-boost1.64_2 bioconda 127.0.0.1 - - [18/Nov/2017:15:08:51 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:54 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:08:58 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:01 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:04 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:07 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" blast-2.5.0-bo 100% |##########################################################################################################################################################| Time: 0:00:17 6.72 MB/s 127.0.0.1 - - [18/Nov/2017:15:09:10 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:13 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:16 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:19 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:22 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:25 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:28 -0400] "GET /admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:28 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:31 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:34 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:37 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:40 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:43 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" # # To activate this environment, use: # > source activate __blast@2.5.0 # # To deactivate an active environment, use: # > source deactivate # galaxy.tools.deps DEBUG 2017-11-18 15:09:44,103 Using dependency blast version 2.5.0 of type conda tool_shed.util.tool_dependency_util DEBUG 2017-11-18 15:09:44,626 Updating an existing record for version 2.5.0 of tool dependency blast for revision 6f386c5dc4fb of repository ncbi_blast_plus by updating the status from Never installed to Installed. galaxy.tools.toolbox.base DEBUG 2017-11-18 15:09:44,676 Appending to tool panel section: Fetch Sequences 127.0.0.1 - - [18/Nov/2017:15:09:46 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.tool_dependency_util DEBUG 2017-11-18 15:09:47,130 Creating a new record for version 2.5.0 of tool dependency blast for revision 5dd2b68c7d04 of repository package_blast_plus_2_5_0. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 15:09:47,202 Updating an existing record for version 2.5.0 of tool dependency blast for revision 5dd2b68c7d04 of repository package_blast_plus_2_5_0 by updating the status from Never installed to Installing. tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 15:09:47,224 Attempting to download via url: https://depot.galaxyproject.org/software/blast_plus/blast_plus_2.5.0_darwin_x64.tar.gz 127.0.0.1 - - [18/Nov/2017:15:09:49 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:52 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:53 -0400] "GET /admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:53 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:56 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:09:59 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:10:02 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:10:05 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:10:08 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:10:11 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:10:14 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 15:10:15,239 Successfully downloaded from url: https://depot.galaxyproject.org/software/blast_plus/blast_plus_2.5.0_darwin_x64.tar.gz tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 15:10:15,262 Changing status for tool dependency blast from Installing to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 15:10:15,262 Updating an existing record for version 2.5.0 of tool dependency blast for revision 5dd2b68c7d04 of repository package_blast_plus_2_5_0 by updating the status from Installing to Installed. 127.0.0.1 - - [18/Nov/2017:15:08:00 -0400] "POST /admin_toolshed/manage_repositories HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 61917) Traceback (most recent call last): File "/galaxydir/galaxy/.venv/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 657, in __init__ self.finish() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 716, in finish self.wfile.close() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 283, in close self.flush() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- 127.0.0.1 - - [18/Nov/2017:15:10:17 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=f597429621d6eb2b,ebfb8f50c6abde6d" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:10:34 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:10:34 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:22 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:23 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:32 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=ebfb8f50c6abde6d HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:32 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=ebfb8f50c6abde6d&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:33 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=ebfb8f50c6abde6d&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:36 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:40 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=f597429621d6eb2b HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.deps DEBUG 2017-11-18 15:12:40,540 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 15:12:40,541 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 15:12:40,541 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 15:12:40,542 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 15:12:40,542 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 15:12:40,542 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 15:12:40,543 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 15:12:40,543 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 15:12:40,543 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 15:12:40,544 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 15:12:40,544 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 15:12:40,544 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 15:12:40,545 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 15:12:40,545 Using dependency blast version 2.5.0 of type tool_shed_package 127.0.0.1 - - [18/Nov/2017:15:12:40 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=f597429621d6eb2b&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:40 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=f597429621d6eb2b&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:50 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:50 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:51 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=f2db41e1fa331b3e HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:51 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:51 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:55 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:55 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:56 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=1cd8e2f6b131e891 HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:56 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=1cd8e2f6b131e891&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:12:57 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=1cd8e2f6b131e891&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:15:46 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:15:46 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:15:46 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:15:46 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:15:46 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:15:50 -0400] "GET /admin_toolshed/browse_tool_sheds HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:15:50 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:15:52 -0400] "GET /admin_toolshed/browse_tool_shed?tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.deps DEBUG 2017-11-18 15:16:30,665 Dependency sra-tools not found. galaxy.tools.deps DEBUG 2017-11-18 15:16:30,666 Dependency sra-tools not found. galaxy.tools.deps DEBUG 2017-11-18 15:16:30,667 Dependency sra-tools not found. 127.0.0.1 - - [18/Nov/2017:15:16:30 -0400] "GET /admin_toolshed/prepare_for_install?changeset_revisions=8c00bc7fd8de&repository_ids=cb2d31dfab58ee88&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:16:31 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=8c00bc7fd8de&repository_ids=cb2d31dfab58ee88&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 15:16:35,742 Creating repository dependency objects... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:36,282 Appending to tool panel section: Get Data tool_shed.util.repository_util DEBUG 2017-11-18 15:16:36,293 Adding new row for repository 'sra_tools' in the tool_shed_repository table, status set to 'New'. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 15:16:36,302 Building repository dependency relationships... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:36,303 Appending to tool panel section: Get Data 127.0.0.1 - - [18/Nov/2017:15:16:35 -0400] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=8c00bc7fd8de&repository_ids=cb2d31dfab58ee88&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:16:36 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:36,499 Appending to tool panel section: Get Data 127.0.0.1 - - [18/Nov/2017:15:16:39 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,036 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.8.1.2, version: 2.8.1.2 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,048 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,057 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.watcher DEBUG 2017-11-18 15:16:42,707 The file './config/shed_tool_conf.xml' has changes. galaxy.queue_worker DEBUG 2017-11-18 15:16:42,707 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 15:16:42,741 Parsing the tool configuration ./config/tool_conf.xml.sample galaxy.tools.toolbox.base ERROR 2017-11-18 15:16:42,750 Error reading tool configuration file from path: extract/liftOver_wrapper.xml 127.0.0.1 - - [18/Nov/2017:15:16:42 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.toolbox.base INFO 2017-11-18 15:16:42,760 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 15:16:42,765 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,765 Reading tools from config files finshed (24.595 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,765 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,766 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.8.1.2, version: 2.8.1.2 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,766 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,767 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,769 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,770 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,770 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,771 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,771 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,773 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,774 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,775 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,775 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,776 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,777 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,779 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,780 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,781 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 15:16:42,781 Loading tool panel finished (15.896 ms) galaxy.tools.deps DEBUG 2017-11-18 15:16:42,784 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 15:16:42,808 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 15:16:42,810 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 15:16:42,811 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 15:16:42,811 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 15:16:42,817 Toolbox reload (110.326 ms) galaxy.tools.deps.conda_util DEBUG 2017-11-18 15:16:42,924 Executing command: /galaxydir/galaxy/database/dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --channel r --name __sra-tools@2.8.1 sra-tools=2.8.1 galaxy.queue_worker INFO 2017-11-18 15:16:43,011 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 15:16:43,011 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 15:16:43,242 Toolbox index finished (230.942 ms) Fetching package metadata .......127.0.0.1 - - [18/Nov/2017:15:16:45 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:16:48 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:16:51 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" .127.0.0.1 - - [18/Nov/2017:15:16:54 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ......... Solving package specifications: . Package plan for installation in environment /galaxydir/galaxy/database/dependencies/_conda/envs/__sra-tools@2.8.1: The following NEW packages will be INSTALLED: sra-tools: 2.8.1-0 bioconda 127.0.0.1 - - [18/Nov/2017:15:16:57 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:00 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:03 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:07 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:10 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:13 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:16 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" sra-tools-2.8. 100% |##########################################################################################################################################################| Time: 0:00:18 6.47 MB/s 127.0.0.1 - - [18/Nov/2017:15:17:19 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:22 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:25 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:28 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:31 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:34 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:37 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:40 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:43 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:46 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:49 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:52 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" # # To activate this environment, use: # > source activate __sra-tools@2.8.1 # # To deactivate an active environment, use: # > source deactivate # galaxy.tools.deps DEBUG 2017-11-18 15:17:53,866 Using dependency sra-tools version 2.8.1 of type conda 127.0.0.1 - - [18/Nov/2017:15:16:36 -0400] "POST /admin_toolshed/manage_repositories HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:53 -0400] "GET /admin_toolshed/monitor_repository_installation?tool_shed_repository_ids=33b43b4e7093c91f HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:17:55 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:00 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:00 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:02 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=33b43b4e7093c91f HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.deps DEBUG 2017-11-18 15:18:03,020 Using dependency sra-tools version 2.8.1 of type conda galaxy.tools.deps DEBUG 2017-11-18 15:18:03,020 Using dependency sra-tools version 2.8.1 of type conda galaxy.tools.deps DEBUG 2017-11-18 15:18:03,021 Using dependency sra-tools version 2.8.1 of type conda 127.0.0.1 - - [18/Nov/2017:15:18:02 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=33b43b4e7093c91f&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:03 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=33b43b4e7093c91f&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:10 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:10 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:10 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:10 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:10 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:10 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:10 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:11 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:11 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:11 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:11 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:18:13 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:26 -0400] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3/build?version=2.8.1.3&__identifer=f62cnesklq4&tool_version=2.8.1.3 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffastq_dump%2F2.8.1.3&version=2.8.1.3&__identifer=f62cnesklq4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:26 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffastq_dump%2F2.8.1.3&version=2.8.1.3&__identifer=f62cnesklq4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" beaker.container DEBUG 2017-11-18 15:20:26,939 lock_createfunc (waiting) beaker.container DEBUG 2017-11-18 15:20:26,939 lock_createfunc (waited) beaker.container DEBUG 2017-11-18 15:20:26,939 get_value creating new value requests.packages.urllib3.connectionpool INFO 2017-11-18 15:20:26,942 Starting new HTTP connection (1): dx.doi.org requests.packages.urllib3.connectionpool DEBUG 2017-11-18 15:20:27,644 "GET /10.1093/nar/gkq1019 HTTP/1.1" 303 183 requests.packages.urllib3.connectionpool INFO 2017-11-18 15:20:27,647 Starting new HTTPS connection (1): data.crossref.org requests.packages.urllib3.connectionpool DEBUG 2017-11-18 15:20:27,836 "GET /10.1093%2Fnar%2Fgkq1019 HTTP/1.1" 200 360 beaker.container DEBUG 2017-11-18 15:20:27,843 set_value stored time 1511036427.843214 expire time None beaker.container DEBUG 2017-11-18 15:20:27,843 released create lock 127.0.0.1 - - [18/Nov/2017:15:20:26 -0400] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffastq_dump%2F2.8.1.3&version=2.8.1.3&__identifer=f62cnesklq4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:28 -0400] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.8.1.2/build?version=2.8.1.2&__identifer=ozigwrgaty9&tool_version=2.8.1.2 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsra_pileup%2F2.8.1.2&version=2.8.1.2&__identifer=ozigwrgaty9" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:28 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsra_pileup%2F2.8.1.2&version=2.8.1.2&__identifer=ozigwrgaty9" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:28 -0400] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.8.1.2/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsra_pileup%2F2.8.1.2&version=2.8.1.2&__identifer=ozigwrgaty9" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:29 -0400] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.3/build?version=2.8.1.3&__identifer=n8bh1pk0que&tool_version=2.8.1.3 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsam_dump%2F2.8.1.3&version=2.8.1.3&__identifer=n8bh1pk0que" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:29 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsam_dump%2F2.8.1.3&version=2.8.1.3&__identifer=n8bh1pk0que" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:29 -0400] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.3/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsam_dump%2F2.8.1.3&version=2.8.1.3&__identifer=n8bh1pk0que" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:32 -0400] "GET /api/tools?q=sfr HTTP/1.1" 200 - "http://localhost:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsam_dump%2F2.8.1.3&version=2.8.1.3&__identifer=n8bh1pk0que" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:34 -0400] "GET /api/tools?q=sra HTTP/1.1" 200 - "http://localhost:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsam_dump%2F2.8.1.3&version=2.8.1.3&__identifer=n8bh1pk0que" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:41 -0400] "GET /api/tools?q=blas HTTP/1.1" 200 - "http://localhost:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsam_dump%2F2.8.1.3&version=2.8.1.3&__identifer=n8bh1pk0que" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:41 -0400] "GET /api/tools?q=blast HTTP/1.1" 200 - "http://localhost:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsam_dump%2F2.8.1.3&version=2.8.1.3&__identifer=n8bh1pk0que" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:49 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsam_dump%2F2.8.1.3&version=2.8.1.3&__identifer=n8bh1pk0que" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:49 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:49 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:49 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:20:49 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:21:07 -0400] "GET /admin_toolshed/browse_tool_sheds HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:21:07 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:21:08 -0400] "GET /admin_toolshed/browse_tool_shed?tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:21:21 -0400] "GET /admin_toolshed/prepare_for_install?changeset_revisions=ec2595e4d313&repository_ids=18e81ffc1cf9369e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:21:23 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=ec2595e4d313&repository_ids=18e81ffc1cf9369e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 15:21:41,643 Creating repository dependency objects... tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 15:21:41,979 Skipping installation of revision ec2595e4d313 of repository 'package_bwa_0_5_9' because it was installed with the (possibly updated) revision ec2595e4d313 and its current installation status is 'Installed'. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 15:21:41,979 Building repository dependency relationships... 127.0.0.1 - - [18/Nov/2017:15:21:41 -0400] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=ec2595e4d313&repository_ids=18e81ffc1cf9369e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:21:41 -0400] "GET /admin_toolshed/manage_repositories?status=done&encoded_updated_metadata=None&updating_repository_id=None&includes_tools_for_display_in_tool_panel=False&message=&updating_to_ctx_rev=None&shed_tool_conf=.%2Fconfig%2Fshed_tool_conf.xml&updating_to_changeset_revision=None&encoded_repo_info_dicts=d57721e138de1268b0a566274a00367d39893c1c%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&install_tool_dependencies=__CHECKED__&install_tool_dependencies=__NOTHING__&includes_tools=False&requirements_status=%5B%5D&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&select_tool_panel_section_button=Install&includes_tool_dependencies=True&updating=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=ec2595e4d313&repository_ids=18e81ffc1cf9369e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:21:42 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repositories?status=done&encoded_updated_metadata=None&updating_repository_id=None&includes_tools_for_display_in_tool_panel=False&message=&updating_to_ctx_rev=None&shed_tool_conf=.%2Fconfig%2Fshed_tool_conf.xml&updating_to_changeset_revision=None&encoded_repo_info_dicts=d57721e138de1268b0a566274a00367d39893c1c%3A7b227061636b6167655f6277615f305f355f39223a205b22436f6e7461696e73206120746f6f6c20646570656e64656e637920646566696e6974696f6e207468617420646f776e6c6f61647320616e6420636f6d70696c65732076657273696f6e20302e352e392d723136206f662074686520425741207061636b616765222c202268747470733a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6465767465616d2f7061636b6167655f6277615f305f355f39222c2022656332353935653464333133222c202232222c20226465767465616d222c207b7d2c207b226277612f302e352e39223a207b227265706f7369746f72795f6e616d65223a20227061636b6167655f6277615f305f355f39222c20226e616d65223a2022627761222c20227265706f7369746f72795f6f776e6572223a20226465767465616d222c202276657273696f6e223a2022302e352e39222c2022726561646d65223a20225c6e5468697320697320746865206c6173742076657273696f6e206f6620425741207468617420757365732073657061726174652066696c657320666f722042575420616e642072657665727365204257542e5c6e5c6e50726f6772616d3a206277612028616c69676e6d656e742076696120427572726f77732d576865656c6572207472616e73666f726d6174696f6e295c6e56657273696f6e3a20302e352e392d7231365c6e436f6e746163743a2048656e67204c69203c6c68334073616e6765722e61632e756b3e5c6e5c6e55736167653a202020627761203c636f6d6d616e643e205b6f7074696f6e735d5c6e5c6e436f6d6d616e643a20696e646578202020202020202020696e6465782073657175656e63657320696e2074686520464153544120666f726d61745c6e202020202020202020616c6e20202020202020202020206761707065642f756e67617070656420616c69676e6d656e745c6e20202020202020202073616d736520202020202020202067656e657261746520616c69676e6d656e74202873696e676c6520656e646564295c6e20202020202020202073616d706520202020202020202067656e657261746520616c69676e6d656e74202870616972656420656e646564295c6e20202020202020202062776173772020202020202020204257412d535720666f72206c6f6e6720717565726965735c6e5c6e2020202020202020206661327061632020202020202020636f6e7665727420464153544120746f2050414320666f726d61745c6e202020202020202020706163326277742020202020202067656e6572617465204257542066726f6d205041435c6e2020202020202020207061633262777467656e20202020616c7465726e617469766520616c676f726974686d20666f722067656e65726174696e67204257545c6e2020202020202020206277747570646174652020202020757064617465202e62777420746f20746865206e657720666f726d61745c6e2020202020202020207061635f7265762020202020202067656e65726174652072657665727365205041435c6e202020202020202020627774327361202020202020202067656e65726174652053412066726f6d2042575420616e64204f63635c6e2020202020202020207061633263737061632020202020636f6e766572742050414320746f20636f6c6f722d7370616365205041435c6e20202020202020202073746473772020202020202020207374616e646172642053572f4e5720616c69676e6d656e745c6e2020202020202020222c20226368616e67657365745f7265766973696f6e223a2022656332353935653464333133222c202274797065223a20227061636b616765227d7d5d7d&install_tool_dependencies=__CHECKED__&install_tool_dependencies=__NOTHING__&includes_tools=False&requirements_status=%5B%5D&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&select_tool_panel_section_button=Install&includes_tool_dependencies=True&updating=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:21:46 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:21:47 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:21:51 -0400] "GET /admin_toolshed/browse_tool_sheds HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:21:51 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:21:52 -0400] "GET /admin_toolshed/browse_tool_shed?tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:03 -0400] "GET /admin_toolshed/prepare_for_install?changeset_revisions=ec2595e4d313&repository_ids=18e81ffc1cf9369e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:04 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=ec2595e4d313&repository_ids=18e81ffc1cf9369e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 15:22:06,599 Creating repository dependency objects... tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 15:22:06,967 Skipping installation of revision ec2595e4d313 of repository 'package_bwa_0_5_9' because it was installed with the (possibly updated) revision ec2595e4d313 and its current installation status is 'Installed'. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 15:22:06,967 Building repository dependency relationships... 127.0.0.1 - - [18/Nov/2017:15:22:06 -0400] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=ec2595e4d313&repository_ids=18e81ffc1cf9369e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:06 -0400] "GET /admin_toolshed/manage_repositories?status=done&encoded_updated_metadata=None&updating_repository_id=None&includes_tools_for_display_in_tool_panel=False&message=&updating_to_ctx_rev=None&shed_tool_conf=.%2Fconfig%2Fshed_tool_conf.xml&updating_to_changeset_revision=None&encoded_repo_info_dicts=d57721e138de1268b0a566274a00367d39893c1c%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&install_tool_dependencies=__CHECKED__&install_tool_dependencies=__NOTHING__&includes_tools=False&requirements_status=%5B%5D&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&select_tool_panel_section_button=Install&includes_tool_dependencies=True&updating=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=ec2595e4d313&repository_ids=18e81ffc1cf9369e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:07 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repositories?status=done&encoded_updated_metadata=None&updating_repository_id=None&includes_tools_for_display_in_tool_panel=False&message=&updating_to_ctx_rev=None&shed_tool_conf=.%2Fconfig%2Fshed_tool_conf.xml&updating_to_changeset_revision=None&encoded_repo_info_dicts=d57721e138de1268b0a566274a00367d39893c1c%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&install_tool_dependencies=__CHECKED__&install_tool_dependencies=__NOTHING__&includes_tools=False&requirements_status=%5B%5D&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&select_tool_panel_section_button=Install&includes_tool_dependencies=True&updating=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:11 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:12 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:12 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:12 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:16 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=f2db41e1fa331b3e HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:16 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:16 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:18 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:19 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:19 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:19 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:19 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:19 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:19 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:19 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:19 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:19 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:19 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:22:21 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 15:23:36,743 Validated and populated state for tool request (51.719 ms) galaxy.tools.actions.upload DEBUG 2017-11-18 15:23:36,800 Persisted uploads (35.572 ms) galaxy.tools.actions.upload DEBUG 2017-11-18 15:23:37,021 Checked and cleaned uploads (214.908 ms) galaxy.tools.actions.upload_common INFO 2017-11-18 15:23:37,084 tool upload1 created job id 1 galaxy.tools.actions.upload DEBUG 2017-11-18 15:23:37,168 Created upload job (147.062 ms) galaxy.tools.execute DEBUG 2017-11-18 15:23:37,168 Tool [upload1] created job [1] (403.514 ms) galaxy.tools.execute DEBUG 2017-11-18 15:23:37,197 Executed 1 job(s) for tool upload1 request: (453.522 ms) 127.0.0.1 - - [18/Nov/2017:15:23:30 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:23:37 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T20%3A22%3A19.387Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 15:23:37,863 (1) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/1 galaxy.jobs.handler DEBUG 2017-11-18 15:23:37,895 (1) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 15:23:37,984 (1) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 15:23:38,007 Job [1] queued (112.055 ms) galaxy.jobs.handler INFO 2017-11-18 15:23:38,038 (1) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 15:23:38,663 Built script [/galaxydir/galaxy/database/jobs_directory/000/1/tool_script.sh] for tool command [python /galaxydir/galaxy/tools/data_source/upload.py /galaxydir/galaxy /galaxydir/galaxy/database/jobs_directory/000/1/registry.xml /galaxydir/galaxy/database/tmp/tmprYN10U 1:/galaxydir/galaxy/database/jobs_directory/000/1/dataset_1_files:/galaxydir/galaxy/database/files/000/dataset_1.dat] galaxy.jobs.runners DEBUG 2017-11-18 15:23:39,018 (1) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/1/tool_script.sh; return_code=$?; cd '/galaxydir/galaxy/database/jobs_directory/000/1'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True python "/galaxydir/galaxy/database/jobs_directory/000/1/set_metadata_44kdrO.py" "/galaxydir/galaxy/database/jobs_directory/000/1/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/1/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/1/metadata_in_HistoryDatasetAssociation_1_iwkYnZ,/galaxydir/galaxy/database/jobs_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_vEsMXK,/galaxydir/galaxy/database/jobs_directory/000/1/metadata_out_HistoryDatasetAssociation_1_b7VwIy,/galaxydir/galaxy/database/jobs_directory/000/1/metadata_results_HistoryDatasetAssociation_1_Lwyc57,/galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/jobs_directory/000/1/metadata_override_HistoryDatasetAssociation_1_yFa6wr" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 15:23:39,063 (1) executing job script: /galaxydir/galaxy/database/jobs_directory/000/1/galaxy_1.sh galaxy.jobs DEBUG 2017-11-18 15:23:39,086 (1) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:15:23:41 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T20%3A23%3A37.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 15:23:45,228 Validated and populated state for tool request (61.918 ms) galaxy.tools.actions.upload DEBUG 2017-11-18 15:23:45,280 Persisted uploads (27.577 ms) galaxy.tools.actions.upload DEBUG 2017-11-18 15:23:45,486 Checked and cleaned uploads (205.768 ms) 127.0.0.1 - - [18/Nov/2017:15:23:45 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T20%3A23%3A41.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.actions.upload_common INFO 2017-11-18 15:23:45,615 tool upload1 created job id 2 galaxy.tools.actions.upload DEBUG 2017-11-18 15:23:45,721 Created upload job (235.381 ms) galaxy.tools.execute DEBUG 2017-11-18 15:23:45,721 Tool [upload1] created job [2] (469.401 ms) galaxy.tools.execute DEBUG 2017-11-18 15:23:45,743 Executed 1 job(s) for tool upload1 request: (514.921 ms) 127.0.0.1 - - [18/Nov/2017:15:23:37 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 15:23:46,370 (2) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/2 galaxy.jobs.handler DEBUG 2017-11-18 15:23:46,385 (2) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 15:23:46,446 (2) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 15:23:46,465 Job [2] queued (79.502 ms) galaxy.jobs.handler INFO 2017-11-18 15:23:46,490 (2) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 15:23:46,892 Built script [/galaxydir/galaxy/database/jobs_directory/000/2/tool_script.sh] for tool command [python /galaxydir/galaxy/tools/data_source/upload.py /galaxydir/galaxy /galaxydir/galaxy/database/jobs_directory/000/2/registry.xml /galaxydir/galaxy/database/tmp/tmpBvlIDY 2:/galaxydir/galaxy/database/jobs_directory/000/2/dataset_2_files:/galaxydir/galaxy/database/files/000/dataset_2.dat] galaxy.jobs.runners DEBUG 2017-11-18 15:23:47,129 (2) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/2/tool_script.sh; return_code=$?; cd '/galaxydir/galaxy/database/jobs_directory/000/2'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True python "/galaxydir/galaxy/database/jobs_directory/000/2/set_metadata_QFxiHy.py" "/galaxydir/galaxy/database/jobs_directory/000/2/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/2/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/2/metadata_in_HistoryDatasetAssociation_2_ENScGA,/galaxydir/galaxy/database/jobs_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_477rLV,/galaxydir/galaxy/database/jobs_directory/000/2/metadata_out_HistoryDatasetAssociation_2_OeEbzr,/galaxydir/galaxy/database/jobs_directory/000/2/metadata_results_HistoryDatasetAssociation_2_HeVjzA,/galaxydir/galaxy/database/files/000/dataset_2.dat,/galaxydir/galaxy/database/jobs_directory/000/2/metadata_override_HistoryDatasetAssociation_2_Zmleoz" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 15:23:47,149 (2) executing job script: /galaxydir/galaxy/database/jobs_directory/000/2/galaxy_2.sh galaxy.jobs DEBUG 2017-11-18 15:23:47,159 (2) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:15:23:49 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T20%3A23%3A45.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:23:53 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T20%3A23%3A49.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 15:23:56,320 execution finished: /galaxydir/galaxy/database/jobs_directory/000/1/galaxy_1.sh 127.0.0.1 - - [18/Nov/2017:15:23:56 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T20%3A23%3A53.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.model.metadata DEBUG 2017-11-18 15:23:56,542 loading metadata from file for: HistoryDatasetAssociation 1 galaxy.jobs INFO 2017-11-18 15:23:56,736 Collecting metrics for Job 1 galaxy.jobs DEBUG 2017-11-18 15:23:56,760 job 1 ended (finish() executed in (440.005 ms)) galaxy.model.metadata DEBUG 2017-11-18 15:23:56,768 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:15:24:00 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T20%3A23%3A56.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 15:24:02,569 execution finished: /galaxydir/galaxy/database/jobs_directory/000/2/galaxy_2.sh galaxy.model.metadata DEBUG 2017-11-18 15:24:02,741 loading metadata from file for: HistoryDatasetAssociation 2 galaxy.jobs INFO 2017-11-18 15:24:02,908 Collecting metrics for Job 2 galaxy.jobs DEBUG 2017-11-18 15:24:02,927 job 2 ended (finish() executed in (357.032 ms)) galaxy.model.metadata DEBUG 2017-11-18 15:24:02,942 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:15:24:04 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T20%3A24%3A00.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:24:04 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:15:24:04 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ^Cgalaxy.jobs.handler INFO 2017-11-18 16:13:41,530 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 16:13:41,530 job handler queue stopped galaxy.jobs.runners INFO 2017-11-18 16:13:41,531 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2017-11-18 16:13:41,531 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 16:13:41,532 job handler stop queue stopped CFM5081985:galaxy charles.strittmatter$ sh run.sh Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv galaxy.tools.deps DEBUG 2017-11-18 16:13:49,214 Unable to find config file './dependency_resolvers_conf.xml' DEBUG:galaxy.app:python path is: /galaxydir/galaxy/scripts, /galaxydir/galaxy/lib, /galaxydir/galaxy/.venv/lib/python27.zip, /galaxydir/galaxy/.venv/lib/python2.7, /galaxydir/galaxy/.venv/lib/python2.7/plat-darwin, /galaxydir/galaxy/.venv/lib/python2.7/plat-mac, /galaxydir/galaxy/.venv/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/Extras/lib/python, /galaxydir/galaxy/.venv/lib/python2.7/lib-tk, /galaxydir/galaxy/.venv/lib/python2.7/lib-old, /galaxydir/galaxy/.venv/lib/python2.7/lib-dynload, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/lib/python2.7/site-packages DEBUG:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config INFO:galaxy.config:Logging at '10' level to 'stdout' galaxy.queue_worker INFO 2017-11-18 16:13:51,560 Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE tool_shed.tool_shed_registry DEBUG 2017-11-18 16:13:51,635 Loading references to tool sheds from ./config/tool_sheds_conf.xml.sample tool_shed.tool_shed_registry DEBUG 2017-11-18 16:13:51,635 Loaded reference to tool shed: Galaxy Main Tool Shed galaxy.app DEBUG 2017-11-18 16:13:51,640 Using "galaxy.ini" config file: /galaxydir/galaxy/config/galaxy.ini migrate.versioning.repository DEBUG 2017-11-18 16:13:51,795 Loading repository lib/galaxy/model/migrate... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,803 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,803 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,804 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,804 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,804 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,804 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,805 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,805 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,806 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,806 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,806 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,806 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,807 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,807 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,808 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,808 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,808 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,808 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,808 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,809 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,809 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,809 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,809 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,809 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,810 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,810 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,810 Loading script lib/galaxy/model/migrate/versions/0014_pages.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,810 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully 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('required_dbs', '[]')]))]) galaxy.model.migrate.check INFO 2017-11-18 16:13:51,933 At database version 135 migrate.versioning.repository DEBUG 2017-11-18 16:13:51,936 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,938 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,938 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,938 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,938 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,938 Loading script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:13:51,938 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'migrate_tools'), ('required_dbs', '[]')]))]) tool_shed.galaxy_install.migrate.check INFO 2017-11-18 16:13:51,960 At migrate_tools version 12 galaxy.config INFO 2017-11-18 16:13:51,986 Install database targetting Galaxy's database configuration. /galaxydir/galaxy/lib/galaxy/datatypes/registry.py:98: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if root_dir and config: galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,083 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,083 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,083 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/binary: No module named binary galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,083 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,084 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,084 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,084 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,095 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,097 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,099 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,099 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,100 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,100 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,100 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,100 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,101 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,130 Loading datatypes from ./config/datatypes_conf.xml.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,130 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,131 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,131 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,132 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,132 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,132 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,132 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,132 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,132 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,133 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,133 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,133 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,133 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,133 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,134 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,134 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,134 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,134 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,134 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,135 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,135 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,135 Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,135 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,136 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,136 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,136 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,137 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,137 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,137 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,137 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,137 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,138 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,138 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,138 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,138 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,139 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,139 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,139 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,139 Retrieved datatype module galaxy.datatypes.sequence:FastqGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,139 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,140 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,140 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,141 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,141 Retrieved datatype module galaxy.datatypes.sequence:FastqBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,141 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,142 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,142 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,142 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,142 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,142 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,143 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,143 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,143 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,143 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,143 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,144 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,144 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,144 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,144 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,144 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,145 Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,145 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,145 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,145 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,146 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,146 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,146 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,147 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,147 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,147 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,147 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,148 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,148 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,148 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,148 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,149 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,149 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,149 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,149 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,149 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,150 Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,150 Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,150 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,150 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,150 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,150 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,151 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,151 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,151 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,151 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,151 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,151 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,151 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,152 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,152 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,152 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,152 Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,152 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,155 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,155 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,155 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,155 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,156 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,156 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,156 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,157 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,157 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,157 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,157 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,157 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,158 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,158 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,158 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,158 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,158 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,159 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,159 Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,159 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,159 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,159 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,159 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,159 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,160 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,160 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,160 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,160 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,160 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,160 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,160 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,161 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,161 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,161 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,161 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,161 Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,161 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,162 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,162 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,162 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,162 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,162 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,163 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,163 Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,163 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,163 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,164 Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,164 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,164 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,164 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,165 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,165 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,165 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,165 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,165 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,165 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,166 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,166 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,166 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,166 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,166 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,166 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,167 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,167 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,167 Roadmaps is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,167 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,167 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,167 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,167 Sequences is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,168 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,168 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,168 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,168 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,168 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,169 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,169 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,169 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,169 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,170 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,170 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,170 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,170 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,170 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,170 Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,171 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,171 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,171 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,171 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,171 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,171 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,172 Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,172 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,172 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,173 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,174 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,174 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,174 Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,174 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,175 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,175 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,178 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,178 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,178 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,178 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,178 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,179 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,179 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,179 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,179 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,179 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,180 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,180 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,180 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,180 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,180 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,181 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,181 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,181 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,181 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,181 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,182 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,182 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,185 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,185 Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,185 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,185 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,186 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,186 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,186 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,186 Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,186 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,188 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,188 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,276 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,276 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,276 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,276 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,277 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,277 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,277 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,278 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,278 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,278 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,278 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,278 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,279 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,279 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,279 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,280 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,280 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,280 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,280 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,281 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,281 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,281 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,281 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,282 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,282 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,282 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,282 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,282 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,283 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,283 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,283 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,283 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,284 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,284 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,284 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,284 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,285 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,285 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,285 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,285 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,286 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,286 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,286 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,286 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,287 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,287 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,287 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,287 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,287 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,288 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,288 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,288 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,288 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,289 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,289 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,289 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,289 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,289 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,290 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,290 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,290 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,291 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,292 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,292 Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,292 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,292 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,293 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,293 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,293 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,293 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,294 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,294 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,294 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,294 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,295 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,295 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,295 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,295 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,296 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,296 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,296 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,296 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,296 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,297 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,297 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,297 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,297 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,298 Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,298 Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,299 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,299 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,300 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,300 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,300 Retrieved datatype module galaxy.datatypes.binary:Cel from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,300 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,300 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,301 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,301 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,301 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,301 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,301 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,302 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,303 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,303 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,303 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,303 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,303 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,304 Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,304 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,306 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,306 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,306 Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,306 Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,307 Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,307 Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,307 Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,307 Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,307 Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,308 Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,308 Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,308 Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,308 Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,308 Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,312 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,312 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,312 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,312 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,312 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,313 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,313 Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,313 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,313 Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,313 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,313 Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,314 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,314 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,314 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,314 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,314 Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,314 Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,314 Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,314 Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,315 Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,315 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,315 Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,315 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,315 Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,315 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,315 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,316 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,317 Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,317 Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,317 Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,317 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,318 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,318 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,318 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,318 Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,318 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,318 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,319 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,319 Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,320 Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,320 Overriding conflicting datatype with extension 'blastxml', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,320 Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,321 Overriding conflicting datatype with extension 'blastdbn', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,321 Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,321 Overriding conflicting datatype with extension 'blastdbp', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,321 Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,321 Overriding conflicting datatype with extension 'blastdbd', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,322 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,322 Overriding conflicting datatype with extension 'maskinfo-asn1', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,323 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,323 Overriding conflicting datatype with extension 'maskinfo-asn1-binary', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,324 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,324 Overriding conflicting datatype with extension 'pssm-asn1', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,328 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,329 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,329 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,330 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,330 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,330 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,330 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,330 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrtho from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,330 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,331 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylip from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,331 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,331 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,331 Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,331 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,331 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,331 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,332 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,332 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,332 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,332 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,332 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,332 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,332 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,332 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,332 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,332 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,333 Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,333 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,333 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,333 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,333 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,333 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,333 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,333 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,333 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,334 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,334 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,334 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,334 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,334 Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,334 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,334 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,334 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,335 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,335 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,335 Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,335 Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,335 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,335 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,335 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,335 Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,335 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,336 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,336 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,336 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,336 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,336 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,336 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,336 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,336 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,337 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,337 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,337 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,337 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,337 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,337 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,337 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,337 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,337 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,338 Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,338 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,338 Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,338 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,338 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,338 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,338 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,338 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,339 Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,339 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,339 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,339 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,339 Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,339 Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,339 Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,339 Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,339 Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,340 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,340 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,340 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerGz' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,340 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerBz2' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,340 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,341 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqGz' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,341 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqBz2' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,341 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,341 Loaded sniffer for datatype 'galaxy.datatypes.text:Html' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,341 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,342 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,342 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,342 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,342 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,342 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,342 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,343 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,343 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,343 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,343 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,343 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,343 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,344 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,344 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,344 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,344 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,344 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,344 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,345 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,345 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,345 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,345 Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,345 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,345 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,345 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,346 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,346 Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,346 Loaded sniffer for datatype 'galaxy.datatypes.binary:Cel' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,346 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,346 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,346 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,347 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,347 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,347 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,347 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,347 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,347 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,347 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,347 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,348 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,348 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,348 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,348 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,348 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,348 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,348 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,349 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,349 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,349 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,349 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,349 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,349 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,355 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,356 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,356 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,356 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,356 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,356 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,356 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,356 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:52,357 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.tools.data INFO 2017-11-18 16:13:53,178 Could not find tool data tool-data/all_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:13:53,179 Loaded 0 lines from 'tool-data/all_fasta.loc.sample' for 'all_fasta' galaxy.tools.data DEBUG 2017-11-18 16:13:53,180 Loaded tool data table 'all_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:13:53,180 Could not find tool data tool-data/bfast_indexes.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:13:53,181 Loaded 0 lines from 'tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' galaxy.tools.data DEBUG 2017-11-18 16:13:53,182 Loaded tool data table 'bfast_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:13:53,183 Loaded 0 lines from 'tool-data/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 16:13:53,184 Loaded tool data table 'blastdb' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:13:53,185 Loaded 0 lines from 'tool-data/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 16:13:53,186 Loaded tool data table 'blastdb_p' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:13:53,187 Loaded 0 lines from 'tool-data/blastdb_d.loc' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 16:13:53,188 Loaded tool data table 'blastdb_d' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data WARNING 2017-11-18 16:13:53,188 Cannot find index file 'tool-data/bwa_index.loc' for tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 16:13:53,188 Loaded tool data table 'bwa_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data WARNING 2017-11-18 16:13:53,189 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 16:13:53,189 Loaded tool data table 'bwa_indexes_color' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:13:53,189 Could not find tool data tool-data/maf_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:13:53,192 Loaded 0 lines from 'tool-data/maf_index.loc.sample' for 'indexed_maf_files' galaxy.tools.data DEBUG 2017-11-18 16:13:53,192 Loaded tool data table 'indexed_maf_files' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:13:53,192 Could not find tool data tool-data/ngs_sim_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:13:53,194 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' galaxy.tools.data DEBUG 2017-11-18 16:13:53,194 Loaded tool data table 'ngs_sim_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:13:53,194 Could not find tool data tool-data/perm_base_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:13:53,196 Loaded 0 lines from 'tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' galaxy.tools.data DEBUG 2017-11-18 16:13:53,196 Loaded tool data table 'perm_base_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:13:53,196 Could not find tool data tool-data/perm_color_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:13:53,198 Loaded 0 lines from 'tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' galaxy.tools.data DEBUG 2017-11-18 16:13:53,198 Loaded tool data table 'perm_color_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:13:53,199 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:13:53,200 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'picard_indexes' galaxy.tools.data DEBUG 2017-11-18 16:13:53,201 Loaded tool data table 'picard_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:13:53,201 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:13:53,202 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'srma_indexes' galaxy.tools.data DEBUG 2017-11-18 16:13:53,202 Loaded tool data table 'srma_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:13:53,202 Could not find tool data tool-data/mosaik_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:13:53,204 Loaded 0 lines from 'tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' galaxy.tools.data DEBUG 2017-11-18 16:13:53,204 Loaded tool data table 'mosaik_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:13:53,205 Could not find tool data tool-data/twobit.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:13:53,206 Loaded 0 lines from 'tool-data/twobit.loc.sample' for 'twobit' galaxy.tools.data DEBUG 2017-11-18 16:13:53,206 Loaded tool data table 'twobit' from file './config/tool_data_table_conf.xml.sample' requests.packages.urllib3.connectionpool INFO 2017-11-18 16:13:53,225 Starting new HTTP connection (1): igv.broadinstitute.org requests.packages.urllib3.connectionpool DEBUG 2017-11-18 16:13:53,320 "GET /genomes/genomes.txt HTTP/1.1" 200 15681 galaxy.tools.data DEBUG 2017-11-18 16:13:53,333 Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-x86ZMT". galaxy.tools.data WARNING 2017-11-18 16:13:53,333 Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields): <Server-Side Genome List> galaxy.tools.data DEBUG 2017-11-18 16:13:53,335 Loaded 156 lines from '/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-x86ZMT' for 'igv_broad_genomes' galaxy.tools.data DEBUG 2017-11-18 16:13:53,338 Loaded tool data table 'igv_broad_genomes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:13:53,338 Could not find tool data tool-data/liftOver.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:13:53,340 Loaded 0 lines from 'tool-data/liftOver.loc.sample' for 'liftOver' galaxy.tools.data DEBUG 2017-11-18 16:13:53,340 Loaded tool data table 'liftOver' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:13:53,341 Could not find tool data tool-data/bam_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:13:53,342 Loaded 1 lines from 'tool-data/bam_iobio.loc.sample' for 'bam_iobio' galaxy.tools.data DEBUG 2017-11-18 16:13:53,343 Loaded tool data table 'bam_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:13:53,343 Could not find tool data tool-data/vcf_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:13:53,345 Loaded 1 lines from 'tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' galaxy.tools.data DEBUG 2017-11-18 16:13:53,345 Loaded tool data table 'vcf_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:13:53,346 Could not find tool data tool-data/biom_simple_display.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:13:53,347 Loaded 1 lines from 'tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' galaxy.tools.data DEBUG 2017-11-18 16:13:53,348 Loaded tool data table 'biom_simple_display' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:13:53,352 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 16:13:53,353 Loading another instance of data table 'blastdb' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 16:13:53,355 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 16:13:53,358 Loading another instance of data table 'blastdb_p' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 16:13:53,360 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb_d.loc' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 16:13:53,360 Loading another instance of data table 'blastdb_d' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.jobs WARNING 2017-11-18 16:13:53,465 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/galaxydir/galaxy/config/galaxy.ini" instead galaxy.jobs DEBUG 2017-11-18 16:13:53,465 Loading job configuration from /galaxydir/galaxy/config/galaxy.ini galaxy.jobs DEBUG 2017-11-18 16:13:53,465 Done loading job configuration beaker.container DEBUG 2017-11-18 16:13:53,698 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache galaxy.tools.toolbox.base INFO 2017-11-18 16:13:53,712 Parsing the tool configuration ./config/tool_conf.xml.sample galaxy.tools.toolbox.base ERROR 2017-11-18 16:13:54,211 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:13:54,490 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:13:55,037 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,037 Reading tools from config files finshed (1325.354 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,038 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,038 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.8.1.2, version: 2.8.1.2 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,038 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,039 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,039 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,039 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,039 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,039 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,040 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,040 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,040 Loaded tool id: biomart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,040 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,040 Loaded tool id: gramenemart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,041 Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,041 Loaded tool id: flymine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,041 Loaded tool id: flymine_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,041 Loaded tool id: modmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,041 Loaded tool id: mousemine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,042 Loaded tool id: ratmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,042 Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,042 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,042 Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,042 Loaded tool id: wormbase, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,042 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,043 Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,043 Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,043 Loaded tool id: hbvar, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,043 Loaded tool id: genomespace_importer, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,043 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,043 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,044 Loaded tool id: genomespace_exporter, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,044 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,044 Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,044 Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,044 Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,044 Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,045 Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,045 Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,045 Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,045 Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,045 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,045 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,046 Loaded tool id: addValue, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,046 Loaded tool id: cat1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,046 Loaded tool id: Cut1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,046 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,046 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,047 Loaded tool id: createInterval, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,047 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,047 Loaded tool id: Paste1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,047 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,047 Loaded tool id: random_lines1, version: 2.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,048 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,048 Loaded tool id: Show tail1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,048 Loaded tool id: trimmer, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,048 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,048 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,048 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,049 Loaded tool id: Filter1, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,049 Loaded tool id: sort1, version: 1.0.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,049 Loaded tool id: Grep1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,049 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,049 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,050 Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,050 Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,050 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,050 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,050 Loaded tool id: join1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,051 Loaded tool id: comp1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,051 Loaded tool id: Grouping1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,051 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,051 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,051 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,052 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,052 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,052 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,052 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,052 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,053 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,053 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,053 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,053 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,053 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,054 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,054 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,054 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,054 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,054 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,055 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,055 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,055 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,055 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_convert2blastmask_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,056 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,056 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,056 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,056 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,057 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_segmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,057 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,057 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,057 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,057 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,058 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,058 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,058 Loaded tool id: Extract genomic DNA 1, version: 2.2.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,058 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,058 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,059 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,059 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,059 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,059 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,059 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,060 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,060 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,060 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,060 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,060 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,060 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,061 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,061 Loaded tool id: Summary_Statistics1, version: 1.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,061 Loaded tool id: Count1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,061 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,061 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,062 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,062 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:13:55,062 Loading tool panel finished (24.195 ms) galaxy.tools.deps DEBUG 2017-11-18 16:13:55,067 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.search DEBUG 2017-11-18 16:13:55,094 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 16:13:57,197 Toolbox index finished (2102.727 ms) galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,203 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,209 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,263 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,265 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,267 Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,269 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,271 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,275 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,277 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,281 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,283 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,286 Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,327 Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,338 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,379 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,381 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,389 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,400 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,404 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,447 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,451 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,455 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,504 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,508 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,511 Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,513 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,569 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,572 Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,574 Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,576 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,576 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,576 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,576 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,576 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,577 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,577 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,577 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,584 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,584 Adding inherited display application 'igv_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,594 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,595 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,595 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,595 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,597 Adding inherited display application 'igv_fasta' to datatype 'sequences' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,597 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,598 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,598 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,598 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,599 Adding inherited display application 'igv_fasta' to datatype 'mothur.align' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,601 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,601 Adding inherited display application 'igv_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,610 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,610 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,610 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,610 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,612 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,612 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,612 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,612 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,615 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,615 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,615 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,615 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,622 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,627 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,630 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,633 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,636 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,639 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,642 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,645 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,648 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,650 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,654 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,656 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,664 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,667 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,670 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,674 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,678 Loaded converter: CONVERTER_fasta_to_fai galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,681 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,683 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,684 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,685 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,686 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,689 Loaded converter: CONVERTER_fastqgz_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,692 Loaded converter: CONVERTER_fastqsangergz_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,696 Loaded converter: CONVERTER_fastqsolexagz_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,700 Loaded converter: CONVERTER_fastqcssangergz_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,702 Loaded converter: CONVERTER_fastqilluminagz_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,705 Loaded converter: CONVERTER_fastqbz2_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,708 Loaded converter: CONVERTER_fastqsangerbz2_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,712 Loaded converter: CONVERTER_fastqsolexabz2_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,714 Loaded converter: CONVERTER_fastqcssangerbz2_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,717 Loaded converter: CONVERTER_fastqilluminabz2_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,720 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,723 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,728 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,731 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,733 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,735 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,738 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,741 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,744 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,747 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,749 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,751 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,755 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,758 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,761 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,763 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,768 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,771 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,772 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,777 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,779 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,781 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,784 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,787 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,790 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,794 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,797 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,800 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,803 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,807 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,812 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,815 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,817 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,820 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,824 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,827 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,829 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,832 Loaded converter: CONVERTER_biom1_to_biom2 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,835 Loaded converter: CONVERTER_biom2_to_biom1 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,840 Loaded converter: CONVERTER_SMILES_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,843 Loaded converter: CONVERTER_SMILES_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,845 Loaded converter: CONVERTER_SMILES_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,849 Loaded converter: CONVERTER_SMILES_to_MOL galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,852 Loaded converter: CONVERTER_SMILES_to_MOL2 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,856 Loaded converter: CONVERTER_smiles_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,862 Loaded converter: CONVERTER_sdf_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,865 Loaded converter: CONVERTER_sdf_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,868 Loaded converter: CONVERTER_sdf_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,871 Loaded converter: CONVERTER_sdf_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,874 Loaded converter: CONVERTER_inchi_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,879 Loaded converter: CONVERTER_inchi_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,881 Loaded converter: CONVERTER_inchi_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,885 Loaded converter: CONVERTER_inchi_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,888 Loaded converter: CONVERTER_inchi_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,892 Loaded converter: CONVERTER_mol_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,896 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,900 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,902 Loaded converter: CONVERTER_mol_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,906 Loaded converter: CONVERTER_mol2_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,911 Loaded converter: CONVERTER_mol2_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,914 Loaded converter: CONVERTER_mol2_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,917 Loaded converter: CONVERTER_mol2_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,920 Loaded converter: CONVERTER_mol2_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,926 Loaded converter: CONVERTER_cml_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,928 Loaded converter: CONVERTER_cml_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,932 Loaded converter: CONVERTER_cml_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,936 Loaded converter: CONVERTER_cml_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,939 Loaded converter: CONVERTER_ref_to_seq_taxomony galaxy.datatypes.registry DEBUG 2017-11-18 16:13:57,946 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 16:13:57,953 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 16:13:57,958 Loaded history export tool: __EXPORT_HISTORY__ galaxy.web.base.pluginframework INFO 2017-11-18 16:13:57,965 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:13:57,972 Visualizations plugin disabled: Circster. Skipping... galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:13:57,976 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 16:13:57,976 VisualizationsRegistry, loaded plugin: csg galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:13:57,979 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 16:13:57,979 VisualizationsRegistry, loaded plugin: graphviz galaxy.web.base.pluginframework INFO 2017-11-18 16:13:57,982 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2017-11-18 16:13:57,985 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:13:57,987 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2017-11-18 16:13:57,990 VisualizationsRegistry, loaded plugin: trackster galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:13:57,993 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 16:13:57,995 VisualizationsRegistry, loaded plugin: unipept galaxy.tours INFO 2017-11-18 16:13:58,042 Loaded tour 'core.galaxy_ui' galaxy.tours INFO 2017-11-18 16:13:58,080 Loaded tour 'core.history' galaxy.tours INFO 2017-11-18 16:13:58,100 Loaded tour 'core.scratchbook' galaxy.webhooks WARNING 2017-11-18 16:13:58,100 directory not found: /galaxydir/galaxy/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config galaxy.jobs.manager DEBUG 2017-11-18 16:13:58,121 Starting job handler galaxy.jobs INFO 2017-11-18 16:13:58,121 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2017-11-18 16:13:58,125 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2017-11-18 16:13:58,125 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2017-11-18 16:13:58,129 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs DEBUG 2017-11-18 16:13:58,129 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2017-11-18 16:13:58,129 Loaded job runners plugins: local galaxy.jobs.handler INFO 2017-11-18 16:13:58,129 job handler stop queue started galaxy.jobs.handler INFO 2017-11-18 16:13:58,142 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 16:13:58,155 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 16:13:58,158 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.workflow.scheduling_manager DEBUG 2017-11-18 16:13:58,173 Starting workflow schedulers galaxy.app INFO 2017-11-18 16:13:58,179 Galaxy app startup finished (6725.329 ms) galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,361 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,749 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,749 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,751 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,753 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,755 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,759 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,761 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,767 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,769 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,773 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,777 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,779 Enabling 'interactive_environments' controller, class: InteractiveEnvironmentsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,790 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,792 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,792 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,797 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,799 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,801 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,804 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,804 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,808 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,811 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,813 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,816 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,818 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,821 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,828 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,836 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,837 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,837 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,838 Enabling 'authenticate' API controller, class: AuthenticationController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,841 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,843 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,846 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,848 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,850 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,850 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,853 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,855 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,858 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,860 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,864 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,866 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,868 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,871 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,875 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,877 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,877 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,877 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,879 Enabling 'job_files' API controller, class: JobFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,882 Enabling 'jobs' API controller, class: JobController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,891 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,895 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,900 Enabling 'library_datasets' API controller, class: LibraryDatasetsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,902 Enabling 'metrics' API controller, class: MetricsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,904 Enabling 'page_revisions' API controller, class: PageRevisionsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,906 Enabling 'pages' API controller, class: PagesController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,908 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,908 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,910 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,920 Enabling 'remote_files' API controller, class: RemoteFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,922 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,924 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,927 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,929 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,970 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,972 Enabling 'tool_data' API controller, class: ToolData galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,975 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,978 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,982 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,984 Enabling 'toolshed' API controller, class: ToolShedController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,986 Enabling 'tours' API controller, class: ToursController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,989 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,991 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,993 Enabling 'webhooks' API controller, class: WebhooksController galaxy.web.framework.base DEBUG 2017-11-18 16:13:58,995 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.webapps.util DEBUG 2017-11-18 16:13:59,465 Enabling 'paste.httpexceptions' middleware galaxy.webapps.util DEBUG 2017-11-18 16:13:59,468 Enabling 'RecursiveMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:13:59,487 Enabling 'ErrorMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:13:59,489 Enabling 'TransLogger' middleware galaxy.webapps.util DEBUG 2017-11-18 16:13:59,491 Enabling 'XForwardedHostMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:13:59,493 Enabling 'RequestIDMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:13:59,496 Enabling 'BatchMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:13:59,496 Enabling 'wrap_in_static' middleware galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,512 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,513 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,513 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,514 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,514 added url, path to static middleware: /plugins/visualizations/unipept/static, ./config/plugins/visualizations/unipept/static galaxy.queue_worker INFO 2017-11-18 16:13:59,514 Binding and starting galaxy control worker for main galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,515 Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 140735112855552)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,523 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145308196864)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,526 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-2, started daemon 123145325023232)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,526 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-0, started daemon 123145316610048)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,526 Prior to webapp return, Galaxy thread <Thread(JobHandlerStopQueue.monitor_thread, started daemon 123145337643008)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,526 Prior to webapp return, Galaxy thread <Thread(WorkflowRequestMonitor.monitor_thread, started daemon 123145346056192)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,527 Prior to webapp return, Galaxy thread <GalaxyQueueWorker(Thread-1, started daemon 123145350262784)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,529 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-3, started daemon 123145329229824)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,530 Prior to webapp return, Galaxy thread <Thread(JobHandlerQueue.monitor_thread, started daemon 123145341849600)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,530 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-1, started daemon 123145320816640)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,530 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-4, started daemon 123145333436416)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:13:59,532 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145312403456)> is alive. Starting server in PID 31120. serving on http://127.0.0.1:8080 /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. 'storage.' % (dialect.name, dialect.driver)) /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. 'strategies for improved performance.' % expr) 127.0.0.1 - - [18/Nov/2017:16:18:50 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:18:50 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:18:50 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:18:50 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:18:50 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:18:50 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:18:50 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:18:51 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:18:51 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:18:51 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:18:51 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:18:53 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:03 -0400] "GET /api/tools?q=tes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:04 -0400] "GET /api/tools?q=test HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:09 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:09 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:09 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:09 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:10 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:11 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:11 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:14 -0400] "GET /admin/reload_tool HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:15 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/reload_tool" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:15 -0400] "GET /admin/tool_errors HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:15 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/tool_errors" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:22 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:22 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:23 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:23 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:23 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:23 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:23 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:23 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:23 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:23 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:23 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:19:25 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ^C ^C 127.0.0.1 - - [18/Nov/2017:16:19:13 -0400] "GET /admin/review_tool_migration_stages HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 62900) Traceback (most recent call last): File "/galaxydir/galaxy/.venv/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 657, in __init__ self.finish() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 716, in finish self.wfile.close() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 283, in close self.flush() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- Exception KeyboardInterrupt in <module 'threading' from '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.pyc'> ignored galaxy.jobs.handler INFO 2017-11-18 16:19:47,022 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 16:19:47,022 job handler queue stopped galaxy.jobs.runners INFO 2017-11-18 16:19:47,022 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2017-11-18 16:19:47,023 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 16:19:47,023 job handler stop queue stopped CFM5081985:galaxy charles.strittmatter$ CFM5081985:galaxy charles.strittmatter$ pwd /galaxydir/galaxy CFM5081985:galaxy charles.strittmatter$ ls CITATION SECURITY_POLICY.md display_applications manage_db.sh run_tests.sh test-data CODE_OF_CONDUCT.md client doc manage_tools.sh run_tool_shed.sh tool-data CONTRIBUTING.md config external_service_types openid scripts tool_list.py CONTRIBUTORS.md contrib extract_dataset_parts.sh requirements.txt setup.cfg tools LICENSE.txt create_db.sh integrated_tool_panel.xml rolling_restart.sh static tox.ini Makefile cron lib run.sh templates README.rst database locale run_reports.sh test CFM5081985:galaxy charles.strittmatter$ sh run.sh Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv galaxy.tools.deps DEBUG 2017-11-18 16:20:01,682 Unable to find config file './dependency_resolvers_conf.xml' DEBUG:galaxy.app:python path is: /galaxydir/galaxy/scripts, /galaxydir/galaxy/lib, /galaxydir/galaxy/.venv/lib/python27.zip, /galaxydir/galaxy/.venv/lib/python2.7, 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lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,118 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,118 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,118 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,118 Loading script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,118 Script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,118 Loading script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,118 Script 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16:20:04,119 Loading script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,119 Script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,120 Loading script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,120 Script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,120 Loading script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,120 Script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,120 Loading script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,120 Script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,120 Loading script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:20:04,120 Script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py loaded successfully migrate.versioning.repository DEBUG 2017-11-18 16:20:04,121 Repository lib/tool_shed/galaxy_install/migrate loaded successfully migrate.versioning.repository DEBUG 2017-11-18 16:20:04,121 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))]) tool_shed.galaxy_install.migrate.check INFO 2017-11-18 16:20:04,140 At migrate_tools version 12 galaxy.config INFO 2017-11-18 16:20:04,163 Install database targetting Galaxy's database configuration. /galaxydir/galaxy/lib/galaxy/datatypes/registry.py:98: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if root_dir and config: galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,213 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,213 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,213 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/binary: No module named binary galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,213 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,213 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,214 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,214 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,224 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,225 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,225 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,225 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,225 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,225 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,225 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,226 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,226 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,240 Loading datatypes from ./config/datatypes_conf.xml.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,241 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,241 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,242 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,242 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,242 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,242 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,242 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,243 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,243 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,243 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,243 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,243 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,244 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,244 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,244 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,244 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,245 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,245 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,245 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,245 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,246 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,246 Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,246 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,247 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,248 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,248 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,248 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,248 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,248 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,249 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,249 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,249 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,250 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,250 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,250 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,251 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,251 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,251 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,251 Retrieved datatype module galaxy.datatypes.sequence:FastqGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,251 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,252 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,252 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,252 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,252 Retrieved datatype module galaxy.datatypes.sequence:FastqBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,252 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,252 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,253 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,253 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,253 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,253 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,253 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,253 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,253 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,253 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,253 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,254 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,254 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,254 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,254 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,254 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,254 Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,254 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,255 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,255 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,255 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,255 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,255 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,256 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,256 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,256 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,256 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,257 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,257 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,257 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,258 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,258 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,258 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,259 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,259 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,259 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,259 Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,260 Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,260 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,260 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,260 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,260 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,261 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,262 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,262 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,262 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,262 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,262 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,263 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,263 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,263 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,263 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,263 Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,263 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,266 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,267 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,268 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,269 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,270 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,271 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,272 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,272 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,272 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,272 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,273 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,273 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,273 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,273 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,273 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,274 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,274 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,274 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,274 Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,274 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,274 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,275 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,275 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,275 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,275 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,275 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,275 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,276 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,276 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,276 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,276 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,276 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,276 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,277 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,277 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,277 Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,277 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,277 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,277 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,278 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,278 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,278 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,279 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,279 Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,279 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,279 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,279 Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,280 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,280 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,280 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,280 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,280 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,280 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,280 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,281 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,281 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,281 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,281 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,282 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,282 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,282 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,282 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,282 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,282 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,283 Roadmaps is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,283 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,283 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,283 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,283 Sequences is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,283 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,283 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,284 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,284 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,284 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,284 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,285 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,285 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,285 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,285 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,285 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,286 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,286 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,286 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,286 Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,286 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,286 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,287 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,287 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,287 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,287 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,287 Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,287 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,288 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,288 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,288 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,288 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,289 Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,289 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,289 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,289 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,292 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,292 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,292 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,293 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,293 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,293 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,293 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,293 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,294 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,294 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,294 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,294 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,295 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,295 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,295 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,295 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,295 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,296 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,296 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,296 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,299 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,300 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,301 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,301 Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,301 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,301 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,301 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,301 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,301 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,301 Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,302 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,302 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,302 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,302 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,302 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,302 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,306 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,400 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,400 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,400 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,401 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,401 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,401 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,402 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,402 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,402 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,402 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,403 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,403 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,403 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,403 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,403 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,404 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,404 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,404 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,404 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,405 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,405 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,405 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,405 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,406 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,406 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,406 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,406 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,407 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,407 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,407 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,407 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,407 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,408 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,408 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,408 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,408 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,409 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,409 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,409 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,409 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,409 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,410 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,410 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,410 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,410 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,411 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,411 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,411 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,411 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,412 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,412 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,412 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,412 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,413 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,413 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,413 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,413 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,414 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,414 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,414 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,414 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,414 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,415 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,415 Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,415 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,415 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,416 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,416 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,416 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,417 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,417 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,417 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,417 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,418 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,418 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,418 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,418 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,419 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,419 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,419 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,419 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,420 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,420 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,420 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,420 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,420 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,421 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,421 Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,421 Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,423 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,423 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,423 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,423 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,423 Retrieved datatype module galaxy.datatypes.binary:Cel from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,423 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,424 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,424 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,424 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,424 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,424 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,424 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,426 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,426 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,426 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,426 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,426 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,426 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,427 Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,427 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,429 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,429 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,429 Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,429 Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,429 Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,430 Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,430 Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,430 Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,430 Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,430 Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,430 Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,431 Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,431 Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,431 Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,434 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,434 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,434 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,435 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,435 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,435 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,436 Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,436 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,436 Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,436 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,436 Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,437 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,437 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,437 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,437 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,438 Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,438 Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,438 Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,438 Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,438 Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,438 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,439 Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,439 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,439 Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,439 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,439 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,440 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,442 Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,442 Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,442 Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,442 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,443 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,444 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,444 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,444 Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,445 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,445 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,445 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,446 Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,447 Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,447 Overriding conflicting datatype with extension 'blastxml', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,447 Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,447 Overriding conflicting datatype with extension 'blastdbn', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,448 Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,448 Overriding conflicting datatype with extension 'blastdbp', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,448 Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,448 Overriding conflicting datatype with extension 'blastdbd', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,449 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,449 Overriding conflicting datatype with extension 'maskinfo-asn1', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,449 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,449 Overriding conflicting datatype with extension 'maskinfo-asn1-binary', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,450 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,450 Overriding conflicting datatype with extension 'pssm-asn1', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,455 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,455 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,455 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,456 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,456 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,456 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,456 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,456 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrtho from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,456 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,457 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylip from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,457 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,457 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,457 Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,457 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,458 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,458 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,458 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,458 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,458 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,458 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,458 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,459 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,459 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,459 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,459 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,459 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,459 Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,459 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,460 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,460 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,460 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,460 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,460 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,460 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,460 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,460 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,460 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,461 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,461 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,461 Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,461 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,461 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,461 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,461 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,461 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,461 Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,462 Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,462 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,462 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,462 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,462 Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,462 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,462 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,462 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,463 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,463 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,463 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,463 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,463 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,463 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,463 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,463 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,463 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,464 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,464 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,464 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,464 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,464 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,464 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,464 Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,465 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,465 Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,465 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,465 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,465 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,465 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,466 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,466 Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,466 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,466 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,466 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,466 Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,466 Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,467 Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,467 Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,467 Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,467 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,467 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,467 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerGz' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,468 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerBz2' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,468 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,468 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqGz' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,468 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqBz2' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,468 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,468 Loaded sniffer for datatype 'galaxy.datatypes.text:Html' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,469 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,469 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,469 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,469 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,469 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,469 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,470 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,470 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,470 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,470 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,470 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,470 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,471 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,471 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,471 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,471 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,471 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,471 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,472 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,472 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,472 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,472 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,472 Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,472 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,472 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,472 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,472 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,472 Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,473 Loaded sniffer for datatype 'galaxy.datatypes.binary:Cel' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,473 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,473 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,473 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,473 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,473 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,473 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,473 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,473 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,473 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,474 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,474 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,474 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,474 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,474 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,474 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,474 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,474 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,474 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,474 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,474 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,475 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,475 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,475 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,475 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,482 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,483 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,483 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,484 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,484 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,484 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,485 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,485 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:04,485 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.tools.data INFO 2017-11-18 16:20:05,264 Could not find tool data tool-data/all_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:20:05,265 Loaded 0 lines from 'tool-data/all_fasta.loc.sample' for 'all_fasta' galaxy.tools.data DEBUG 2017-11-18 16:20:05,265 Loaded tool data table 'all_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:20:05,265 Could not find tool data tool-data/bfast_indexes.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:20:05,265 Loaded 0 lines from 'tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' galaxy.tools.data DEBUG 2017-11-18 16:20:05,266 Loaded tool data table 'bfast_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:20:05,266 Loaded 0 lines from 'tool-data/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 16:20:05,266 Loaded tool data table 'blastdb' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:20:05,266 Loaded 0 lines from 'tool-data/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 16:20:05,267 Loaded tool data table 'blastdb_p' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:20:05,267 Loaded 0 lines from 'tool-data/blastdb_d.loc' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 16:20:05,267 Loaded tool data table 'blastdb_d' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data WARNING 2017-11-18 16:20:05,268 Cannot find index file 'tool-data/bwa_index.loc' for tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 16:20:05,268 Loaded tool data table 'bwa_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data WARNING 2017-11-18 16:20:05,268 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 16:20:05,268 Loaded tool data table 'bwa_indexes_color' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:20:05,269 Could not find tool data tool-data/maf_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:20:05,269 Loaded 0 lines from 'tool-data/maf_index.loc.sample' for 'indexed_maf_files' galaxy.tools.data DEBUG 2017-11-18 16:20:05,269 Loaded tool data table 'indexed_maf_files' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:20:05,269 Could not find tool data tool-data/ngs_sim_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:20:05,269 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' galaxy.tools.data DEBUG 2017-11-18 16:20:05,270 Loaded tool data table 'ngs_sim_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:20:05,270 Could not find tool data tool-data/perm_base_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:20:05,270 Loaded 0 lines from 'tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' galaxy.tools.data DEBUG 2017-11-18 16:20:05,270 Loaded tool data table 'perm_base_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:20:05,270 Could not find tool data tool-data/perm_color_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:20:05,271 Loaded 0 lines from 'tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' galaxy.tools.data DEBUG 2017-11-18 16:20:05,271 Loaded tool data table 'perm_color_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:20:05,271 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:20:05,271 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'picard_indexes' galaxy.tools.data DEBUG 2017-11-18 16:20:05,271 Loaded tool data table 'picard_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:20:05,272 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:20:05,272 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'srma_indexes' galaxy.tools.data DEBUG 2017-11-18 16:20:05,272 Loaded tool data table 'srma_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:20:05,272 Could not find tool data tool-data/mosaik_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:20:05,272 Loaded 0 lines from 'tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' galaxy.tools.data DEBUG 2017-11-18 16:20:05,273 Loaded tool data table 'mosaik_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:20:05,273 Could not find tool data tool-data/twobit.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:20:05,273 Loaded 0 lines from 'tool-data/twobit.loc.sample' for 'twobit' galaxy.tools.data DEBUG 2017-11-18 16:20:05,273 Loaded tool data table 'twobit' from file './config/tool_data_table_conf.xml.sample' requests.packages.urllib3.connectionpool INFO 2017-11-18 16:20:05,284 Starting new HTTP connection (1): igv.broadinstitute.org requests.packages.urllib3.connectionpool DEBUG 2017-11-18 16:20:05,362 "GET /genomes/genomes.txt HTTP/1.1" 200 15681 galaxy.tools.data DEBUG 2017-11-18 16:20:05,370 Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-xygNMv". galaxy.tools.data WARNING 2017-11-18 16:20:05,370 Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields): <Server-Side Genome List> galaxy.tools.data DEBUG 2017-11-18 16:20:05,373 Loaded 156 lines from '/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-xygNMv' for 'igv_broad_genomes' galaxy.tools.data DEBUG 2017-11-18 16:20:05,375 Loaded tool data table 'igv_broad_genomes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:20:05,376 Could not find tool data tool-data/liftOver.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:20:05,376 Loaded 0 lines from 'tool-data/liftOver.loc.sample' for 'liftOver' galaxy.tools.data DEBUG 2017-11-18 16:20:05,376 Loaded tool data table 'liftOver' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:20:05,377 Could not find tool data tool-data/bam_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:20:05,377 Loaded 1 lines from 'tool-data/bam_iobio.loc.sample' for 'bam_iobio' galaxy.tools.data DEBUG 2017-11-18 16:20:05,377 Loaded tool data table 'bam_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:20:05,378 Could not find tool data tool-data/vcf_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:20:05,378 Loaded 1 lines from 'tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' galaxy.tools.data DEBUG 2017-11-18 16:20:05,379 Loaded tool data table 'vcf_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:20:05,379 Could not find tool data tool-data/biom_simple_display.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:20:05,380 Loaded 1 lines from 'tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' galaxy.tools.data DEBUG 2017-11-18 16:20:05,380 Loaded tool data table 'biom_simple_display' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:20:05,382 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 16:20:05,382 Loading another instance of data table 'blastdb' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 16:20:05,383 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 16:20:05,383 Loading another instance of data table 'blastdb_p' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 16:20:05,384 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb_d.loc' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 16:20:05,384 Loading another instance of data table 'blastdb_d' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.jobs WARNING 2017-11-18 16:20:05,448 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/galaxydir/galaxy/config/galaxy.ini" instead galaxy.jobs DEBUG 2017-11-18 16:20:05,448 Loading job configuration from /galaxydir/galaxy/config/galaxy.ini galaxy.jobs DEBUG 2017-11-18 16:20:05,449 Done loading job configuration beaker.container DEBUG 2017-11-18 16:20:05,532 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache galaxy.tools.toolbox.base INFO 2017-11-18 16:20:05,537 Parsing the tool configuration ./config/tool_conf.xml.sample galaxy.tools.toolbox.base ERROR 2017-11-18 16:20:05,720 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:20:05,866 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:20:06,371 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,372 Reading tools from config files finshed (835.338 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,372 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,373 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.8.1.2, version: 2.8.1.2 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,373 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,374 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,374 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,374 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,374 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,375 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,375 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,375 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,375 Loaded tool id: biomart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,375 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,376 Loaded tool id: gramenemart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,376 Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,376 Loaded tool id: flymine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,376 Loaded tool id: flymine_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,376 Loaded tool id: modmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,377 Loaded tool id: mousemine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,377 Loaded tool id: ratmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,377 Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,377 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,378 Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,378 Loaded tool id: wormbase, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,378 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,378 Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,378 Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,379 Loaded tool id: hbvar, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,379 Loaded tool id: genomespace_importer, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,379 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,379 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,379 Loaded tool id: genomespace_exporter, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,380 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,380 Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,380 Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,380 Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,381 Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,381 Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,381 Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,381 Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,381 Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,381 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,382 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,382 Loaded tool id: addValue, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,382 Loaded tool id: cat1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,382 Loaded tool id: Cut1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,382 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,383 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,383 Loaded tool id: createInterval, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,383 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,383 Loaded tool id: Paste1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,383 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,384 Loaded tool id: random_lines1, version: 2.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,384 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,384 Loaded tool id: Show tail1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,384 Loaded tool id: trimmer, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,384 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,385 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,385 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,385 Loaded tool id: Filter1, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,385 Loaded tool id: sort1, version: 1.0.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,385 Loaded tool id: Grep1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,385 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,386 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,386 Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,386 Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,386 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,386 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,387 Loaded tool id: join1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,387 Loaded tool id: comp1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,387 Loaded tool id: Grouping1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,387 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,387 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,387 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,388 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,388 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,388 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,389 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,389 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,389 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,389 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,390 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,390 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,390 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,390 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,390 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,391 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,391 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,391 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,391 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,391 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,392 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,392 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_convert2blastmask_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,392 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,392 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,392 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,393 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,393 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_segmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,393 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,393 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,394 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,394 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,394 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,394 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,394 Loaded tool id: Extract genomic DNA 1, version: 2.2.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,394 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,395 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,395 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,395 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,395 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,395 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,396 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,396 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,396 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,396 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,396 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,397 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,397 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,397 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,397 Loaded tool id: Summary_Statistics1, version: 1.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,397 Loaded tool id: Count1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,397 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,398 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,398 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,398 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:20:06,398 Loading tool panel finished (26.018 ms) galaxy.tools.deps DEBUG 2017-11-18 16:20:06,402 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.search DEBUG 2017-11-18 16:20:06,428 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 16:20:08,419 Toolbox index finished (1990.766 ms) galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,423 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,425 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,471 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,472 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,473 Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,474 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,474 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,476 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,477 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,482 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,484 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,486 Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,520 Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,525 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,567 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,567 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,574 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,586 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,587 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,636 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,638 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,640 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,688 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,689 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,690 Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,690 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,752 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,753 Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,753 Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,756 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,756 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,756 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,756 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,756 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,756 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,756 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,756 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,764 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,764 Adding inherited display application 'igv_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,778 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,778 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,778 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,779 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,783 Adding inherited display application 'igv_fasta' to datatype 'sequences' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,784 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,784 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,784 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,784 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,786 Adding inherited display application 'igv_fasta' to datatype 'mothur.align' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,790 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,791 Adding inherited display application 'igv_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,803 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,804 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,804 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,804 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,805 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,805 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,805 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,806 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,809 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,809 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,810 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,810 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,819 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,820 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,822 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,824 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,827 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,830 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,832 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,834 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,837 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,840 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,841 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,842 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,844 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,846 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,847 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,850 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,851 Loaded converter: CONVERTER_fasta_to_fai galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,852 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,853 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,855 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,856 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,857 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,858 Loaded converter: CONVERTER_fastqgz_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,859 Loaded converter: CONVERTER_fastqsangergz_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,861 Loaded converter: CONVERTER_fastqsolexagz_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,863 Loaded converter: CONVERTER_fastqcssangergz_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,868 Loaded converter: CONVERTER_fastqilluminagz_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,869 Loaded converter: CONVERTER_fastqbz2_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,870 Loaded converter: CONVERTER_fastqsangerbz2_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,872 Loaded converter: CONVERTER_fastqsolexabz2_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,873 Loaded converter: CONVERTER_fastqcssangerbz2_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,874 Loaded converter: CONVERTER_fastqilluminabz2_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,875 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,877 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,878 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,879 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,881 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,882 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,885 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,887 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,889 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,891 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,893 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,895 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,897 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,898 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,899 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,900 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,901 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,903 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,905 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,906 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,909 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,911 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,914 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,918 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,920 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,921 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,922 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,923 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,925 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,926 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,928 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,931 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,933 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,934 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,936 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,939 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,941 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,942 Loaded converter: CONVERTER_biom1_to_biom2 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,943 Loaded converter: CONVERTER_biom2_to_biom1 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,945 Loaded converter: CONVERTER_SMILES_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,951 Loaded converter: CONVERTER_SMILES_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,953 Loaded converter: CONVERTER_SMILES_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,954 Loaded converter: CONVERTER_SMILES_to_MOL galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,956 Loaded converter: CONVERTER_SMILES_to_MOL2 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,957 Loaded converter: CONVERTER_smiles_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,959 Loaded converter: CONVERTER_sdf_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,960 Loaded converter: CONVERTER_sdf_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,962 Loaded converter: CONVERTER_sdf_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,963 Loaded converter: CONVERTER_sdf_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,964 Loaded converter: CONVERTER_inchi_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,966 Loaded converter: CONVERTER_inchi_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,967 Loaded converter: CONVERTER_inchi_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,968 Loaded converter: CONVERTER_inchi_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,970 Loaded converter: CONVERTER_inchi_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,971 Loaded converter: CONVERTER_mol_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,973 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,976 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,978 Loaded converter: CONVERTER_mol_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,981 Loaded converter: CONVERTER_mol2_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,983 Loaded converter: CONVERTER_mol2_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,986 Loaded converter: CONVERTER_mol2_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,988 Loaded converter: CONVERTER_mol2_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,989 Loaded converter: CONVERTER_mol2_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,992 Loaded converter: CONVERTER_cml_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,994 Loaded converter: CONVERTER_cml_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:20:08,998 Loaded converter: CONVERTER_cml_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:20:09,002 Loaded converter: CONVERTER_cml_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:20:09,003 Loaded converter: CONVERTER_ref_to_seq_taxomony galaxy.datatypes.registry DEBUG 2017-11-18 16:20:09,005 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 16:20:09,007 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 16:20:09,009 Loaded history export tool: __EXPORT_HISTORY__ galaxy.web.base.pluginframework INFO 2017-11-18 16:20:09,010 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:20:09,011 Visualizations plugin disabled: Circster. Skipping... galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:20:09,013 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 16:20:09,013 VisualizationsRegistry, loaded plugin: csg galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:20:09,014 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 16:20:09,015 VisualizationsRegistry, loaded plugin: graphviz galaxy.web.base.pluginframework INFO 2017-11-18 16:20:09,016 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2017-11-18 16:20:09,016 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:20:09,017 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2017-11-18 16:20:09,018 VisualizationsRegistry, loaded plugin: trackster galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:20:09,019 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 16:20:09,019 VisualizationsRegistry, loaded plugin: unipept galaxy.tours INFO 2017-11-18 16:20:09,068 Loaded tour 'core.galaxy_ui' galaxy.tours INFO 2017-11-18 16:20:09,099 Loaded tour 'core.history' galaxy.tours INFO 2017-11-18 16:20:09,122 Loaded tour 'core.scratchbook' galaxy.webhooks WARNING 2017-11-18 16:20:09,123 directory not found: /galaxydir/galaxy/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config galaxy.jobs.manager DEBUG 2017-11-18 16:20:09,126 Starting job handler galaxy.jobs INFO 2017-11-18 16:20:09,126 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2017-11-18 16:20:09,127 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2017-11-18 16:20:09,128 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2017-11-18 16:20:09,129 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs DEBUG 2017-11-18 16:20:09,129 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2017-11-18 16:20:09,129 Loaded job runners plugins: local galaxy.jobs.handler INFO 2017-11-18 16:20:09,130 job handler stop queue started galaxy.jobs.handler INFO 2017-11-18 16:20:09,149 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 16:20:09,156 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 16:20:09,160 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.workflow.scheduling_manager DEBUG 2017-11-18 16:20:09,166 Starting workflow schedulers galaxy.app INFO 2017-11-18 16:20:09,174 Galaxy app startup finished (5375.393 ms) galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,188 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,473 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,473 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,474 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,474 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,475 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,476 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,477 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,478 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,479 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,480 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,482 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,482 Enabling 'interactive_environments' controller, class: InteractiveEnvironmentsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,488 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,488 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,489 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,491 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,492 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,492 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,493 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,493 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,495 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,496 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,496 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,497 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,498 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,499 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,501 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,502 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,502 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,503 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,503 Enabling 'authenticate' API controller, class: AuthenticationController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,504 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,504 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,507 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,508 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,509 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,509 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,510 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,511 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,511 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,512 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,512 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,513 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,514 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,515 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,518 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,518 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,518 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,519 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,519 Enabling 'job_files' API controller, class: JobFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,520 Enabling 'jobs' API controller, class: JobController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,521 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,521 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,522 Enabling 'library_datasets' API controller, class: LibraryDatasetsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,523 Enabling 'metrics' API controller, class: MetricsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,523 Enabling 'page_revisions' API controller, class: PageRevisionsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,524 Enabling 'pages' API controller, class: PagesController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,524 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,524 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,525 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,527 Enabling 'remote_files' API controller, class: RemoteFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,528 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,528 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,529 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,529 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,544 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,545 Enabling 'tool_data' API controller, class: ToolData galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,545 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,547 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,548 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,549 Enabling 'toolshed' API controller, class: ToolShedController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,549 Enabling 'tours' API controller, class: ToursController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,550 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,551 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,551 Enabling 'webhooks' API controller, class: WebhooksController galaxy.web.framework.base DEBUG 2017-11-18 16:20:09,553 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.webapps.util DEBUG 2017-11-18 16:20:09,940 Enabling 'paste.httpexceptions' middleware galaxy.webapps.util DEBUG 2017-11-18 16:20:09,941 Enabling 'RecursiveMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:20:09,946 Enabling 'ErrorMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:20:09,947 Enabling 'TransLogger' middleware galaxy.webapps.util DEBUG 2017-11-18 16:20:09,948 Enabling 'XForwardedHostMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:20:09,948 Enabling 'RequestIDMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:20:09,949 Enabling 'BatchMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:20:09,949 Enabling 'wrap_in_static' middleware galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,955 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,955 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,955 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,956 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,956 added url, path to static middleware: /plugins/visualizations/unipept/static, ./config/plugins/visualizations/unipept/static galaxy.queue_worker INFO 2017-11-18 16:20:09,956 Binding and starting galaxy control worker for main galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,957 Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 140735112855552)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,965 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145308196864)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,967 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-2, started daemon 123145325023232)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,968 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-0, started daemon 123145316610048)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,969 Prior to webapp return, Galaxy thread <Thread(JobHandlerStopQueue.monitor_thread, started daemon 123145337643008)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,970 Prior to webapp return, Galaxy thread <Thread(WorkflowRequestMonitor.monitor_thread, started daemon 123145346056192)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,970 Prior to webapp return, Galaxy thread <GalaxyQueueWorker(Thread-1, started daemon 123145350262784)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,971 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-3, started daemon 123145329229824)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,971 Prior to webapp return, Galaxy thread <Thread(JobHandlerQueue.monitor_thread, started daemon 123145341849600)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,972 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-1, started daemon 123145320816640)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,972 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-4, started daemon 123145333436416)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:20:09,973 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145312403456)> is alive. Starting server in PID 31196. serving on http://127.0.0.1:8080 /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. 'storage.' % (dialect.name, dialect.driver)) /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. 'strategies for improved performance.' % expr) 127.0.0.1 - - [18/Nov/2017:16:20:33 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:20:33 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:20:34 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:20:34 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:20:34 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:20:34 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:20:34 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:20:34 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:20:34 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:20:34 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:20:34 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:20:36 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:21:16 -0400] "GET /api/tools?q=test HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ^Cgalaxy.jobs.handler INFO 2017-11-18 16:22:32,145 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 16:22:32,145 job handler queue stopped galaxy.jobs.runners INFO 2017-11-18 16:22:32,145 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2017-11-18 16:22:32,146 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 16:22:32,146 job handler stop queue stopped CFM5081985:galaxy charles.strittmatter$ sh run.sh Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv galaxy.tools.deps DEBUG 2017-11-18 16:22:38,023 Unable to find config file './dependency_resolvers_conf.xml' DEBUG:galaxy.app:python path is: /galaxydir/galaxy/scripts, /galaxydir/galaxy/lib, /galaxydir/galaxy/.venv/lib/python27.zip, /galaxydir/galaxy/.venv/lib/python2.7, /galaxydir/galaxy/.venv/lib/python2.7/plat-darwin, /galaxydir/galaxy/.venv/lib/python2.7/plat-mac, /galaxydir/galaxy/.venv/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/Extras/lib/python, /galaxydir/galaxy/.venv/lib/python2.7/lib-tk, /galaxydir/galaxy/.venv/lib/python2.7/lib-old, /galaxydir/galaxy/.venv/lib/python2.7/lib-dynload, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/lib/python2.7/site-packages DEBUG:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config INFO:galaxy.config:Logging at '10' level to 'stdout' galaxy.queue_worker INFO 2017-11-18 16:22:40,322 Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE tool_shed.tool_shed_registry DEBUG 2017-11-18 16:22:40,352 Loading references to tool sheds from ./config/tool_sheds_conf.xml.sample tool_shed.tool_shed_registry DEBUG 2017-11-18 16:22:40,353 Loaded reference to tool shed: Galaxy Main Tool Shed galaxy.app DEBUG 2017-11-18 16:22:40,354 Using "galaxy.ini" config file: /galaxydir/galaxy/config/galaxy.ini migrate.versioning.repository DEBUG 2017-11-18 16:22:40,406 Loading repository lib/galaxy/model/migrate... migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,407 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,407 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,407 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,407 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,408 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,408 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,408 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,408 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,408 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,408 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,409 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,409 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,409 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,409 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,409 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py... migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,409 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,409 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py... migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,410 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,410 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py... migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,410 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,410 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,410 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:22:40,410 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py... 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/galaxydir/galaxy/lib/galaxy/datatypes/registry.py:98: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if root_dir and config: galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,643 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,643 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,643 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/binary: No module named binary galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,643 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,644 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,644 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,644 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,650 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,650 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,651 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,651 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,651 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,651 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,651 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,651 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,651 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,670 Loading datatypes from ./config/datatypes_conf.xml.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,671 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,672 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,672 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,672 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,673 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,673 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,674 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,674 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,674 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,675 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,676 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,676 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,676 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,676 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,676 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,677 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,677 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,677 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,677 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,677 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,678 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,678 Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,678 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,678 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,679 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,679 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,679 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,679 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,679 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,679 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,679 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,679 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,680 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,680 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,680 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,680 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,680 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,680 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,680 Retrieved datatype module galaxy.datatypes.sequence:FastqGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,681 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,681 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,681 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,681 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,681 Retrieved datatype module galaxy.datatypes.sequence:FastqBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,681 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,681 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,681 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,681 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,681 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,682 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,682 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,682 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,682 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,682 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,682 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,682 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,682 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,683 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,683 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,683 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,683 Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,683 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,683 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,683 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,684 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,684 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,684 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,684 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,685 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,685 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,685 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,685 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,685 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,685 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,686 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,686 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,686 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,686 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,687 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,687 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,687 Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,688 Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,689 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,689 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,689 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,689 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,689 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,689 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,690 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,690 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,690 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,690 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,690 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,691 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,691 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,691 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,691 Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,691 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,694 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,694 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,694 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,695 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,695 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,695 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,695 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,695 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,696 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,696 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,696 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,696 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,696 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,697 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,697 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,697 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,697 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,697 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,697 Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,698 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,698 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,698 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,698 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,698 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,699 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,699 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,699 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,699 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,699 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,699 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,699 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,700 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,700 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,700 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,700 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,700 Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,700 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,701 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,701 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,701 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,701 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,702 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,702 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,702 Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,702 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,703 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,703 Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,703 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,703 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,704 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,704 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,704 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,704 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,704 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,704 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,705 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,705 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,705 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,705 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,705 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,706 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,706 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,706 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,707 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,708 Roadmaps is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,708 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,709 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,709 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,710 Sequences is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,711 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,712 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,712 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,712 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,713 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,713 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,713 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,713 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,714 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,714 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,714 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,714 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,714 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,715 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,715 Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,715 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,715 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,715 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,715 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,716 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,716 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,716 Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,716 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,716 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,717 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,717 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,717 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,717 Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,718 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,718 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,718 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,721 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,721 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,721 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,721 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,722 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,722 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,722 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,722 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,722 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,723 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,723 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,723 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,724 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,724 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,724 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,724 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,728 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,729 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,729 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,729 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,733 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,733 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,734 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,735 Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,735 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,735 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,735 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,735 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,736 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,736 Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,736 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,736 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,736 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,737 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,737 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,737 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,737 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,831 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,832 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,832 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,832 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,832 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,833 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,833 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,833 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,833 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,834 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,834 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,834 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,834 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,835 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,835 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,835 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,835 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,836 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,836 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,836 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,836 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,836 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,837 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,837 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,837 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,837 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,838 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,838 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,838 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,838 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,838 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,839 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,840 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,840 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,841 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,841 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,841 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,841 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,842 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,842 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,842 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,842 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,843 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,843 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,843 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,843 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,844 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,844 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,844 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,844 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,845 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,845 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,845 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,845 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,845 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,846 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,846 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,846 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,846 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,847 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,847 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,847 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,847 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,847 Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,848 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,848 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,848 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,848 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,848 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,849 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,849 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,849 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,849 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,849 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,850 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,850 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,850 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,850 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,851 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,851 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,851 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,851 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,851 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,852 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,852 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,852 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,852 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,853 Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,853 Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,854 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,854 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,855 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,855 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,855 Retrieved datatype module galaxy.datatypes.binary:Cel from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,855 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,855 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,856 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,856 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,856 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,856 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,857 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,858 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,858 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,858 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,858 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,859 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,859 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,859 Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,859 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,861 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,861 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,862 Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,862 Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,862 Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,862 Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,862 Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,863 Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,863 Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,863 Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,863 Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,863 Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,864 Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,864 Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,867 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,867 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,868 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,868 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,868 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,868 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,869 Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,869 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,869 Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,869 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,869 Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,870 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,870 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,870 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,870 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,871 Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,871 Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,871 Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,871 Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,871 Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,871 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,872 Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,872 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,872 Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,872 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,872 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,873 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,875 Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,875 Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,875 Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,875 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,875 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,876 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,877 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,877 Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,877 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,877 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,878 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,879 Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,879 Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,879 Overriding conflicting datatype with extension 'blastxml', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,880 Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,880 Overriding conflicting datatype with extension 'blastdbn', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,880 Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,880 Overriding conflicting datatype with extension 'blastdbp', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,881 Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,881 Overriding conflicting datatype with extension 'blastdbd', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,881 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,881 Overriding conflicting datatype with extension 'maskinfo-asn1', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,881 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,881 Overriding conflicting datatype with extension 'maskinfo-asn1-binary', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,882 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,882 Overriding conflicting datatype with extension 'pssm-asn1', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,883 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,884 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,884 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,884 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,884 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,884 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,885 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,885 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrtho from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,885 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,885 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylip from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,885 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,885 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,886 Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,886 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,886 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,886 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,887 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,887 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,887 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,887 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,887 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,887 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,887 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,888 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,888 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,888 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,888 Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,888 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,888 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,889 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,889 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,889 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,889 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,889 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,889 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,890 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,890 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,890 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,890 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,890 Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,891 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,891 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,892 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,892 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,892 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,893 Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,893 Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,894 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,895 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,895 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,896 Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,896 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,896 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,896 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,896 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,896 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,897 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,897 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,897 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,897 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,897 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,897 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,897 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,898 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,898 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,898 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,898 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,898 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,898 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,899 Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,899 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,899 Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,899 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,899 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,899 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,900 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,900 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,900 Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,900 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,900 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,900 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,901 Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,901 Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,901 Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,901 Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,901 Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,901 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,902 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,902 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerGz' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,902 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerBz2' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,902 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,902 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqGz' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,902 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqBz2' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,903 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,903 Loaded sniffer for datatype 'galaxy.datatypes.text:Html' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,903 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,903 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,903 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,903 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,904 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,904 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,904 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,904 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,904 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,905 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,905 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,905 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,905 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,905 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,906 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,906 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,906 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,906 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,906 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,906 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,907 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,907 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,907 Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,907 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,907 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,908 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,908 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,908 Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,908 Loaded sniffer for datatype 'galaxy.datatypes.binary:Cel' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,908 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,908 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,909 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,909 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,909 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,909 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,909 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,909 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,910 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,910 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,910 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,910 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,910 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,910 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,910 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,911 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,911 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,911 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,911 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,912 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,912 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,912 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,912 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,912 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,921 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,922 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,922 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,922 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,922 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,922 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,922 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,923 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:40,923 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.tools.data INFO 2017-11-18 16:22:41,731 Could not find tool data tool-data/all_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:22:41,731 Loaded 0 lines from 'tool-data/all_fasta.loc.sample' for 'all_fasta' galaxy.tools.data DEBUG 2017-11-18 16:22:41,731 Loaded tool data table 'all_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:22:41,732 Could not find tool data tool-data/bfast_indexes.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:22:41,732 Loaded 0 lines from 'tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' galaxy.tools.data DEBUG 2017-11-18 16:22:41,732 Loaded tool data table 'bfast_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:22:41,732 Loaded 0 lines from 'tool-data/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 16:22:41,732 Loaded tool data table 'blastdb' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:22:41,733 Loaded 0 lines from 'tool-data/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 16:22:41,733 Loaded tool data table 'blastdb_p' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:22:41,733 Loaded 0 lines from 'tool-data/blastdb_d.loc' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 16:22:41,733 Loaded tool data table 'blastdb_d' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data WARNING 2017-11-18 16:22:41,734 Cannot find index file 'tool-data/bwa_index.loc' for tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 16:22:41,734 Loaded tool data table 'bwa_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data WARNING 2017-11-18 16:22:41,734 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 16:22:41,734 Loaded tool data table 'bwa_indexes_color' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:22:41,734 Could not find tool data tool-data/maf_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:22:41,735 Loaded 0 lines from 'tool-data/maf_index.loc.sample' for 'indexed_maf_files' galaxy.tools.data DEBUG 2017-11-18 16:22:41,735 Loaded tool data table 'indexed_maf_files' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:22:41,735 Could not find tool data tool-data/ngs_sim_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:22:41,735 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' galaxy.tools.data DEBUG 2017-11-18 16:22:41,735 Loaded tool data table 'ngs_sim_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:22:41,736 Could not find tool data tool-data/perm_base_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:22:41,736 Loaded 0 lines from 'tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' galaxy.tools.data DEBUG 2017-11-18 16:22:41,736 Loaded tool data table 'perm_base_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:22:41,736 Could not find tool data tool-data/perm_color_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:22:41,737 Loaded 0 lines from 'tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' galaxy.tools.data DEBUG 2017-11-18 16:22:41,737 Loaded tool data table 'perm_color_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:22:41,737 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:22:41,737 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'picard_indexes' galaxy.tools.data DEBUG 2017-11-18 16:22:41,737 Loaded tool data table 'picard_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:22:41,738 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:22:41,738 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'srma_indexes' galaxy.tools.data DEBUG 2017-11-18 16:22:41,738 Loaded tool data table 'srma_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:22:41,738 Could not find tool data tool-data/mosaik_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:22:41,738 Loaded 0 lines from 'tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' galaxy.tools.data DEBUG 2017-11-18 16:22:41,739 Loaded tool data table 'mosaik_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:22:41,739 Could not find tool data tool-data/twobit.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:22:41,739 Loaded 0 lines from 'tool-data/twobit.loc.sample' for 'twobit' galaxy.tools.data DEBUG 2017-11-18 16:22:41,739 Loaded tool data table 'twobit' from file './config/tool_data_table_conf.xml.sample' requests.packages.urllib3.connectionpool INFO 2017-11-18 16:22:41,749 Starting new HTTP connection (1): igv.broadinstitute.org requests.packages.urllib3.connectionpool DEBUG 2017-11-18 16:22:42,207 "GET /genomes/genomes.txt HTTP/1.1" 200 15681 galaxy.tools.data DEBUG 2017-11-18 16:22:42,214 Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-e_bDPi". galaxy.tools.data WARNING 2017-11-18 16:22:42,214 Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields): <Server-Side Genome List> galaxy.tools.data DEBUG 2017-11-18 16:22:42,216 Loaded 156 lines from '/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-e_bDPi' for 'igv_broad_genomes' galaxy.tools.data DEBUG 2017-11-18 16:22:42,219 Loaded tool data table 'igv_broad_genomes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:22:42,219 Could not find tool data tool-data/liftOver.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:22:42,220 Loaded 0 lines from 'tool-data/liftOver.loc.sample' for 'liftOver' galaxy.tools.data DEBUG 2017-11-18 16:22:42,220 Loaded tool data table 'liftOver' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:22:42,220 Could not find tool data tool-data/bam_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:22:42,221 Loaded 1 lines from 'tool-data/bam_iobio.loc.sample' for 'bam_iobio' galaxy.tools.data DEBUG 2017-11-18 16:22:42,221 Loaded tool data table 'bam_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:22:42,221 Could not find tool data tool-data/vcf_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:22:42,222 Loaded 1 lines from 'tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' galaxy.tools.data DEBUG 2017-11-18 16:22:42,222 Loaded tool data table 'vcf_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:22:42,223 Could not find tool data tool-data/biom_simple_display.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:22:42,223 Loaded 1 lines from 'tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' galaxy.tools.data DEBUG 2017-11-18 16:22:42,223 Loaded tool data table 'biom_simple_display' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:22:42,225 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 16:22:42,226 Loading another instance of data table 'blastdb' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 16:22:42,226 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 16:22:42,227 Loading another instance of data table 'blastdb_p' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 16:22:42,227 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb_d.loc' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 16:22:42,228 Loading another instance of data table 'blastdb_d' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.jobs WARNING 2017-11-18 16:22:42,293 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/galaxydir/galaxy/config/galaxy.ini" instead galaxy.jobs DEBUG 2017-11-18 16:22:42,293 Loading job configuration from /galaxydir/galaxy/config/galaxy.ini galaxy.jobs DEBUG 2017-11-18 16:22:42,293 Done loading job configuration beaker.container DEBUG 2017-11-18 16:22:42,378 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache galaxy.tools.toolbox.base INFO 2017-11-18 16:22:42,382 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:22:42,504 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:22:42,630 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:22:42,696 Error reading tool configuration file from path: evolution/codingSnps.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:22:42,701 Error reading tool configuration file from path: evolution/add_scores.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:22:42,704 Error reading tool configuration file from path: phenotype_association/sift.xml galaxy.tools.parameters.basic WARNING 2017-11-18 16:22:42,738 Datatype class not found for extension 'tab', which is used in the 'format' attribute of parameter 'input1' galaxy.tools.toolbox.base INFO 2017-11-18 16:22:42,751 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:22:43,272 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,272 Reading tools from config files finshed (890.836 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,273 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,273 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.8.1.2, version: 2.8.1.2 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,274 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,274 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,274 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,274 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,275 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,275 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,275 Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,275 Loaded tool id: flymine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,275 Loaded tool id: modmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,276 Loaded tool id: mousemine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,276 Loaded tool id: ratmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,276 Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,276 Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,276 Loaded tool id: wormbase, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,277 Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,277 Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,277 Loaded tool id: genomespace_importer, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,277 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,277 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,277 Loaded tool id: genomespace_exporter, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,278 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,278 Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,278 Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,278 Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,278 Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,279 Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,279 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,279 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,279 Loaded tool id: addValue, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,279 Skipping tool panel addition of hidden tool: cat1, version: 1.0.0 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,280 Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,280 Skipping tool panel addition of hidden tool: Cut1, version: 1.0.2 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,280 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,280 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,280 Loaded tool id: createInterval, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,281 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,281 Loaded tool id: Paste1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,281 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,281 Loaded tool id: random_lines1, version: 2.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,281 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,282 Loaded tool id: Show tail1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,282 Loaded tool id: trimmer, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,282 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,282 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,282 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,282 Loaded tool id: Filter1, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,283 Loaded tool id: sort1, version: 1.0.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,283 Loaded tool id: Grep1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,283 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,283 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,283 Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,284 Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,284 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,284 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,284 Loaded tool id: join1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,284 Loaded tool id: comp1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,285 Loaded tool id: Grouping1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,285 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,285 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,285 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,285 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,285 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,286 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,286 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,286 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,286 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,286 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,287 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,287 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,287 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,287 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,287 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,288 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,288 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,288 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,288 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,288 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,288 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,289 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,289 Loaded tool id: Extract genomic DNA 1, version: 2.2.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,289 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,289 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,289 Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,290 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,290 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,290 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,290 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,290 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,291 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,291 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_convert2blastmask_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,291 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,291 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,292 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,292 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,292 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_segmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,292 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,292 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,293 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,293 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,293 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,293 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,294 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,294 Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,294 Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,294 Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,294 Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,295 Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,295 Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,295 Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,295 Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,296 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,296 Loaded label: Illumina data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,296 Loaded label: Roche-454 data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,296 Loaded label: AB-SOLiD data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,296 Loaded tool id: solid2fastq, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,297 Loaded tool id: solid_qual_stats, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,297 Loaded tool id: solid_qual_boxplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,297 Loaded label: Generic FASTQ manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,297 Loaded label: FASTX-Toolkit for FASTQ data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,297 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,298 Loaded label: Illumina galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,298 Loaded label: Roche-454 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,298 Loaded label: AB-SOLiD galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,298 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,298 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,298 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,299 Loaded tool id: Summary_Statistics1, version: 1.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,299 Loaded tool id: Count1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,299 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,299 Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.0 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,300 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:22:43,300 Loading tool panel finished (27.067 ms) galaxy.tools.deps DEBUG 2017-11-18 16:22:43,306 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.search DEBUG 2017-11-18 16:22:43,340 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 16:22:45,535 Toolbox index finished (2195.246 ms) galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,539 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,542 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,585 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,586 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,588 Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,590 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,592 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,594 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,594 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,596 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,597 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,599 Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,633 Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,644 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,679 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,681 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,688 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,699 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,700 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,739 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,743 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,745 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,792 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,793 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,794 Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,795 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,845 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,846 Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,847 Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,849 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,849 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,849 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,849 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,849 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,849 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,849 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,850 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,861 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,862 Adding inherited display application 'igv_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,876 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,876 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,876 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,876 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,880 Adding inherited display application 'igv_fasta' to datatype 'sequences' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,881 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,881 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,881 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,881 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,884 Adding inherited display application 'igv_fasta' to datatype 'mothur.align' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,886 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,886 Adding inherited display application 'igv_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,900 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,900 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,900 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,900 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,901 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,901 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,901 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,901 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,905 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,905 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,905 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,905 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,911 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,912 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,914 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,915 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,916 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,918 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,921 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,923 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,925 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,927 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,929 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,932 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,933 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,934 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,935 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,937 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,943 Loaded converter: CONVERTER_fasta_to_fai galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,944 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,946 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,947 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,948 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,949 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,950 Loaded converter: CONVERTER_fastqgz_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,952 Loaded converter: CONVERTER_fastqsangergz_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,953 Loaded converter: CONVERTER_fastqsolexagz_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,955 Loaded converter: CONVERTER_fastqcssangergz_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,956 Loaded converter: CONVERTER_fastqilluminagz_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,958 Loaded converter: CONVERTER_fastqbz2_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,959 Loaded converter: CONVERTER_fastqsangerbz2_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,960 Loaded converter: CONVERTER_fastqsolexabz2_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,961 Loaded converter: CONVERTER_fastqcssangerbz2_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,962 Loaded converter: CONVERTER_fastqilluminabz2_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,964 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,966 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,968 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,970 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,976 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,977 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,979 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,980 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,981 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,982 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,983 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,985 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,986 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,988 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,992 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,994 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,995 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,996 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,998 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:45,999 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,000 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,001 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,003 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,004 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,005 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,007 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,008 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,011 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,013 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,015 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,016 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,017 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,019 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,020 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,023 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,024 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,026 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,027 Loaded converter: CONVERTER_biom1_to_biom2 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,028 Loaded converter: CONVERTER_biom2_to_biom1 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,030 Loaded converter: CONVERTER_SMILES_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,031 Loaded converter: CONVERTER_SMILES_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,032 Loaded converter: CONVERTER_SMILES_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,034 Loaded converter: CONVERTER_SMILES_to_MOL galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,035 Loaded converter: CONVERTER_SMILES_to_MOL2 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,039 Loaded converter: CONVERTER_smiles_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,043 Loaded converter: CONVERTER_sdf_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,045 Loaded converter: CONVERTER_sdf_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,046 Loaded converter: CONVERTER_sdf_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,047 Loaded converter: CONVERTER_sdf_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,050 Loaded converter: CONVERTER_inchi_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,052 Loaded converter: CONVERTER_inchi_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,054 Loaded converter: CONVERTER_inchi_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,056 Loaded converter: CONVERTER_inchi_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,059 Loaded converter: CONVERTER_inchi_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,061 Loaded converter: CONVERTER_mol_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,063 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,065 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,067 Loaded converter: CONVERTER_mol_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,069 Loaded converter: CONVERTER_mol2_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,071 Loaded converter: CONVERTER_mol2_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,076 Loaded converter: CONVERTER_mol2_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,078 Loaded converter: CONVERTER_mol2_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,079 Loaded converter: CONVERTER_mol2_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,081 Loaded converter: CONVERTER_cml_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,082 Loaded converter: CONVERTER_cml_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,084 Loaded converter: CONVERTER_cml_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,085 Loaded converter: CONVERTER_cml_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,087 Loaded converter: CONVERTER_ref_to_seq_taxomony galaxy.datatypes.registry DEBUG 2017-11-18 16:22:46,088 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 16:22:46,090 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 16:22:46,092 Loaded history export tool: __EXPORT_HISTORY__ galaxy.web.base.pluginframework INFO 2017-11-18 16:22:46,093 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:22:46,094 Visualizations plugin disabled: Circster. Skipping... galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:22:46,095 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 16:22:46,095 VisualizationsRegistry, loaded plugin: csg galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:22:46,096 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 16:22:46,096 VisualizationsRegistry, loaded plugin: graphviz galaxy.web.base.pluginframework INFO 2017-11-18 16:22:46,097 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2017-11-18 16:22:46,098 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:22:46,099 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2017-11-18 16:22:46,100 VisualizationsRegistry, loaded plugin: trackster galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:22:46,100 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 16:22:46,101 VisualizationsRegistry, loaded plugin: unipept galaxy.tours INFO 2017-11-18 16:22:46,148 Loaded tour 'core.galaxy_ui' galaxy.tours INFO 2017-11-18 16:22:46,180 Loaded tour 'core.history' galaxy.tours INFO 2017-11-18 16:22:46,197 Loaded tour 'core.scratchbook' galaxy.webhooks WARNING 2017-11-18 16:22:46,198 directory not found: /galaxydir/galaxy/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config galaxy.jobs.manager DEBUG 2017-11-18 16:22:46,201 Starting job handler galaxy.jobs INFO 2017-11-18 16:22:46,201 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2017-11-18 16:22:46,202 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2017-11-18 16:22:46,202 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2017-11-18 16:22:46,204 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs DEBUG 2017-11-18 16:22:46,204 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2017-11-18 16:22:46,204 Loaded job runners plugins: local galaxy.jobs.handler INFO 2017-11-18 16:22:46,204 job handler stop queue started galaxy.jobs.handler INFO 2017-11-18 16:22:46,391 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 16:22:46,397 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 16:22:46,399 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.workflow.scheduling_manager DEBUG 2017-11-18 16:22:46,401 Starting workflow schedulers galaxy.app INFO 2017-11-18 16:22:46,404 Galaxy app startup finished (6192.752 ms) galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,411 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,543 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,544 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,545 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,545 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,546 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,548 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,548 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,550 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,550 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,552 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,554 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,554 Enabling 'interactive_environments' controller, class: InteractiveEnvironmentsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,560 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,561 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,561 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,565 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,566 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,566 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,567 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,567 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,569 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,569 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,570 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,571 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,571 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,572 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,574 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,576 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,576 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,576 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,577 Enabling 'authenticate' API controller, class: AuthenticationController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,577 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,579 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,580 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,581 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,582 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,582 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,583 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,584 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,584 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,585 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,585 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,586 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,586 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,589 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,590 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,591 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,591 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,591 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,591 Enabling 'job_files' API controller, class: JobFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,592 Enabling 'jobs' API controller, class: JobController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,593 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,593 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,595 Enabling 'library_datasets' API controller, class: LibraryDatasetsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,595 Enabling 'metrics' API controller, class: MetricsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,596 Enabling 'page_revisions' API controller, class: PageRevisionsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,596 Enabling 'pages' API controller, class: PagesController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,597 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,597 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,598 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,601 Enabling 'remote_files' API controller, class: RemoteFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,602 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,602 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,603 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,603 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,617 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,617 Enabling 'tool_data' API controller, class: ToolData galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,618 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,619 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,620 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,620 Enabling 'toolshed' API controller, class: ToolShedController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,621 Enabling 'tours' API controller, class: ToursController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,622 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,623 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,624 Enabling 'webhooks' API controller, class: WebhooksController galaxy.web.framework.base DEBUG 2017-11-18 16:22:46,625 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.webapps.util DEBUG 2017-11-18 16:22:47,006 Enabling 'paste.httpexceptions' middleware galaxy.webapps.util DEBUG 2017-11-18 16:22:47,008 Enabling 'RecursiveMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:22:47,012 Enabling 'ErrorMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:22:47,012 Enabling 'TransLogger' middleware galaxy.webapps.util DEBUG 2017-11-18 16:22:47,013 Enabling 'XForwardedHostMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:22:47,013 Enabling 'RequestIDMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:22:47,014 Enabling 'BatchMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:22:47,014 Enabling 'wrap_in_static' middleware galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,018 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,018 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,018 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,018 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,019 added url, path to static middleware: /plugins/visualizations/unipept/static, ./config/plugins/visualizations/unipept/static galaxy.queue_worker INFO 2017-11-18 16:22:47,019 Binding and starting galaxy control worker for main galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,019 Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 140735112855552)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,020 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145308196864)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,028 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-2, started daemon 123145325023232)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,030 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-0, started daemon 123145316610048)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,030 Prior to webapp return, Galaxy thread <Thread(JobHandlerStopQueue.monitor_thread, started daemon 123145337643008)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,030 Prior to webapp return, Galaxy thread <Thread(WorkflowRequestMonitor.monitor_thread, started daemon 123145346056192)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,030 Prior to webapp return, Galaxy thread <GalaxyQueueWorker(Thread-1, started daemon 123145350262784)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,031 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-3, started daemon 123145329229824)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,031 Prior to webapp return, Galaxy thread <Thread(JobHandlerQueue.monitor_thread, started daemon 123145341849600)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,031 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-1, started daemon 123145320816640)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,032 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-4, started daemon 123145333436416)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:22:47,033 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145312403456)> is alive. Starting server in PID 31254. serving on http://127.0.0.1:8080 /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. 'storage.' % (dialect.name, dialect.driver)) /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. 'strategies for improved performance.' % expr) 127.0.0.1 - - [18/Nov/2017:16:22:55 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:22:55 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:22:56 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:22:56 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:22:56 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:22:56 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:22:56 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:22:56 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:22:56 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:22:56 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:22:56 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:22:58 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:23:03 -0400] "GET /api/tools?q=tes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:23:03 -0400] "GET /api/tools?q=test HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.toolbox.watcher DEBUG 2017-11-18 16:29:14,757 The file './config/tool_conf.xml' has changes. galaxy.queue_worker DEBUG 2017-11-18 16:29:14,758 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 16:29:14,783 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:29:14,788 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:29:14,793 Error reading tool configuration file from path: evolution/codingSnps.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:29:14,794 Error reading tool configuration file from path: evolution/add_scores.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:29:14,797 Error reading tool configuration file from path: phenotype_association/sift.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:29:14,798 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:29:14,802 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,810 Reading tools from config files finshed (26.855 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,810 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,812 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,812 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,812 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,813 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,813 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,813 Skipping tool panel addition of hidden tool: cat1, version: 1.0.0 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,813 Skipping tool panel addition of hidden tool: Cut1, version: 1.0.2 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,814 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,815 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,816 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,816 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,817 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,819 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,820 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,820 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,822 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,824 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,826 Loaded label: Illumina data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,826 Loaded label: Roche-454 data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,826 Loaded label: AB-SOLiD data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,827 Loaded label: Generic FASTQ manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,827 Loaded label: FASTX-Toolkit for FASTQ data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,827 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,827 Loaded label: Illumina galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,827 Loaded label: Roche-454 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,828 Loaded label: AB-SOLiD galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,828 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,828 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,828 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,828 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,828 Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.0 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:29:14,829 Loading tool panel finished (18.478 ms) galaxy.tools.deps DEBUG 2017-11-18 16:29:14,830 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,857 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,857 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,857 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,858 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,858 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,858 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,858 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,858 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,858 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,858 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,859 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,859 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,859 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,859 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,859 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,859 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,859 Loaded converter: CONVERTER_fasta_to_fai galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,859 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,860 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,860 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,860 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,860 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,860 Loaded converter: CONVERTER_fastqgz_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,860 Loaded converter: CONVERTER_fastqsangergz_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,861 Loaded converter: CONVERTER_fastqsolexagz_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,861 Loaded converter: CONVERTER_fastqcssangergz_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,861 Loaded converter: CONVERTER_fastqilluminagz_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,861 Loaded converter: CONVERTER_fastqbz2_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,861 Loaded converter: CONVERTER_fastqsangerbz2_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,861 Loaded converter: CONVERTER_fastqsolexabz2_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,861 Loaded converter: CONVERTER_fastqcssangerbz2_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,861 Loaded converter: CONVERTER_fastqilluminabz2_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,862 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,862 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,862 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,862 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,862 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,862 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,862 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,863 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,863 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,863 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,863 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,863 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,863 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,864 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,864 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,864 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,864 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,864 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,864 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,864 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,865 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,865 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,865 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,865 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,865 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,865 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,865 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,866 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,866 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,866 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,866 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,866 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,866 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,866 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,866 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,866 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,867 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,867 Loaded converter: CONVERTER_biom1_to_biom2 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,867 Loaded converter: CONVERTER_biom2_to_biom1 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,867 Loaded converter: CONVERTER_SMILES_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,867 Loaded converter: CONVERTER_SMILES_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,867 Loaded converter: CONVERTER_SMILES_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,867 Loaded converter: CONVERTER_SMILES_to_MOL galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,868 Loaded converter: CONVERTER_SMILES_to_MOL2 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,868 Loaded converter: CONVERTER_smiles_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,868 Loaded converter: CONVERTER_sdf_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,868 Loaded converter: CONVERTER_sdf_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,868 Loaded converter: CONVERTER_sdf_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,868 Loaded converter: CONVERTER_sdf_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,868 Loaded converter: CONVERTER_inchi_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,869 Loaded converter: CONVERTER_inchi_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,869 Loaded converter: CONVERTER_inchi_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,869 Loaded converter: CONVERTER_inchi_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,869 Loaded converter: CONVERTER_inchi_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,869 Loaded converter: CONVERTER_mol_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,869 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,869 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,869 Loaded converter: CONVERTER_mol_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,870 Loaded converter: CONVERTER_mol2_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,870 Loaded converter: CONVERTER_mol2_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,870 Loaded converter: CONVERTER_mol2_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,870 Loaded converter: CONVERTER_mol2_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,870 Loaded converter: CONVERTER_mol2_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,870 Loaded converter: CONVERTER_cml_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,870 Loaded converter: CONVERTER_cml_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,871 Loaded converter: CONVERTER_cml_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,871 Loaded converter: CONVERTER_cml_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,871 Loaded converter: CONVERTER_ref_to_seq_taxomony galaxy.datatypes.registry DEBUG 2017-11-18 16:29:14,873 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 16:29:14,874 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 16:29:14,876 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 16:29:14,876 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 16:29:14,905 Toolbox reload (147.417 ms) galaxy.queue_worker INFO 2017-11-18 16:29:15,625 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 16:29:15,625 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 16:29:16,140 Toolbox index finished (514.961 ms) 127.0.0.1 - - [18/Nov/2017:16:31:38 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:31:38 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:31:38 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:31:38 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:31:38 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:31:40 -0400] "GET /admin_toolshed/browse_tool_sheds HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:31:40 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:31:41 -0400] "GET /admin_toolshed/browse_tool_sheds HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:31:41 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:31:41 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:31:41 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:31:48 -0400] "GET /admin/tool_errors HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:31:48 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/tool_errors" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.toolbox.watcher DEBUG 2017-11-18 16:44:48,321 The file './config/tool_conf.xml' has changes. galaxy.queue_worker DEBUG 2017-11-18 16:44:48,322 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 16:44:48,339 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:44:48,368 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:44:48,389 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:44:48,392 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,393 Reading tools from config files finshed (54.218 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,393 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,394 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,394 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,394 Loaded tool id: biomart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,394 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,394 Loaded tool id: gramenemart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,395 Loaded tool id: flymine_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,395 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,395 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,396 Loaded tool id: hbvar, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,396 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,396 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,396 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,397 Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,397 Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,397 Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,397 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,397 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,398 Skipping tool panel addition of hidden tool: cat1, version: 1.0.0 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,398 Skipping tool panel addition of hidden tool: Cut1, version: 1.0.2 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,399 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,399 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,399 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,400 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,400 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,400 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,400 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,400 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,401 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,401 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,401 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,401 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,401 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,405 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,405 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,405 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,405 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,405 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,405 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,406 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,406 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,407 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,407 Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.0 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:44:48,407 Loading tool panel finished (13.939 ms) galaxy.tools.deps DEBUG 2017-11-18 16:44:48,409 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 16:44:48,434 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 16:44:48,436 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 16:44:48,440 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 16:44:48,440 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 16:44:48,446 Toolbox reload (124.543 ms) galaxy.queue_worker INFO 2017-11-18 16:44:49,136 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 16:44:49,137 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 16:44:49,397 Toolbox index finished (260.244 ms) galaxy.tools.toolbox.watcher DEBUG 2017-11-18 16:45:27,008 The file './config/tool_conf.xml' has changes. galaxy.queue_worker DEBUG 2017-11-18 16:45:27,008 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 16:45:27,028 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:45:27,033 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:45:27,035 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:45:27,041 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:45:27,055 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,055 Reading tools from config files finshed (26.892 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,055 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,058 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,058 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,058 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,060 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,060 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,060 Skipping tool panel addition of hidden tool: cat1, version: 1.0.0 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,060 Skipping tool panel addition of hidden tool: Cut1, version: 1.0.2 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,061 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,062 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,062 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,062 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,063 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,064 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,064 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,064 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,066 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,066 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,066 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,066 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,066 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,067 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,067 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,067 Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.0 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:27,067 Loading tool panel finished (12.273 ms) galaxy.tools.deps DEBUG 2017-11-18 16:45:27,069 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:27,096 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 16:45:27,097 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 16:45:27,098 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 16:45:27,098 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 16:45:27,106 Toolbox reload (98.306 ms) galaxy.queue_worker INFO 2017-11-18 16:45:28,292 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 16:45:28,292 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 16:45:28,302 Toolbox index finished (10.049 ms) ^Cgalaxy.jobs.handler INFO 2017-11-18 16:45:34,468 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 16:45:34,469 job handler queue stopped galaxy.jobs.runners INFO 2017-11-18 16:45:34,469 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2017-11-18 16:45:34,469 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 16:45:34,470 job handler stop queue stopped CFM5081985:galaxy charles.strittmatter$ sh run.sh Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) 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/galaxydir/galaxy/.venv/lib/python2.7/lib-dynload, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/lib/python2.7/site-packages DEBUG:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config INFO:galaxy.config:Logging at '10' level to 'stdout' galaxy.queue_worker INFO 2017-11-18 16:45:43,472 Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE tool_shed.tool_shed_registry DEBUG 2017-11-18 16:45:43,502 Loading references to tool sheds from ./config/tool_sheds_conf.xml.sample 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lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,592 Script lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,592 Loading script lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,592 Script lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,592 Loading script lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,592 Script lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,592 Loading script lib/galaxy/model/migrate/versions/0135_add_library_tags.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,592 Script lib/galaxy/model/migrate/versions/0135_add_library_tags.py loaded successfully migrate.versioning.repository DEBUG 2017-11-18 16:45:43,592 Repository lib/galaxy/model/migrate loaded successfully migrate.versioning.repository DEBUG 2017-11-18 16:45:43,593 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) galaxy.model.migrate.check INFO 2017-11-18 16:45:43,694 At database version 135 migrate.versioning.repository DEBUG 2017-11-18 16:45:43,695 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,696 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,696 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,696 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,696 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,697 Loading script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,697 Script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,697 Loading script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,697 Script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,697 Loading script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,697 Script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,698 Loading script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,698 Script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,698 Loading script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,698 Script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,698 Loading script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,698 Script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,699 Loading script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,699 Script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,699 Loading script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,699 Script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,699 Loading script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,699 Script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,700 Loading script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 16:45:43,700 Script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py loaded successfully migrate.versioning.repository DEBUG 2017-11-18 16:45:43,700 Repository lib/tool_shed/galaxy_install/migrate loaded successfully migrate.versioning.repository DEBUG 2017-11-18 16:45:43,700 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))]) tool_shed.galaxy_install.migrate.check INFO 2017-11-18 16:45:43,719 At migrate_tools version 12 galaxy.config INFO 2017-11-18 16:45:43,741 Install database targetting Galaxy's database configuration. /galaxydir/galaxy/lib/galaxy/datatypes/registry.py:98: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if root_dir and config: galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,796 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,796 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,796 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/binary: No module named binary galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,796 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,796 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,797 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,797 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,803 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,803 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,803 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,804 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,804 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,804 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,804 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,805 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,805 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,822 Loading datatypes from ./config/datatypes_conf.xml.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,822 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,823 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,823 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,823 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,824 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,824 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,824 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,824 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,824 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,825 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,825 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,825 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,825 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,825 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,826 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,826 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,827 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,827 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,828 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,828 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,828 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,829 Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,829 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,830 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,833 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,833 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,833 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,833 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,833 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,833 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,834 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,834 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,834 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,834 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,834 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,834 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,834 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,835 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,835 Retrieved datatype module galaxy.datatypes.sequence:FastqGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,835 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,835 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,835 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,835 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,835 Retrieved datatype module galaxy.datatypes.sequence:FastqBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,835 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,835 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,835 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,836 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,836 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,836 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,836 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,836 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,836 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,836 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,837 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,837 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,837 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,837 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,838 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,838 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,838 Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,838 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,838 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,839 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,839 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,840 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,840 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,840 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,841 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,841 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,841 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,841 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,842 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,842 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,842 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,842 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,843 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,843 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,843 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,843 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,843 Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,844 Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,844 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,844 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,844 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,844 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,844 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,845 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,845 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,845 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,845 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,845 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,845 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,846 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,846 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,846 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,846 Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,846 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,849 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,849 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,849 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,849 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,850 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,850 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,850 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,850 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,850 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,851 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,851 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,851 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,851 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,851 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,852 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,852 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,852 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,852 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,853 Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,853 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,853 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,853 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,854 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,854 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,854 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,855 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,855 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,856 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,856 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,858 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,859 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,859 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,859 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,859 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,859 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,860 Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,860 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,860 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,860 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,860 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,861 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,861 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,861 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,862 Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,862 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,862 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,863 Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,863 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,863 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,863 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,863 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,863 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,864 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,864 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,867 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,867 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,867 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,868 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,868 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,868 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,868 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,868 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,868 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,868 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,868 Roadmaps is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,868 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,868 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,869 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,869 Sequences is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,869 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,869 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,869 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,869 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,869 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,870 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,870 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,870 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,870 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,870 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,871 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,871 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,871 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,872 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,872 Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,872 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,873 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,873 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,873 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,873 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,873 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,874 Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,874 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,874 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,874 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,874 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,875 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,875 Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,875 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,875 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,875 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,879 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,879 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,879 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,880 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,880 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,880 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,881 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,881 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,881 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,881 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,882 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,882 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,882 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,883 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,883 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,883 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,883 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,883 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,884 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,884 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,886 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,886 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,887 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,888 Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,888 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,889 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,890 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,890 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,891 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,892 Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,893 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,893 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,893 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,893 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,894 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,894 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,894 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,982 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,982 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,983 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,983 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,983 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,984 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,984 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,984 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,984 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,985 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,985 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,985 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,985 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,986 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,986 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,986 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,986 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,987 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,987 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,988 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,988 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,989 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,989 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,989 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,989 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,990 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,990 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,990 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,990 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,991 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,991 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,991 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,991 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,992 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,992 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,992 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,992 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,993 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,993 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,993 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,993 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,993 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,994 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,994 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,994 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,994 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,995 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,995 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,995 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,995 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,996 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,996 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,996 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,996 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,996 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,997 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,997 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,997 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,997 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,997 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,998 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,998 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,998 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,998 Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,999 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,999 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,999 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,999 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:43,999 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,000 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,000 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,000 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,000 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,001 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,001 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,001 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,001 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,001 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,002 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,002 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,002 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,002 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,003 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,003 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,003 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,003 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,004 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,004 Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,004 Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,006 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,006 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,006 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,006 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,006 Retrieved datatype module galaxy.datatypes.binary:Cel from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,006 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,006 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,007 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,007 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,007 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,007 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,007 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,008 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,009 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,009 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,009 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,009 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,010 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,010 Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,010 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,012 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,012 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,012 Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,013 Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,013 Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,013 Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,013 Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,013 Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,014 Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,014 Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,014 Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,014 Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,014 Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,015 Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,018 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,018 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,018 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,018 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,018 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,019 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,019 Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,019 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,019 Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,019 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,019 Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,019 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,020 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,020 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,020 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,020 Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,020 Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,021 Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,021 Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,021 Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,021 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,022 Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,022 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,022 Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,022 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,022 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,023 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,025 Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,025 Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,026 Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,026 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,026 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,026 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,027 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,027 Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,027 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,028 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,028 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,029 Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,030 Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,031 Overriding conflicting datatype with extension 'blastxml', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,031 Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,031 Overriding conflicting datatype with extension 'blastdbn', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,032 Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,032 Overriding conflicting datatype with extension 'blastdbp', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,032 Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,032 Overriding conflicting datatype with extension 'blastdbd', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,033 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,033 Overriding conflicting datatype with extension 'maskinfo-asn1', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,033 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,033 Overriding conflicting datatype with extension 'maskinfo-asn1-binary', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,034 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,034 Overriding conflicting datatype with extension 'pssm-asn1', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,035 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,035 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,036 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,036 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,036 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,036 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,036 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,037 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrtho from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,037 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,037 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylip from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,037 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,038 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,038 Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,039 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,039 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,040 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,040 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,041 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,041 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,042 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,043 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,043 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,043 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,043 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,044 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,044 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,044 Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,044 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,044 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,044 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,045 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,045 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,045 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,045 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,045 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,045 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,045 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,046 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,046 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,046 Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,046 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,046 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,046 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,046 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,047 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,047 Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,047 Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,047 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,047 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,047 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,048 Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,048 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,048 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,048 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,048 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,048 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,048 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,049 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,049 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,049 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,049 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,049 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,049 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,049 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,050 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,050 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,050 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,050 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,050 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,050 Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,051 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,051 Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,051 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,051 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,051 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,051 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,051 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,052 Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,052 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,052 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,052 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,052 Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,052 Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,052 Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,053 Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,053 Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,053 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,053 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,053 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerGz' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,054 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerBz2' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,054 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,055 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqGz' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,055 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqBz2' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,055 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,055 Loaded sniffer for datatype 'galaxy.datatypes.text:Html' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,056 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,056 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,056 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,056 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,056 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,056 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,057 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,057 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,057 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,057 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,057 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,057 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,058 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,058 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,058 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,058 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,058 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,059 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,059 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,059 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,059 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,059 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,059 Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,060 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,060 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,060 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,060 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,060 Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,060 Loaded sniffer for datatype 'galaxy.datatypes.binary:Cel' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,061 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,061 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,061 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,061 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,061 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,061 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,062 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,062 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,062 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,062 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,062 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,064 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,064 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,064 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,064 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,064 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,064 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,065 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,071 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,071 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,071 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,072 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,072 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,072 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,072 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,072 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:44,072 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.tools.data INFO 2017-11-18 16:45:44,848 Could not find tool data tool-data/all_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:45:44,848 Loaded 0 lines from 'tool-data/all_fasta.loc.sample' for 'all_fasta' galaxy.tools.data DEBUG 2017-11-18 16:45:44,849 Loaded tool data table 'all_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:45:44,849 Could not find tool data tool-data/bfast_indexes.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:45:44,849 Loaded 0 lines from 'tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' galaxy.tools.data DEBUG 2017-11-18 16:45:44,849 Loaded tool data table 'bfast_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:45:44,850 Loaded 0 lines from 'tool-data/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 16:45:44,850 Loaded tool data table 'blastdb' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:45:44,850 Loaded 0 lines from 'tool-data/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 16:45:44,850 Loaded tool data table 'blastdb_p' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:45:44,851 Loaded 0 lines from 'tool-data/blastdb_d.loc' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 16:45:44,851 Loaded tool data table 'blastdb_d' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data WARNING 2017-11-18 16:45:44,851 Cannot find index file 'tool-data/bwa_index.loc' for tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 16:45:44,851 Loaded tool data table 'bwa_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data WARNING 2017-11-18 16:45:44,851 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 16:45:44,852 Loaded tool data table 'bwa_indexes_color' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:45:44,852 Could not find tool data tool-data/maf_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:45:44,852 Loaded 0 lines from 'tool-data/maf_index.loc.sample' for 'indexed_maf_files' galaxy.tools.data DEBUG 2017-11-18 16:45:44,852 Loaded tool data table 'indexed_maf_files' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:45:44,852 Could not find tool data tool-data/ngs_sim_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:45:44,853 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' galaxy.tools.data DEBUG 2017-11-18 16:45:44,853 Loaded tool data table 'ngs_sim_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:45:44,853 Could not find tool data tool-data/perm_base_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:45:44,853 Loaded 0 lines from 'tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' galaxy.tools.data DEBUG 2017-11-18 16:45:44,853 Loaded tool data table 'perm_base_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:45:44,854 Could not find tool data tool-data/perm_color_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:45:44,854 Loaded 0 lines from 'tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' galaxy.tools.data DEBUG 2017-11-18 16:45:44,854 Loaded tool data table 'perm_color_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:45:44,854 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:45:44,854 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'picard_indexes' galaxy.tools.data DEBUG 2017-11-18 16:45:44,854 Loaded tool data table 'picard_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:45:44,855 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:45:44,855 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'srma_indexes' galaxy.tools.data DEBUG 2017-11-18 16:45:44,855 Loaded tool data table 'srma_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:45:44,855 Could not find tool data tool-data/mosaik_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:45:44,856 Loaded 0 lines from 'tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' galaxy.tools.data DEBUG 2017-11-18 16:45:44,856 Loaded tool data table 'mosaik_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:45:44,856 Could not find tool data tool-data/twobit.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:45:44,856 Loaded 0 lines from 'tool-data/twobit.loc.sample' for 'twobit' galaxy.tools.data DEBUG 2017-11-18 16:45:44,857 Loaded tool data table 'twobit' from file './config/tool_data_table_conf.xml.sample' requests.packages.urllib3.connectionpool INFO 2017-11-18 16:45:44,868 Starting new HTTP connection (1): igv.broadinstitute.org requests.packages.urllib3.connectionpool DEBUG 2017-11-18 16:45:45,333 "GET /genomes/genomes.txt HTTP/1.1" 200 15681 galaxy.tools.data DEBUG 2017-11-18 16:45:45,338 Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-AX_c1c". galaxy.tools.data WARNING 2017-11-18 16:45:45,338 Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields): <Server-Side Genome List> galaxy.tools.data DEBUG 2017-11-18 16:45:45,341 Loaded 156 lines from '/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-AX_c1c' for 'igv_broad_genomes' galaxy.tools.data DEBUG 2017-11-18 16:45:45,344 Loaded tool data table 'igv_broad_genomes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:45:45,345 Could not find tool data tool-data/liftOver.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:45:45,346 Loaded 0 lines from 'tool-data/liftOver.loc.sample' for 'liftOver' galaxy.tools.data DEBUG 2017-11-18 16:45:45,346 Loaded tool data table 'liftOver' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:45:45,347 Could not find tool data tool-data/bam_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:45:45,347 Loaded 1 lines from 'tool-data/bam_iobio.loc.sample' for 'bam_iobio' galaxy.tools.data DEBUG 2017-11-18 16:45:45,347 Loaded tool data table 'bam_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:45:45,348 Could not find tool data tool-data/vcf_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:45:45,348 Loaded 1 lines from 'tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' galaxy.tools.data DEBUG 2017-11-18 16:45:45,349 Loaded tool data table 'vcf_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 16:45:45,349 Could not find tool data tool-data/biom_simple_display.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 16:45:45,350 Loaded 1 lines from 'tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' galaxy.tools.data DEBUG 2017-11-18 16:45:45,350 Loaded tool data table 'biom_simple_display' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 16:45:45,352 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 16:45:45,352 Loading another instance of data table 'blastdb' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 16:45:45,353 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 16:45:45,353 Loading another instance of data table 'blastdb_p' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 16:45:45,354 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb_d.loc' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 16:45:45,354 Loading another instance of data table 'blastdb_d' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.jobs WARNING 2017-11-18 16:45:45,417 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/galaxydir/galaxy/config/galaxy.ini" instead galaxy.jobs DEBUG 2017-11-18 16:45:45,417 Loading job configuration from /galaxydir/galaxy/config/galaxy.ini galaxy.jobs DEBUG 2017-11-18 16:45:45,418 Done loading job configuration beaker.container DEBUG 2017-11-18 16:45:45,523 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache galaxy.tools.toolbox.base INFO 2017-11-18 16:45:45,529 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:45:45,733 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:45:45,827 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:45:45,886 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:45:46,358 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,358 Reading tools from config files finshed (829.774 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,358 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,359 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.8.1.2, version: 2.8.1.2 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,359 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,359 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,359 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,360 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,360 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,360 Loaded tool id: biomart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,361 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,361 Loaded tool id: gramenemart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,361 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,362 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,362 Loaded tool id: flymine_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,362 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,362 Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,362 Loaded tool id: flymine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,363 Loaded tool id: modmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,363 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,363 Loaded tool id: mousemine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,363 Loaded tool id: ratmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,363 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,364 Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,364 Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,364 Loaded tool id: hbvar, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,364 Loaded tool id: wormbase, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,364 Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,364 Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,365 Loaded tool id: genomespace_importer, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,365 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,365 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,365 Loaded tool id: genomespace_exporter, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,365 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,365 Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,366 Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,366 Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,366 Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,366 Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,366 Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,367 Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,367 Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,367 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,367 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,367 Loaded tool id: addValue, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,367 Loaded tool id: cat1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,368 Loaded tool id: Cut1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,368 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,368 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,368 Loaded tool id: createInterval, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,368 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,369 Loaded tool id: Paste1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,369 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,369 Loaded tool id: random_lines1, version: 2.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,369 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,369 Loaded tool id: Show tail1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,370 Loaded tool id: trimmer, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,370 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,370 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,370 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,370 Loaded tool id: Filter1, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,371 Loaded tool id: sort1, version: 1.0.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,371 Loaded tool id: Grep1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,371 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,371 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,371 Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,371 Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,372 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,372 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,372 Loaded tool id: join1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,372 Loaded tool id: comp1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,372 Loaded tool id: Grouping1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,372 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,373 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,373 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,373 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,373 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,373 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,374 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,374 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,374 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,374 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,374 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,375 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,375 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,375 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,375 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,375 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,376 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,376 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,376 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,376 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,376 Loaded tool id: Extract genomic DNA 1, version: 2.2.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,377 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,377 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,377 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,378 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,378 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_convert2blastmask_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,378 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,378 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,379 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,379 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,379 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_segmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,379 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,380 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,380 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,380 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,380 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,381 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,381 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,381 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,381 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,381 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,381 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,381 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,382 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,382 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,382 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,382 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,382 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,383 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,383 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,383 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,383 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,383 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,384 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,384 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,384 Loaded tool id: Summary_Statistics1, version: 1.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,384 Loaded tool id: Count1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,384 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,384 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,385 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,385 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:45:46,385 Loading tool panel finished (26.593 ms) galaxy.tools.deps DEBUG 2017-11-18 16:45:46,389 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.search DEBUG 2017-11-18 16:45:46,417 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 16:45:48,443 Toolbox index finished (2026.684 ms) galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,447 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,449 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,493 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,494 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,494 Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,495 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,495 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,497 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,498 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,500 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,502 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,507 Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,549 Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,559 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,605 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,606 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,612 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,620 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,621 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,662 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,663 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,666 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,719 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,723 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,724 Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,725 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,775 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,776 Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,777 Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,779 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,779 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,780 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,780 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,780 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,780 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,780 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,780 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,792 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,792 Adding inherited display application 'igv_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,802 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,802 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,802 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,802 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,804 Adding inherited display application 'igv_fasta' to datatype 'sequences' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,805 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,805 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,806 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,806 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,808 Adding inherited display application 'igv_fasta' to datatype 'mothur.align' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,810 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,810 Adding inherited display application 'igv_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,820 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,820 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,820 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,820 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,821 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,821 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,821 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,822 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,825 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,825 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,825 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,825 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,828 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,829 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,830 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,831 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,836 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,840 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,841 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,843 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,844 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,845 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,846 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,849 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,852 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,853 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,855 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,856 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,857 Loaded converter: CONVERTER_fasta_to_fai galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,859 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,861 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,863 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,865 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,866 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,867 Loaded converter: CONVERTER_fastqgz_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,870 Loaded converter: CONVERTER_fastqsangergz_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,874 Loaded converter: CONVERTER_fastqsolexagz_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,875 Loaded converter: CONVERTER_fastqcssangergz_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,877 Loaded converter: CONVERTER_fastqilluminagz_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,878 Loaded converter: CONVERTER_fastqbz2_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,879 Loaded converter: CONVERTER_fastqsangerbz2_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,880 Loaded converter: CONVERTER_fastqsolexabz2_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,881 Loaded converter: CONVERTER_fastqcssangerbz2_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,882 Loaded converter: CONVERTER_fastqilluminabz2_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,886 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,888 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,890 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,891 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,893 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,894 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,896 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,898 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,899 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,900 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,903 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,907 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,908 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,910 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,911 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,912 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,913 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,914 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,916 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,917 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,920 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,921 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,922 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,924 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,925 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,926 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,927 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,929 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,931 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,933 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,935 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,940 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,941 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,943 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,944 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,945 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,946 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,947 Loaded converter: CONVERTER_biom1_to_biom2 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,949 Loaded converter: CONVERTER_biom2_to_biom1 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,950 Loaded converter: CONVERTER_SMILES_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,952 Loaded converter: CONVERTER_SMILES_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,957 Loaded converter: CONVERTER_SMILES_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,958 Loaded converter: CONVERTER_SMILES_to_MOL galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,960 Loaded converter: CONVERTER_SMILES_to_MOL2 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,962 Loaded converter: CONVERTER_smiles_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,964 Loaded converter: CONVERTER_sdf_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,966 Loaded converter: CONVERTER_sdf_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,968 Loaded converter: CONVERTER_sdf_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,969 Loaded converter: CONVERTER_sdf_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,972 Loaded converter: CONVERTER_inchi_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,973 Loaded converter: CONVERTER_inchi_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,977 Loaded converter: CONVERTER_inchi_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,979 Loaded converter: CONVERTER_inchi_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,981 Loaded converter: CONVERTER_inchi_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,983 Loaded converter: CONVERTER_mol_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,986 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,989 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,991 Loaded converter: CONVERTER_mol_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,993 Loaded converter: CONVERTER_mol2_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,995 Loaded converter: CONVERTER_mol2_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,997 Loaded converter: CONVERTER_mol2_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:45:48,998 Loaded converter: CONVERTER_mol2_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 16:45:49,000 Loaded converter: CONVERTER_mol2_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:45:49,008 Loaded converter: CONVERTER_cml_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:45:49,009 Loaded converter: CONVERTER_cml_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:45:49,014 Loaded converter: CONVERTER_cml_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:45:49,016 Loaded converter: CONVERTER_cml_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:45:49,019 Loaded converter: CONVERTER_ref_to_seq_taxomony galaxy.datatypes.registry DEBUG 2017-11-18 16:45:49,022 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 16:45:49,025 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 16:45:49,026 Loaded history export tool: __EXPORT_HISTORY__ galaxy.web.base.pluginframework INFO 2017-11-18 16:45:49,027 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:45:49,028 Visualizations plugin disabled: Circster. Skipping... galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:45:49,029 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 16:45:49,029 VisualizationsRegistry, loaded plugin: csg galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:45:49,030 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 16:45:49,030 VisualizationsRegistry, loaded plugin: graphviz galaxy.web.base.pluginframework INFO 2017-11-18 16:45:49,031 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2017-11-18 16:45:49,032 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:45:49,033 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2017-11-18 16:45:49,034 VisualizationsRegistry, loaded plugin: trackster galaxy.visualization.plugins.config_parser INFO 2017-11-18 16:45:49,037 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 16:45:49,037 VisualizationsRegistry, loaded plugin: unipept galaxy.tours INFO 2017-11-18 16:45:49,086 Loaded tour 'core.galaxy_ui' galaxy.tours INFO 2017-11-18 16:45:49,114 Loaded tour 'core.history' galaxy.tours INFO 2017-11-18 16:45:49,130 Loaded tour 'core.scratchbook' galaxy.webhooks WARNING 2017-11-18 16:45:49,130 directory not found: /galaxydir/galaxy/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config galaxy.jobs.manager DEBUG 2017-11-18 16:45:49,137 Starting job handler galaxy.jobs INFO 2017-11-18 16:45:49,137 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2017-11-18 16:45:49,141 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2017-11-18 16:45:49,141 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2017-11-18 16:45:49,142 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs DEBUG 2017-11-18 16:45:49,142 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2017-11-18 16:45:49,142 Loaded job runners plugins: local galaxy.jobs.handler INFO 2017-11-18 16:45:49,143 job handler stop queue started galaxy.jobs.handler INFO 2017-11-18 16:45:49,161 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 16:45:49,170 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 16:45:49,172 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.workflow.scheduling_manager DEBUG 2017-11-18 16:45:49,175 Starting workflow schedulers galaxy.app INFO 2017-11-18 16:45:49,186 Galaxy app startup finished (5819.193 ms) galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,194 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,474 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,475 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,475 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,476 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,476 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,478 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,478 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,480 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,480 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,481 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,483 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,483 Enabling 'interactive_environments' controller, class: InteractiveEnvironmentsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,491 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,492 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,493 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,494 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,495 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,496 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,497 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,497 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,498 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,498 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,499 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,500 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,500 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,502 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,504 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,506 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,506 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,506 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,506 Enabling 'authenticate' API controller, class: AuthenticationController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,507 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,508 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,508 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,510 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,511 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,511 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,512 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,513 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,513 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,514 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,514 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,515 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,516 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,517 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,520 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,521 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,521 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,521 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,521 Enabling 'job_files' API controller, class: JobFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,523 Enabling 'jobs' API controller, class: JobController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,524 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,525 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,526 Enabling 'library_datasets' API controller, class: LibraryDatasetsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,526 Enabling 'metrics' API controller, class: MetricsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,527 Enabling 'page_revisions' API controller, class: PageRevisionsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,527 Enabling 'pages' API controller, class: PagesController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,528 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,528 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,528 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,530 Enabling 'remote_files' API controller, class: RemoteFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,531 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,531 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,532 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,532 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,546 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,547 Enabling 'tool_data' API controller, class: ToolData galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,548 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,548 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,549 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,550 Enabling 'toolshed' API controller, class: ToolShedController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,550 Enabling 'tours' API controller, class: ToursController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,551 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,552 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,553 Enabling 'webhooks' API controller, class: WebhooksController galaxy.web.framework.base DEBUG 2017-11-18 16:45:49,555 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.webapps.util DEBUG 2017-11-18 16:45:49,934 Enabling 'paste.httpexceptions' middleware galaxy.webapps.util DEBUG 2017-11-18 16:45:49,936 Enabling 'RecursiveMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:45:49,940 Enabling 'ErrorMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:45:49,941 Enabling 'TransLogger' middleware galaxy.webapps.util DEBUG 2017-11-18 16:45:49,941 Enabling 'XForwardedHostMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:45:49,942 Enabling 'RequestIDMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:45:49,942 Enabling 'BatchMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 16:45:49,943 Enabling 'wrap_in_static' middleware galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,946 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,947 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,947 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,947 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,947 added url, path to static middleware: /plugins/visualizations/unipept/static, ./config/plugins/visualizations/unipept/static galaxy.queue_worker INFO 2017-11-18 16:45:49,948 Binding and starting galaxy control worker for main galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,948 Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 140735112855552)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,956 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145308196864)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,958 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-2, started daemon 123145325023232)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,958 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-0, started daemon 123145316610048)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,959 Prior to webapp return, Galaxy thread <Thread(JobHandlerStopQueue.monitor_thread, started daemon 123145337643008)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,959 Prior to webapp return, Galaxy thread <Thread(WorkflowRequestMonitor.monitor_thread, started daemon 123145346056192)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,960 Prior to webapp return, Galaxy thread <GalaxyQueueWorker(Thread-1, started daemon 123145350262784)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,961 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-3, started daemon 123145329229824)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,961 Prior to webapp return, Galaxy thread <Thread(JobHandlerQueue.monitor_thread, started daemon 123145341849600)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,962 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-1, started daemon 123145320816640)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,962 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-4, started daemon 123145333436416)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 16:45:49,962 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145312403456)> is alive. Starting server in PID 31465. serving on http://127.0.0.1:8080 /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. 'storage.' % (dialect.name, dialect.driver)) 127.0.0.1 - - [18/Nov/2017:16:46:04 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:05 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:05 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:05 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:05 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. 'strategies for improved performance.' % expr) 127.0.0.1 - - [18/Nov/2017:16:46:07 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:08 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:08 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:08 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:08 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:08 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:08 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:08 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:08 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:08 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:08 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:10 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:13 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=4kjdbu93pt6&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4kjdbu93pt6" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:13 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4kjdbu93pt6" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:13 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4kjdbu93pt6" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:20 -0400] "GET /api/tools?q=test HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4kjdbu93pt6" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:26 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4kjdbu93pt6" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:26 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:26 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:26 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:26 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:28 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:28 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:34 -0400] "GET /admin/tool_errors HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:46:34 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/tool_errors" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:18 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:18 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:18 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:18 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:18 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:18 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:18 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:19 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:19 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:19 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:19 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:21 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:45 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=tnk0x9x9f3&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:45 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:45 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:47 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 16:47:48,410 Validated and populated state for tool request (41.169 ms) galaxy.tools.actions INFO 2017-11-18 16:47:48,689 Handled output named html_file for tool seq_sero_reads_multiple (33.593 ms) galaxy.tools.actions INFO 2017-11-18 16:47:48,730 Handled output named text_file for tool seq_sero_reads_multiple (41.204 ms) galaxy.tools.actions INFO 2017-11-18 16:47:48,753 Added output datasets to history (22.720 ms) galaxy.tools.actions INFO 2017-11-18 16:47:48,816 Verified access to datasets for Job[unflushed,tool_id=seq_sero_reads_multiple] (27.794 ms) galaxy.tools.actions INFO 2017-11-18 16:47:48,816 Setup for job Job[unflushed,tool_id=seq_sero_reads_multiple] complete, ready to flush (62.914 ms) galaxy.tools.actions INFO 2017-11-18 16:47:48,858 Flushed transaction for job Job[id=3,tool_id=seq_sero_reads_multiple] (41.967 ms) galaxy.tools.execute DEBUG 2017-11-18 16:47:48,860 Tool [seq_sero_reads_multiple] created job [3] (226.243 ms) galaxy.tools.execute DEBUG 2017-11-18 16:47:48,881 Executed 1 job(s) for tool seq_sero_reads_multiple request: (469.912 ms) 127.0.0.1 - - [18/Nov/2017:16:47:48 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:48 -0400] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:48 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T21%3A47%3A19.074Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 16:47:49,669 (3) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/3 galaxy.jobs.handler DEBUG 2017-11-18 16:47:49,681 (3) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 16:47:49,723 (3) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 16:47:49,736 Job [3] queued (54.800 ms) galaxy.jobs.handler INFO 2017-11-18 16:47:49,750 (3) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 16:47:50,067 Built script [/galaxydir/galaxy/database/jobs_directory/000/3/tool_script.sh] for tool command [bwa /galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/files/000/dataset_2.dat /galaxydir/galaxy/tools/GalaxySeqsero/] galaxy.jobs.runners DEBUG 2017-11-18 16:47:50,378 (3) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/3/tool_script.sh; return_code=$?; if [ -f /galaxydir/galaxy/database/jobs_directory/000/3/working/Seqsero_result.html ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/3/working/Seqsero_result.html /galaxydir/galaxy/database/files/000/dataset_3.dat ; fi; if [ -f /galaxydir/galaxy/database/jobs_directory/000/3/working/Seqsero_result.txt ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/3/working/Seqsero_result.txt /galaxydir/galaxy/database/files/000/dataset_4.dat ; fi; cd '/galaxydir/galaxy/database/jobs_directory/000/3'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True python "/galaxydir/galaxy/database/jobs_directory/000/3/set_metadata_LCxXRl.py" "/galaxydir/galaxy/database/jobs_directory/000/3/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/3/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/3/metadata_in_HistoryDatasetAssociation_3__mT1kk,/galaxydir/galaxy/database/jobs_directory/000/3/metadata_kwds_HistoryDatasetAssociation_3_b0rAHZ,/galaxydir/galaxy/database/jobs_directory/000/3/metadata_out_HistoryDatasetAssociation_3_Bsc9Jd,/galaxydir/galaxy/database/jobs_directory/000/3/metadata_results_HistoryDatasetAssociation_3_qYaVVS,/galaxydir/galaxy/database/files/000/dataset_3.dat,/galaxydir/galaxy/database/jobs_directory/000/3/metadata_override_HistoryDatasetAssociation_3_xZdasC" "/galaxydir/galaxy/database/jobs_directory/000/3/metadata_in_HistoryDatasetAssociation_4_wWKadJ,/galaxydir/galaxy/database/jobs_directory/000/3/metadata_kwds_HistoryDatasetAssociation_4_y0yJjo,/galaxydir/galaxy/database/jobs_directory/000/3/metadata_out_HistoryDatasetAssociation_4_fYZu3G,/galaxydir/galaxy/database/jobs_directory/000/3/metadata_results_HistoryDatasetAssociation_4_YvwCD7,/galaxydir/galaxy/database/files/000/dataset_4.dat,/galaxydir/galaxy/database/jobs_directory/000/3/metadata_override_HistoryDatasetAssociation_4_514Jdd" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 16:47:50,394 (3) executing job script: /galaxydir/galaxy/database/jobs_directory/000/3/galaxy_3.sh galaxy.jobs DEBUG 2017-11-18 16:47:50,403 (3) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:16:47:51 -0400] "GET /?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3 HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:51 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:51 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:51 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:51 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:51 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:51 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:52 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=tnk0x9x9f3&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:52 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:52 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:52 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:52 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 16:47:54,234 execution finished: /galaxydir/galaxy/database/jobs_directory/000/3/galaxy_3.sh galaxy.jobs.output_checker INFO 2017-11-18 16:47:54,245 Job 3: Warning: Exit code 127 () 127.0.0.1 - - [18/Nov/2017:16:47:54 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs INFO 2017-11-18 16:47:54,568 Collecting metrics for Job 3 galaxy.jobs DEBUG 2017-11-18 16:47:54,587 job 3 ended (finish() executed in (352.403 ms)) galaxy.model.metadata DEBUG 2017-11-18 16:47:54,596 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:16:47:56 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T21%3A47%3A52.116Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:56 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:56 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:56 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:47:59 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/ebfb8f50c6abde6d HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:48:00 -0400] "GET /datasets/ebfb8f50c6abde6d/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:48:01 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/ebfb8f50c6abde6d/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:48:03 -0400] "GET /datasets/ebfb8f50c6abde6d/stdout HTTP/1.1" 200 - "http://localhost:8080/datasets/ebfb8f50c6abde6d/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:48:05 -0400] "GET /datasets/ebfb8f50c6abde6d/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tnk0x9x9f3" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:48:05 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/ebfb8f50c6abde6d/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:48:08 -0400] "GET /datasets/ebfb8f50c6abde6d/stderr HTTP/1.1" 200 - "http://localhost:8080/datasets/ebfb8f50c6abde6d/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.queue_worker DEBUG 2017-11-18 16:49:43,113 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 16:49:43,131 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:49:43,136 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 16:49:43,138 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:49:43,142 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 16:49:43,145 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,146 Reading tools from config files finshed (15.637 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,146 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,149 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,149 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,149 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,150 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,150 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,151 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,151 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,152 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,152 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,153 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,153 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,153 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,153 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,154 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,155 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,155 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,156 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,156 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,156 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,157 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,158 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 16:49:43,158 Loading tool panel finished (12.048 ms) galaxy.tools.deps DEBUG 2017-11-18 16:49:43,160 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,185 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,185 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,186 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,186 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,186 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,186 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,186 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,186 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,186 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,186 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,187 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,187 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,187 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,187 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,187 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,187 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,187 Loaded converter: CONVERTER_fasta_to_fai galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,188 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,188 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,188 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,189 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,189 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,189 Loaded converter: CONVERTER_fastqgz_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,189 Loaded converter: CONVERTER_fastqsangergz_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,189 Loaded converter: CONVERTER_fastqsolexagz_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,189 Loaded converter: CONVERTER_fastqcssangergz_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,189 Loaded converter: CONVERTER_fastqilluminagz_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,190 Loaded converter: CONVERTER_fastqbz2_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,190 Loaded converter: CONVERTER_fastqsangerbz2_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,190 Loaded converter: CONVERTER_fastqsolexabz2_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,190 Loaded converter: CONVERTER_fastqcssangerbz2_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,190 Loaded converter: CONVERTER_fastqilluminabz2_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,190 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,191 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,191 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,191 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,191 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,191 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,192 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,192 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,192 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,192 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,192 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,192 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,192 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,192 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,192 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,193 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,193 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,193 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,193 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,193 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,193 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,193 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,193 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,193 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,193 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,193 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,193 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,193 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,193 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: CONVERTER_biom1_to_biom2 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: CONVERTER_biom2_to_biom1 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: CONVERTER_SMILES_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: CONVERTER_SMILES_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: CONVERTER_SMILES_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: CONVERTER_SMILES_to_MOL galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: CONVERTER_SMILES_to_MOL2 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,194 Loaded converter: CONVERTER_smiles_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,195 Loaded converter: CONVERTER_sdf_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,195 Loaded converter: CONVERTER_sdf_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,195 Loaded converter: CONVERTER_sdf_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,195 Loaded converter: CONVERTER_sdf_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,195 Loaded converter: CONVERTER_inchi_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,195 Loaded converter: CONVERTER_inchi_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,195 Loaded converter: CONVERTER_inchi_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,195 Loaded converter: CONVERTER_inchi_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,195 Loaded converter: CONVERTER_inchi_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,195 Loaded converter: CONVERTER_mol_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,195 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,195 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,195 Loaded converter: CONVERTER_mol_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,195 Loaded converter: CONVERTER_mol2_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,196 Loaded converter: CONVERTER_mol2_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,196 Loaded converter: CONVERTER_mol2_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,196 Loaded converter: CONVERTER_mol2_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,196 Loaded converter: CONVERTER_mol2_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,196 Loaded converter: CONVERTER_cml_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,196 Loaded converter: CONVERTER_cml_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,196 Loaded converter: CONVERTER_cml_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,196 Loaded converter: CONVERTER_cml_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,196 Loaded converter: CONVERTER_ref_to_seq_taxomony galaxy.datatypes.registry DEBUG 2017-11-18 16:49:43,198 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 16:49:43,199 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 16:49:43,200 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 16:49:43,200 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 16:49:43,232 Toolbox reload (118.643 ms) galaxy.queue_worker INFO 2017-11-18 16:49:44,132 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 16:49:44,132 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 16:49:44,737 Toolbox index finished (603.928 ms) 127.0.0.1 - - [18/Nov/2017:16:49:55 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=hlxki40ajtm&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:49:55 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:49:55 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.queue_worker INFO 2017-11-18 16:49:58,863 Sending reload_tool control task. 127.0.0.1 - - [18/Nov/2017:16:49:58 -0400] "GET /api/tools/seq_sero_reads_multiple/reload HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:09 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 16:50:10,976 Validated and populated state for tool request (40.298 ms) galaxy.tools.actions INFO 2017-11-18 16:50:11,060 Handled output named html_file for tool seq_sero_reads_multiple (31.313 ms) galaxy.tools.actions INFO 2017-11-18 16:50:11,102 Handled output named text_file for tool seq_sero_reads_multiple (42.044 ms) galaxy.tools.actions INFO 2017-11-18 16:50:11,125 Added output datasets to history (22.845 ms) galaxy.tools.actions INFO 2017-11-18 16:50:11,188 Verified access to datasets for Job[unflushed,tool_id=seq_sero_reads_multiple] (26.945 ms) galaxy.tools.actions INFO 2017-11-18 16:50:11,188 Setup for job Job[unflushed,tool_id=seq_sero_reads_multiple] complete, ready to flush (63.128 ms) galaxy.tools.actions INFO 2017-11-18 16:50:11,218 Flushed transaction for job Job[id=4,tool_id=seq_sero_reads_multiple] (29.498 ms) galaxy.tools.execute DEBUG 2017-11-18 16:50:11,218 Tool [seq_sero_reads_multiple] created job [4] (217.756 ms) galaxy.tools.execute DEBUG 2017-11-18 16:50:11,239 Executed 1 job(s) for tool seq_sero_reads_multiple request: (263.062 ms) 127.0.0.1 - - [18/Nov/2017:16:50:10 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:11 -0400] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:11 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T21%3A47%3A56.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 16:50:11,579 (4) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/4 galaxy.jobs.handler DEBUG 2017-11-18 16:50:11,592 (4) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 16:50:11,632 (4) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 16:50:11,648 Job [4] queued (55.760 ms) galaxy.jobs.handler INFO 2017-11-18 16:50:11,660 (4) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 16:50:11,946 Built script [/galaxydir/galaxy/database/jobs_directory/000/4/tool_script.sh] for tool command [/galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/files/000/dataset_2.dat /galaxydir/galaxy/tools/GalaxySeqsero/] galaxy.jobs.runners DEBUG 2017-11-18 16:50:12,214 (4) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/4/tool_script.sh; return_code=$?; if [ -f /galaxydir/galaxy/database/jobs_directory/000/4/working/Seqsero_result.html ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/4/working/Seqsero_result.html /galaxydir/galaxy/database/files/000/dataset_5.dat ; fi; if [ -f /galaxydir/galaxy/database/jobs_directory/000/4/working/Seqsero_result.txt ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/4/working/Seqsero_result.txt /galaxydir/galaxy/database/files/000/dataset_6.dat ; fi; cd '/galaxydir/galaxy/database/jobs_directory/000/4'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True python "/galaxydir/galaxy/database/jobs_directory/000/4/set_metadata_YBmJls.py" "/galaxydir/galaxy/database/jobs_directory/000/4/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/4/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/4/metadata_in_HistoryDatasetAssociation_5_GnbG2d,/galaxydir/galaxy/database/jobs_directory/000/4/metadata_kwds_HistoryDatasetAssociation_5_Dz7imH,/galaxydir/galaxy/database/jobs_directory/000/4/metadata_out_HistoryDatasetAssociation_5_4mQf5Z,/galaxydir/galaxy/database/jobs_directory/000/4/metadata_results_HistoryDatasetAssociation_5_EB8XGm,/galaxydir/galaxy/database/files/000/dataset_5.dat,/galaxydir/galaxy/database/jobs_directory/000/4/metadata_override_HistoryDatasetAssociation_5_Ey4AkG" "/galaxydir/galaxy/database/jobs_directory/000/4/metadata_in_HistoryDatasetAssociation_6_l78uJw,/galaxydir/galaxy/database/jobs_directory/000/4/metadata_kwds_HistoryDatasetAssociation_6__AHdQZ,/galaxydir/galaxy/database/jobs_directory/000/4/metadata_out_HistoryDatasetAssociation_6_IfFaWS,/galaxydir/galaxy/database/jobs_directory/000/4/metadata_results_HistoryDatasetAssociation_6_f96_q2,/galaxydir/galaxy/database/files/000/dataset_6.dat,/galaxydir/galaxy/database/jobs_directory/000/4/metadata_override_HistoryDatasetAssociation_6_hYkbZI" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 16:50:12,228 (4) executing job script: /galaxydir/galaxy/database/jobs_directory/000/4/galaxy_4.sh galaxy.jobs DEBUG 2017-11-18 16:50:12,236 (4) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:16:50:15 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T21%3A50%3A11.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:15 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:15 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 16:50:17,210 execution finished: /galaxydir/galaxy/database/jobs_directory/000/4/galaxy_4.sh galaxy.jobs.output_checker INFO 2017-11-18 16:50:17,221 Job 4: Warning: Exit code 0 () galaxy.jobs.output_checker INFO 2017-11-18 16:50:17,222 Job 4: Fatal error: Matched on Error: galaxy.jobs.output_checker DEBUG 2017-11-18 16:50:17,222 Tool exit code indicates an error, failing job. galaxy.jobs DEBUG 2017-11-18 16:50:17,294 (4) setting dataset 5 state to ERROR galaxy.jobs DEBUG 2017-11-18 16:50:17,336 (4) setting dataset 6 state to ERROR galaxy.jobs INFO 2017-11-18 16:50:17,547 Collecting metrics for Job 4 galaxy.jobs DEBUG 2017-11-18 16:50:17,563 job 4 ended (finish() executed in (353.420 ms)) galaxy.tools.error_reports DEBUG 2017-11-18 16:50:17,594 Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x107a71710> generated response None galaxy.tools.error_reports DEBUG 2017-11-18 16:50:17,594 Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x107a71710> generated response None galaxy.model.metadata DEBUG 2017-11-18 16:50:17,595 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:16:50:19 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T21%3A50%3A15.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:19 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:19 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:19 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:19 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:22 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/a799d38679e985db HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=hlxki40ajtm" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:26 -0400] "GET /api/datasets/a799d38679e985db HTTP/1.1" 200 - "http://localhost:8080/datasets/error?dataset_id=a799d38679e985db&__identifer=9nms4ovms1v" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:26 -0400] "GET /api/jobs/ebfb8f50c6abde6d?full=True HTTP/1.1" 200 - "http://localhost:8080/datasets/error?dataset_id=a799d38679e985db&__identifer=9nms4ovms1v" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:40 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/datasets/error?dataset_id=a799d38679e985db&__identifer=9nms4ovms1v" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:40 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:40 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:40 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:40 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:43 -0400] "GET /admin_toolshed/browse_tool_sheds HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:43 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:50:44 -0400] "GET /admin_toolshed/browse_tool_shed?tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:53:23 -0400] "GET /admin_toolshed/prepare_for_install?changeset_revisions=a12f73c3b116&repository_ids=82ee0646f4d9c1d1&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:53:29 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=a12f73c3b116&repository_ids=82ee0646f4d9c1d1&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 16:54:55,152 Creating repository dependency objects... tool_shed.util.repository_util DEBUG 2017-11-18 16:54:57,224 Adding new row for repository 'package_biopython_1_67' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_util DEBUG 2017-11-18 16:54:57,431 Adding new row for repository 'package_numpy_1_9' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_util DEBUG 2017-11-18 16:54:57,665 Adding new row for repository 'package_atlas_3_10' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_util DEBUG 2017-11-18 16:54:57,901 Adding new row for repository 'package_python_2_7' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_util DEBUG 2017-11-18 16:54:58,162 Adding new row for repository 'package_readline_6_3' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_util DEBUG 2017-11-18 16:54:58,405 Adding new row for repository 'package_ncurses_6_0' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_util DEBUG 2017-11-18 16:54:58,661 Adding new row for repository 'package_xz_5_0_5' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_util DEBUG 2017-11-18 16:54:58,933 Adding new row for repository 'package_libtool_2_4' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_util DEBUG 2017-11-18 16:54:59,190 Adding new row for repository 'package_zlib_1_2_8' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_util DEBUG 2017-11-18 16:54:59,459 Adding new row for repository 'package_bzlib_1_0' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_util DEBUG 2017-11-18 16:54:59,729 Adding new row for repository 'package_sqlite_3_8_3' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_util DEBUG 2017-11-18 16:55:00,022 Adding new row for repository 'package_gdbm_1_11' in the tool_shed_repository table, status set to 'New'. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 16:55:00,033 Building repository dependency relationships... tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 16:55:00,074 Creating new repository_dependency record for installed revision 98c017ec230d of repository: package_atlas_3_10 owned by iuc. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 16:55:00,155 Creating new repository_dependency record for installed revision 8b09fe018cac of repository: package_python_2_7 owned by iuc. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 16:55:00,239 Creating new repository_dependency record for installed revision 0efde9889efd of repository: package_ncurses_6_0 owned by iuc. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 16:55:00,339 Creating new repository_dependency record for installed revision 7f67694b167c of repository: package_libtool_2_4 owned by iuc. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 16:55:00,404 Creating new repository_dependency record for installed revision 83d12e13dbbd of repository: package_numpy_1_9 owned by iuc. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 16:55:00,505 Creating new repository_dependency record for installed revision 411985b46ae8 of repository: package_zlib_1_2_8 owned by iuc. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 16:55:00,613 Creating new repository_dependency record for installed revision ca1a9400d4e1 of repository: package_readline_6_3 owned by iuc. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 16:55:00,748 Creating new repository_dependency record for installed revision af4887e1f595 of repository: package_bzlib_1_0 owned by iuc. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 16:55:00,870 Creating new repository_dependency record for installed revision 944f93d45594 of repository: package_xz_5_0_5 owned by iuc. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 16:55:01,011 Creating new repository_dependency record for installed revision c8a5c11cc921 of repository: package_sqlite_3_8_3 owned by iuc. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 16:55:01,174 Creating new repository_dependency record for installed revision ed2537bccffc of repository: package_gdbm_1_11 owned by iuc. 127.0.0.1 - - [18/Nov/2017:16:54:55 -0400] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=a12f73c3b116&repository_ids=82ee0646f4d9c1d1&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:55:01 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:55:04,775 Creating a new record for version 1.11 of tool dependency gdbm for revision ed2537bccffc of repository package_gdbm_1_11. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:55:04,862 Updating an existing record for version 1.11 of tool dependency gdbm for revision ed2537bccffc of repository package_gdbm_1_11 by updating the status from Never installed to Installing. tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 16:55:04,896 Attempting to download via url: ftp://ftp.gnu.org/gnu/gdbm/gdbm-1.11.tar.gz 127.0.0.1 - - [18/Nov/2017:16:55:04 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 16:55:05,593 Successfully downloaded from url: ftp://ftp.gnu.org/gnu/gdbm/gdbm-1.11.tar.gz tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:05,593 + ./configure --prefix=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc --enable-libgdbm-compat && make && make install install_environment.STDOUT DEBUG 2017-11-18 16:55:05,951 checking whether build environment is sane... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:05,973 checking for gawk... no install_environment.STDOUT DEBUG 2017-11-18 16:55:05,974 checking for nawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,011 checking for a BSD-compatible install... /usr/bin/install -c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,011 checking whether build environment is sane... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,011 checking for a thread-safe mkdir -p... build-aux/install-sh -c -d tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,011 checking for gawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,011 checking for mawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,011 checking for nawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,011 checking for awk... awk install_environment.STDOUT DEBUG 2017-11-18 16:55:06,013 checking whether make sets $(MAKE)... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:06,068 checking whether make supports nested variables... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,112 checking whether make sets $(MAKE)... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,113 checking whether make supports nested variables... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,113 checking whether make supports nested variables... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,113 checking for gcc... gcc install_environment.STDOUT DEBUG 2017-11-18 16:55:06,702 checking whether the C compiler works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,728 checking whether the C compiler works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,728 checking for C compiler default output file name... a.out install_environment.STDOUT DEBUG 2017-11-18 16:55:06,752 checking for suffix of executables... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,829 checking for suffix of executables... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:06,931 checking whether we are cross compiling... no install_environment.STDOUT DEBUG 2017-11-18 16:55:06,932 checking for suffix of object files... o install_environment.STDOUT DEBUG 2017-11-18 16:55:07,008 checking whether gcc accepts -g... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:07,032 checking for suffix of object files... o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:07,032 checking whether we are using the GNU C compiler... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:07,033 checking whether gcc accepts -g... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:07,297 checking whether gcc understands -c and -o together... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:07,339 checking for gcc option to accept ISO C89... none needed tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:07,339 checking whether gcc understands -c and -o together... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:07,339 checking for style of include used by make... GNU install_environment.STDOUT DEBUG 2017-11-18 16:55:07,405 checking dependency style of gcc... gcc3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:07,439 checking dependency style of gcc... gcc3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:07,544 checking how to run the C preprocessor... gcc -E install_environment.STDOUT DEBUG 2017-11-18 16:55:07,693 checking build system type... x86_64-apple-darwin15.6.0 install_environment.STDOUT DEBUG 2017-11-18 16:55:07,699 checking how to print strings... printf tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:07,747 checking build system type... x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:07,747 checking host system type... x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:07,748 checking how to print strings... printf tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:07,952 checking for a sed that does not truncate output... /usr/bin/sed 127.0.0.1 - - [18/Nov/2017:16:55:07 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:55:08,119 checking for grep that handles long lines and -e... /usr/bin/grep install_environment.STDOUT DEBUG 2017-11-18 16:55:08,136 checking for fgrep... /usr/bin/grep -F tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,156 checking for grep that handles long lines and -e... /usr/bin/grep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,157 checking for egrep... /usr/bin/grep -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,157 checking for fgrep... /usr/bin/grep -F tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,257 checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld install_environment.STDOUT DEBUG 2017-11-18 16:55:08,271 checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,361 checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,361 checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B install_environment.STDOUT DEBUG 2017-11-18 16:55:08,418 checking the name lister (/usr/bin/nm -B) interface... BSD nm install_environment.STDOUT DEBUG 2017-11-18 16:55:08,429 checking the maximum length of command line arguments... 196608 install_environment.STDOUT DEBUG 2017-11-18 16:55:08,432 checking whether the shell understands "+="... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:08,444 func_convert_file_noop install_environment.STDOUT DEBUG 2017-11-18 16:55:08,444 t_file_noop install_environment.STDOUT DEBUG 2017-11-18 16:55:08,445 /usr/bin/ld option to reload object files... -r install_environment.STDOUT DEBUG 2017-11-18 16:55:08,447 checking how to recognize dependent libraries... pass_all install_environment.STDOUT DEBUG 2017-11-18 16:55:08,448 checking how to associate runtime and link libraries... printf %s\n tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,465 checking the name lister (/usr/bin/nm -B) interface... BSD nm tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,465 checking whether ln -s works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,465 checking the maximum length of command line arguments... 196608 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,465 checking whether the shell understands some XSI constructs... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,465 checking whether the shell understands "+="... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,465 func_convert_file_noop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,466 t_file_noop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,466 /usr/bin/ld option to reload object files... -r tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,466 checking how to convert x86_64-apple-darwin15.6.0 file names to x86_64-apple-darwin15.6.0 format... checking how to convert x86_64-apple-darwin15.6.0 file names to toolchain format... func_converchecking for /Library/Developer/CommandLineToolschecking for objdump... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,466 checking how to recognize dependent libraries... pass_all tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,466 checking for dlltool... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,466 checking how to associate runtime and link libraries... printf %s\n tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,467 checking for ar... ar install_environment.STDOUT DEBUG 2017-11-18 16:55:08,509 checking for archiver @FILE support... no install_environment.STDOUT DEBUG 2017-11-18 16:55:08,513 checking for ranlib... ranlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,568 checking for archiver @FILE support... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,569 checking for strip... strip tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,569 checking for ranlib... ranlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,872 checking command to parse /usr/bin/nm -B output from gcc object... ok install_environment.STDOUT DEBUG 2017-11-18 16:55:08,875 checking for sysroot... no install_environment.STDOUT DEBUG 2017-11-18 16:55:08,884 checking if : is a manifest tool... no install_environment.STDOUT DEBUG 2017-11-18 16:55:08,888 checking for nmedit... nmedit install_environment.STDOUT DEBUG 2017-11-18 16:55:08,890 checking for otool... otool tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,975 checking for sysroot... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,975 checking for mt... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,975 checking if : is a manifest tool... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,975 checking for dsymutil... dsymutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,975 checking for nmedit... nmedit tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,975 checking for lipo... lipo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,975 checking for otool64... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,975 checking for otool... otool tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:08,975 checking for -single_module linker flag... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:09,022 checking for -exported_symbols_list linker flag... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:09,076 checking for -exported_symbols_list linker flag... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:09,177 checking for -force_load linker flag... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:09,442 checking for ANSI C header files... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:09,485 checking for ANSI C header files... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:09,584 checking for sys/stat.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:09,590 checking for sys/types.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:09,590 checking for sys/stat.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:09,691 checking for stdlib.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:09,725 checking for string.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:09,791 checking for string.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:09,870 checking for strings.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:09,892 checking for memory.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:09,892 checking for strings.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:09,993 checking for inttypes.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:10,018 checking for stdint.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,098 checking for stdint.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,099 checking for unistd.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:10,180 checking for dlfcn.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,201 checking for dlfcn.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,201 checking for objdir... .libs install_environment.STDOUT DEBUG 2017-11-18 16:55:10,350 checking if gcc supports -fno-rtti -fno-exceptions... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:10,405 checking if gcc PIC flag -fno-common -DPIC works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,407 checking if gcc supports -fno-rtti -fno-exceptions... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,407 checking for gcc option to produce PIC... -fno-common -DPIC tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,407 checking if gcc PIC flag -fno-common -DPIC works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,508 checking if gcc static flag -static works... no install_environment.STDOUT DEBUG 2017-11-18 16:55:10,518 checking if gcc supports -c -o file.o... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:10,587 checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libchecking dynamic linker cchecking how to hardcode librarchecking whether stripping libraries ischecking if libtool supports shared libraries...checking whether to build shared libraries... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:10,591 checking for special C compiler options needed for large files... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,610 checking if gcc supports -c -o file.o... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,610 checking if gcc supports -c -o file.o... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,611 raries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,611 haracteristics... darwin15.6.0 dyld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,611 y paths into programs... immediate tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,611 possible... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,611 yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,611 checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libchecking dynamic linker cchecking how to hardcode librarchecking whether stripping libraries ischecking if libtool supports shared libraries...checking whether to build shared libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,611 checking whether to build static libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,611 checking for special C compiler options needed for large files... no install_environment.STDOUT DEBUG 2017-11-18 16:55:10,646 checking for bison... bison -y install_environment.STDOUT DEBUG 2017-11-18 16:55:10,704 checking lex output file root... lex.yy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,715 checking for _FILE_OFFSET_BITS value needed for large files... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,716 checking for bison... bison -y tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,716 checking for flex... flex tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:10,716 checking lex output file root... lex.yy 127.0.0.1 - - [18/Nov/2017:16:55:11 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:11,535 checking lex library... -ll install_environment.STDOUT DEBUG 2017-11-18 16:55:11,681 checking whether yytext is a pointer... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:11,743 checking whether yytext is a pointer... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:11,743 checking for an ANSI C-conforming const... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:11,816 checking for unsigned long long int... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:11,827 checking for msgfmt... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:11,844 checking for unsigned long long int... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:11,844 checking whether NLS is requested... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:11,844 checking for msgfmt... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:11,844 checking for gmsgfmt... : install_environment.STDOUT DEBUG 2017-11-18 16:55:11,849 checking for xgettext... no install_environment.STDOUT DEBUG 2017-11-18 16:55:11,898 checking for ld used by GCC... /Library/Developer/CommandLineTools/usr/bin/ld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:11,948 checking for xgettext... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:11,948 checking for msgmerge... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:11,948 checking for ld used by GCC... /Library/Developer/CommandLineTools/usr/bin/ld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:11,948 checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no install_environment.STDOUT DEBUG 2017-11-18 16:55:11,955 checking for shared library run path origin... done tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,049 checking for shared library run path origin... done tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,149 checking for CFPreferencesCopyAppValue... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:12,188 checking for CFLocaleCopyCurrent... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,250 checking for CFLocaleCopyCurrent... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,250 checking for GNU gettext in libc... no install_environment.STDOUT DEBUG 2017-11-18 16:55:12,420 checking for iconv... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,455 checking for iconv... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:12,512 checking how to link with libiconv... -liconv tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,560 checking for working iconv... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,560 checking how to link with libiconv... -liconv install_environment.STDOUT DEBUG 2017-11-18 16:55:12,626 checking whether to use NLS... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,661 checking for GNU gettext in libintl... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,661 checking whether to use NLS... no install_environment.STDOUT DEBUG 2017-11-18 16:55:12,751 checking sys/file.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,764 checking sys/file.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,764 checking sys/file.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,765 checking for sys/file.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:12,835 checking sys/termios.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:12,867 checking for sys/termios.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,868 checking sys/termios.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,869 checking sys/termios.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,869 checking for sys/termios.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:12,961 checking locale.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,971 checking for string.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:12,971 checking locale.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:12,993 checking for locale.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:13,076 checking locale.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:13,076 checking for locale.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:13,077 checking getopt.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:13,109 checking getopt.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:13,179 checking getopt.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:13,179 checking for getopt.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:13,190 checking for main in -ldbm... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:13,280 checking for main in -ldbm... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:13,281 checking for main in -lndbm... no install_environment.STDOUT DEBUG 2017-11-18 16:55:13,332 checking for rename... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:13,384 checking for rename... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:13,485 checking for ftruncate... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:13,500 checking for flock... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:13,588 checking for flock... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:13,690 checking for lockf... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:13,733 checking for fsync... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:13,790 checking for fsync... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:13,892 checking for setlocale... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:14,007 checking for getopt_long... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:14,043 checking for unistd.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:14,097 checking for getopt_long... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:14,097 checking for stdlib.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:14,097 checking for unistd.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:14,198 checking for sys/param.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:14,229 checking for getpagesize... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:14,303 checking for getpagesize... yes 127.0.0.1 - - [18/Nov/2017:16:55:14 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:14,407 checking for working mmap... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:14,461 checking for msync... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:14,510 checking for msync... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:14,611 checking for off_t... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:14,708 checking size of off_t... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:14,714 checking size of off_t... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:14,817 checking for struct stat.st_blksize... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:14,846 checking that generated files are newer than configure... done tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:14,922 checking that generated files are newer than configure... done tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:14,922 configure: creating ./config.status install_environment.STDOUT DEBUG 2017-11-18 16:55:15,952 config.status: creating tests/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:16,029 config.status: creating tests/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:16,029 config.status: creating tests/atlocal install_environment.STDOUT DEBUG 2017-11-18 16:55:16,044 config.status: creating po/Makefile.in install_environment.STDOUT DEBUG 2017-11-18 16:55:16,131 config.status: creating src/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:16,133 config.status: creating po/Makefile.in tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:16,133 config.status: creating Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:16,133 config.status: creating src/Makefile install_environment.STDOUT DEBUG 2017-11-18 16:55:16,229 config.status: creating doc/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:16,234 config.status: creating src/gdbm.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:16,235 config.status: creating doc/Makefile install_environment.STDOUT DEBUG 2017-11-18 16:55:16,329 config.status: creating export/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:16,339 config.status: creating compat/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:16,340 config.status: creating export/Makefile install_environment.STDOUT DEBUG 2017-11-18 16:55:16,403 config.status: executing depfiles commands tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:16,443 config.status: creating autoconf.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:16,443 config.status: executing depfiles commands tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:16,954 config.status: executing libtool commands install_environment.STDOUT DEBUG 2017-11-18 16:55:17,282 config.status: executing po-directories commands install_environment.STDOUT DEBUG 2017-11-18 16:55:17,321 config.status: creating po/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:17,362 config.status: executing po-directories commands tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:17,362 config.status: creating po/POTFILES tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:17,362 config.status: creating po/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:17,362 config.status: executing tests/atconfig commands install_environment.STDOUT DEBUG 2017-11-18 16:55:17,484 /Library/Developer/CommandLineTools/usr/bin/make all-recursive install_environment.STDOUT DEBUG 2017-11-18 16:55:17,522 Making all in src tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:17,565 /Library/Developer/CommandLineTools/usr/bin/make all-recursive tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:17,566 Making all in po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:17,566 Making all in src tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:17,566 CC err.o 127.0.0.1 - - [18/Nov/2017:16:55:17 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:55:17,676 CC mem.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:17,767 CC mem.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:17,767 CC parseopt.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:17,868 parseopt.c:243:18: warning: field width should have type 'int', but argument has type 'size_t' (aka 'unsigned long') [-Wformat] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:17,868 printf ("%*.*s\n", s, s, descr); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:17,868 ~~^~~ ~ install_environment.STDOUT DEBUG 2017-11-18 16:55:18,040 CC progname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:18,075 CC progname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:18,076 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 16:55:18,150 CC gdbmclose.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:18,178 AR libgdbmapp.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:18,178 CC gdbmclose.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:18,382 CC gdbmcount.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:18,578 CC gdbmdelete.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:18,585 CC gdbmdelete.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:18,788 CC gdbmdump.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:19,008 CC gdbmerrno.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:19,093 CC gdbmerrno.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:19,196 CC gdbmexists.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:19,363 CC gdbmexp.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:19,400 CC gdbmexp.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:19,604 CC gdbmfdesc.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:19,775 CC gdbmfetch.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:19,810 CC gdbmfetch.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:20,011 CC gdbmload.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:20,436 CC gdbmopen.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:20,522 CC gdbmopen.lo 127.0.0.1 - - [18/Nov/2017:16:55:20 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:20,831 CC gdbmimp.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:20,991 CC gdbmreorg.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:21,036 CC gdbmreorg.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:21,343 CC gdbmseq.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:21,489 CC gdbmsetopt.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:21,546 CC gdbmsetopt.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:21,751 CC gdbmstore.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:21,931 CC gdbmsync.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:21,957 CC gdbmsync.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:22,163 CC base64.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:22,358 CC bucket.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:22,370 CC bucket.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:22,880 CC falloc.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:23,200 CC findkey.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:23,290 CC findkey.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:23,492 CC fullio.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:23,687 CC hash.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:23,693 CC hash.lo 127.0.0.1 - - [18/Nov/2017:16:55:23 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:24,002 CC lock.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:24,160 CC mmap.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:24,205 CC mmap.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:24,513 CC update.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:24,656 CC version.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:24,723 CC version.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:24,827 CCLD libgdbm.la install_environment.STDOUT DEBUG 2017-11-18 16:55:25,089 CC datconv.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,130 CC datconv.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,333 CC gram.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,433 gram.y:333:17: warning: implicit declaration of function 'variable_unset' is invalid in C99 [-Wimplicit-function-declaration] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,433 int rc = variable_unset ((yyvsp[(1) - (1)].string)); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,433 ^ install_environment.STDOUT DEBUG 2017-11-18 16:55:25,564 CC lex.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,639 CC lex.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,639 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,640 lex.l:227:13: warning: passing 'const char *' to parameter of type 'char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,640 yyerror (_("invalid #line statement")); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,640 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,640 ./gdbmdefs.h:26:14: note: expanded from macro '_' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,640 #define _(s) gettext (s) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,640 ^~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,640 ./gettext.h:69:25: note: expanded from macro 'gettext' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,640 # define gettext(Msgid) ((const char *) (Msgid)) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,641 ^~~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,641 ./gdbmtool.h:253:20: note: passing argument to parameter 's' here tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,641 int yyerror (char *s); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,641 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,641 lex.l:237:16: warning: passing 'const char *' to parameter of type 'char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,641 yyerror (_("invalid #line statement")); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,641 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,641 ./gdbmdefs.h:26:14: note: expanded from macro '_' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,641 #define _(s) gettext (s) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,641 ^~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,642 ./gettext.h:69:25: note: expanded from macro 'gettext' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,642 # define gettext(Msgid) ((const char *) (Msgid)) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,642 ^~~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,642 ./gdbmtool.h:253:20: note: passing argument to parameter 's' here tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,642 int yyerror (char *s); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,642 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:25,947 2 warnings generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,048 CC gdbmtool.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,048 gdbmtool.c:274:3: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,048 dbf->cache_size); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,049 ^~~~~~~~~~~~~~~ install_environment.STDOUT DEBUG 2017-11-18 16:55:26,326 CC var.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,360 CC var.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,361 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,463 var.c:55:40: warning: use of GNU old-style field designator extension [-Wgnu-designator] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,463 { "confirm", VART_BOOL, VARF_INIT, { num: 1 } }, tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,463 ^~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,463 .num = tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,463 var.c:59:37: warning: use of GNU old-style field designator extension [-Wgnu-designator] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,464 { "lock", VART_BOOL, VARF_INIT, { num: 1 } }, tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,464 ^~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,464 .num = tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,464 var.c:60:37: warning: use of GNU old-style field designator extension [-Wgnu-designator] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,464 { "mmap", VART_BOOL, VARF_INIT, { num: 1 } }, tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,464 ^~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,464 .num = tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,465 var.c:61:37: warning: use of GNU old-style field designator extension [-Wgnu-designator] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,465 { "sync", VART_BOOL, VARF_INIT, { num: 0 } }, tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,465 ^~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,465 .num = tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,465 var.c:62:61: warning: use of GNU old-style field designator extension [-Wgnu-designator] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,465 { "filemode", VART_INT, VARF_INIT|VARF_OCTAL|VARF_PROT, { num: 0644 } }, tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,465 ^~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,465 .num = tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,466 5 warnings generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,570 CC util.o install_environment.STDOUT DEBUG 2017-11-18 16:55:26,571 CCLD gdbmtool tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,675 CCLD gdbmtool tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,778 CC gdbm_load.o install_environment.STDOUT DEBUG 2017-11-18 16:55:26,894 CCLD gdbm_load tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:26,984 CCLD gdbm_load 127.0.0.1 - - [18/Nov/2017:16:55:27 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:27,187 CC gdbm_dump.o install_environment.STDOUT DEBUG 2017-11-18 16:55:27,248 CCLD gdbm_dump tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:27,287 CCLD gdbm_dump install_environment.STDOUT DEBUG 2017-11-18 16:55:27,454 make[2]: Nothing to be done for `all'. install_environment.STDOUT DEBUG 2017-11-18 16:55:27,464 CC dbminit.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:27,489 Making all in doc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:27,489 make[2]: Nothing to be done for `all'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:27,489 Making all in compat tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:27,489 CC dbminit.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:27,696 CC delete.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:27,827 CC fetch.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:27,904 CC fetch.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:28,009 CC store.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:28,192 CC seq.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:28,213 CC seq.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:28,421 CC close.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:28,546 CC dbmopen.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:28,628 CC dbmopen.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:28,832 CC dbmdelete.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:28,943 CC dbmerr.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:29,038 CC dbmerr.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:29,139 CC dbmfetch.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:29,329 CC dbmstore.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:29,341 CC dbmstore.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:29,547 CC dbmseq.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:29,680 CC dbmclose.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:29,753 CC dbmclose.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:29,954 CC dbmdirfno.lo install_environment.STDOUT DEBUG 2017-11-18 16:55:30,053 CC dbmpagfno.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,058 CC dbmpagfno.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,263 CC dbmrdonly.lo 127.0.0.1 - - [18/Nov/2017:16:55:30 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:55:30,455 CCLD libgdbm_compat.la tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,467 CCLD libgdbm_compat.la install_environment.STDOUT DEBUG 2017-11-18 16:55:30,721 make[2]: Nothing to be done for `all'. install_environment.STDOUT DEBUG 2017-11-18 16:55:30,743 Making install in po install_environment.STDOUT DEBUG 2017-11-18 16:55:30,751 ../build-aux/install-sh -c -d /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_ for file in Makefile.in.in remove-potcdate.sin quot.sed boldquot.sed en@quot.header en@boldquot.header insert-header.sin Rules-quot Makevars.template; do \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,770 Making all in tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,771 make[2]: Nothing to be done for `all'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,771 make[2]: Nothing to be done for `all-am'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,771 Making install in po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,771 if test "gdbm" = "gettext-tools"; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,771 1_11/ed2537bccffc/share/gettext/po; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,772 /usr/bin/install -c -m 644 ./$file \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,772 /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/share/gettext/po/$file; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,772 done; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,772 for file in Makevars; do \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,772 rm -f /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/share/gettext/po/$file; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,772 done; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,772 else \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,772 : ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,773 fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,773 ../build-aux/install-sh -c -d /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_ for file in Makefile.in.in remove-potcdate.sin quot.sed boldquot.sed en@quot.header en@boldquot.header insert-header.sin Rules-quot Makevars.template; do \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,773 Making install in src install_environment.STDOUT DEBUG 2017-11-18 16:55:30,953 ../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1 /bin/sh ../libtool --mpackage_gdbm_1_11/ed2537bccffc/libtool: install: /usr/bin/install -c .ccffc/lib/libgdbm.4.dylib install_environment.STDOUT DEBUG 2017-11-18 16:55:30,957 laxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib && { ln -s -f | { rm -f libgdbm.dylib &}; }) install_environment.STDOUT DEBUG 2017-11-18 16:55:30,964 dbm.lai /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib/liblibtool: install: /usr/bi/ed2537bccffc/lib/libgdbm.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,975 _11/ed2537bccffc/lib' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,975 ode=install /usr/bin/install -c libgdbm.la '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/lib' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,975 ../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1 /bin/sh ../libtool --mpackage_gdbm_1_11/ed2537bccffc/libtool: install: /usr/bin/install -c .ccffc/lib/libgdbm.4.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,975 laxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib && { ln -s -f | { rm -f libgdbm.dylib &}; }) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,975 libs/libgdbm.4.dylib /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537blibtool: install: (cd /galibgdbm.4.dylib libgdbm.dylib |& ln -s libgdbm.4.dylib libgdbm.dylib; libtool: install: /usr/bin/install -c .libs/libggdbm.la tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,975 dbm.lai /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib/liblibtool: install: /usr/bi/ed2537bccffc/lib/libgdbm.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,976 n/install -c .libs/libgdbm.a /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11libtool: install: chmod 6a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:30,976 /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib/libgdbm.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,079 '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/bin' install_environment.STDOUT DEBUG 2017-11-18 16:55:31,080 44 /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib/libgdbm.libtool: install: ranlib ../build-aux/install-sh -c -d /bin/sh ../libtool --mode=install /uc/package_gdbm_1_11/ed2537bccffc/bin' install_environment.STDOUT DEBUG 2017-11-18 16:55:31,160 n/install -c .libs/gdbmtool /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/libtool: install: /usr/bi/ed2537bccffc/bin/gdbm_load tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,180 44 /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib/libgdbm.libtool: install: ranlib ../build-aux/install-sh -c -d /bin/sh ../libtool --mode=install /uc/package_gdbm_1_11/ed2537bccffc/bin' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,180 usr/bin/install -c gdbmtool gdbm_load gdbm_dump '/galaxydir/galaxy/database/dependencies/gdbm/1.11/ilibtool: install: /usr/bied2537bccffc/bin/gdbmtool tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,180 n/install -c .libs/gdbmtool /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/libtool: install: /usr/bi/ed2537bccffc/bin/gdbm_load install_environment.STDOUT DEBUG 2017-11-18 16:55:31,196 n/install -c .libs/gdbm_dump /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11 ../build-aux/install-sh install_environment.STDOUT DEBUG 2017-11-18 16:55:31,251 44 gdbm.h '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/inclMaking install in doc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,284 n/install -c .libs/gdbm_load /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11libtool: install: /usr/bi/ed2537bccffc/bin/gdbm_dump tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,284 n/install -c .libs/gdbm_dump /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11 ../build-aux/install-sh tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,284 -c -d '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/include' /usr/bin/install -c -m 6ude' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,284 44 gdbm.h '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/inclMaking install in doc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,284 make[2]: Nothing to be done for `install-exec-am'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,284 _11/ed2537bccffc/share/info' install_environment.STDOUT DEBUG 2017-11-18 16:55:31,333 ../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1 /usr/bin/install -c -m 6/share/info' install_environment.STDOUT DEBUG 2017-11-18 16:55:31,350 '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/share/info' '/dencies/gdbm/1.11/iuc/pacgdbm.info' install_environment.STDOUT DEBUG 2017-11-18 16:55:31,360 y/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/share/man/man1' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,389 ../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1 /usr/bin/install -c -m 6/share/info' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,390 '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/share/info' '/dencies/gdbm/1.11/iuc/pacgdbm.info' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,390 y/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/share/man/man1' install_environment.STDOUT DEBUG 2017-11-18 16:55:31,437 .1 '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/share/man/m ../build-aux/install-sh n/man3' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,493 44 ./gdbm.info '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc install-info --info-dir=galaxydir/galaxy/database/depenkage_gdbm_1_11/ed2537bccffc/share/info/ ../build-aux/install-sh -c -d '/galaxydir/galax /usr/bin/install -c -m 644 gdbm_dump.1 gdbm_load.1 gdbmtoolan1' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,494 .1 '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/share/man/m ../build-aux/install-sh n/man3' install_environment.STDOUT DEBUG 2017-11-18 16:55:31,519 44 gdbm.3 '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/sharMaking install in compat tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,594 -c -d '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/share/ma /usr/bin/install -c -m 6e/man/man3' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,595 44 gdbm.3 '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/sharMaking install in compat install_environment.STDOUT DEBUG 2017-11-18 16:55:31,612 _11/ed2537bccffc/lib' install_environment.STDOUT DEBUG 2017-11-18 16:55:31,619 ode=install /usr/bin/install -c libgdbm_compat.la '/galaxydir/galaxy/database/dependencies/gdbm/1.bccffc/lib' install_environment.STDOUT DEBUG 2017-11-18 16:55:31,661 libs/libgdbm_compat.4.dylib /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/libtool: install: (cd /galibgdbm_compat.4.dylib libgdbm_ibgdbm_compat.dylib && ln -s libgdbm_coib; }; }) install_environment.STDOUT DEBUG 2017-11-18 16:55:31,670 libs/libgdbm_compat.lai /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed25/gdbm/1.11/iuc/package_gdlibgdbm_compat.a install_environment.STDOUT DEBUG 2017-11-18 16:55:31,678 laxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib/libgdbm_compatlibtool: install: ranlib pat.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,706 _11/ed2537bccffc/lib' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,714 ode=install /usr/bin/install -c libgdbm_compat.la '/galaxydir/galaxy/database/dependencies/gdbm/1.bccffc/lib' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,714 ../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1 /bin/sh ../libtool --m11/iuc/package_gdbm_1_11/ed2537libtool: install: /usr/bin/install -c .ed2537bccffc/lib/libgdbm_compat.4.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,714 libs/libgdbm_compat.4.dylib /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/libtool: install: (cd /galibgdbm_compat.4.dylib libgdbm_ibgdbm_compat.dylib && ln -s libgdbm_coib; }; }) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,715 laxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib && { ln -s -f compat.dylib || { rm -f lmpat.4.dylib libgdbm_compat.dyllibtool: install: /usr/bin/install -c .37bccffc/lib/libgdbm_compat.la tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,715 libs/libgdbm_compat.lai /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed25/gdbm/1.11/iuc/package_gdlibgdbm_compat.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,715 libtool: install: /usr/bin/install -c .libs/libgdbm_compat.a /galaxydir/galaxy/database/dependenciesbm_1_11/ed2537bccffc/lib/libtool: install: chmod 644 /ga.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,715 laxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib/libgdbm_compatlibtool: install: ranlib pat.a install_environment.STDOUT DEBUG 2017-11-18 16:55:31,762 -c -d '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/include' /usr/bin/install -c -m 6c/include' install_environment.STDOUT DEBUG 2017-11-18 16:55:31,795 make[2]: Nothing to be done for `install-exec-am'. install_environment.STDOUT DEBUG 2017-11-18 16:55:31,813 make[2]: Nothing to be done for `install-exec-am'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,815 /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib/libgdbm_com ../build-aux/install-sh tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,815 -c -d '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/include' /usr/bin/install -c -m 6c/include' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,816 44 dbm.h ndbm.h '/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffMaking install in tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,816 make[2]: Nothing to be done for `install-exec-am'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,816 make[2]: Nothing to be done for `install-data-am'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,816 make[2]: Nothing to be done for `install-exec-am'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:gdbm DEBUG 2017-11-18 16:55:31,816 make[2]: Nothing to be done for `install-data-am'. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 16:55:32,094 Changing status for tool dependency gdbm from Installing to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:55:32,095 Updating an existing record for version 1.11 of tool dependency gdbm for revision ed2537bccffc of repository package_gdbm_1_11 by updating the status from Installing to Installed. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 16:55:32,141 Tool dependency gdbm version 1.11 has been installed in /galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc. 127.0.0.1 - - [18/Nov/2017:16:55:33 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:55:34,643 Creating a new record for version 1.2.8 of tool dependency zlib for revision 411985b46ae8 of repository package_zlib_1_2_8. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:55:34,704 Updating an existing record for version 1.2.8 of tool dependency zlib for revision 411985b46ae8 of repository package_zlib_1_2_8 by updating the status from Never installed to Installing. tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 16:55:34,730 Attempting to download via url: https://depot.galaxyproject.org/software/zlib/zlib_1.2.8_src_all.tar.gz tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 16:55:35,402 Successfully downloaded from url: https://depot.galaxyproject.org/software/zlib/zlib_1.2.8_src_all.tar.gz tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:35,402 + ./configure --prefix=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8 && make && make install tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:35,525 Checking for gcc... install_environment.STDOUT DEBUG 2017-11-18 16:55:35,724 Checking for shared library support... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:35,731 Checking for shared library support... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:35,835 Building shared library libz.1.2.8.dylib with gcc. install_environment.STDOUT DEBUG 2017-11-18 16:55:35,847 Checking for off64_t... No. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:35,936 Checking for off64_t... No. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:35,936 Checking for fseeko... Yes. install_environment.STDOUT DEBUG 2017-11-18 16:55:35,987 Checking for strerror... Yes. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:36,040 Checking for strerror... Yes. install_environment.STDOUT DEBUG 2017-11-18 16:55:36,137 Checking for stdarg.h... Yes. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:36,141 Checking for unistd.h... Yes. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:36,142 Checking for stdarg.h... Yes. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:36,247 Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf(). install_environment.STDOUT DEBUG 2017-11-18 16:55:36,276 Checking for vsnprintf() in stdio.h... Yes. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:36,352 Checking for vsnprintf() in stdio.h... Yes. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:36,352 Checking for return value of vsnprintf()... Yes. install_environment.STDOUT DEBUG 2017-11-18 16:55:36,395 Checking for attribute(visibility) support... Yes. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:36,454 Checking for attribute(visibility) support... Yes. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:36,454 gcc -O3 -DHAVE_HIDDEN -I. -c -o example.o test/example.c install_environment.STDOUT DEBUG 2017-11-18 16:55:36,570 gcc -O3 -DHAVE_HIDDEN -c -o adler32.o adler32.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:36,659 gcc -O3 -DHAVE_HIDDEN -c -o adler32.o adler32.c 127.0.0.1 - - [18/Nov/2017:16:55:36 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:36,760 gcc -O3 -DHAVE_HIDDEN -c -o crc32.o crc32.c install_environment.STDOUT DEBUG 2017-11-18 16:55:36,903 gcc -O3 -DHAVE_HIDDEN -c -o deflate.o deflate.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:36,971 gcc -O3 -DHAVE_HIDDEN -c -o deflate.o deflate.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:37,382 gcc -O3 -DHAVE_HIDDEN -c -o infback.o infback.c install_environment.STDOUT DEBUG 2017-11-18 16:55:37,660 gcc -O3 -DHAVE_HIDDEN -c -o inffast.o inffast.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:37,691 gcc -O3 -DHAVE_HIDDEN -c -o inffast.o inffast.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:37,898 gcc -O3 -DHAVE_HIDDEN -c -o inflate.o inflate.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:38,000 inflate.c:1507:61: warning: shifting a negative signed value is undefined [-Wshift-negative-value] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:38,000 if (strm == Z_NULL || strm->state == Z_NULL) return -1L << 16; tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:38,000 ~~~ ^ install_environment.STDOUT DEBUG 2017-11-18 16:55:38,481 gcc -O3 -DHAVE_HIDDEN -c -o inftrees.o inftrees.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:38,510 gcc -O3 -DHAVE_HIDDEN -c -o inftrees.o inftrees.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:38,510 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:38,712 gcc -O3 -DHAVE_HIDDEN -c -o trees.o trees.c install_environment.STDOUT DEBUG 2017-11-18 16:55:38,969 gcc -O3 -DHAVE_HIDDEN -c -o zutil.o zutil.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:39,017 gcc -O3 -DHAVE_HIDDEN -c -o zutil.o zutil.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:39,120 gcc -O3 -DHAVE_HIDDEN -c -o compress.o compress.c install_environment.STDOUT DEBUG 2017-11-18 16:55:39,122 gcc -O3 -DHAVE_HIDDEN -c -o uncompr.o uncompr.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:39,225 gcc -O3 -DHAVE_HIDDEN -c -o uncompr.o uncompr.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:39,225 gcc -O3 -DHAVE_HIDDEN -c -o gzclose.o gzclose.c install_environment.STDOUT DEBUG 2017-11-18 16:55:39,247 gcc -O3 -DHAVE_HIDDEN -c -o gzlib.o gzlib.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:39,329 gcc -O3 -DHAVE_HIDDEN -c -o gzlib.o gzlib.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:39,433 gcc -O3 -DHAVE_HIDDEN -c -o gzread.o gzread.c install_environment.STDOUT DEBUG 2017-11-18 16:55:39,509 gcc -O3 -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:39,533 gcc -O3 -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c install_environment.STDOUT DEBUG 2017-11-18 16:55:39,639 .o compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o install_environment.STDOUT DEBUG 2017-11-18 16:55:39,659 example example.o -L. libz.a install_environment.STDOUT DEBUG 2017-11-18 16:55:39,703 o minigzip.o test/minigzip.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:39,736 .o compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:39,737 example example.o -L. libz.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:39,737 o minigzip.o test/minigzip.c install_environment.STDOUT DEBUG 2017-11-18 16:55:39,811 gzip.o -L. libz.a 127.0.0.1 - - [18/Nov/2017:16:55:39 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:39,837 gzip.o -L. libz.a install_environment.STDOUT DEBUG 2017-11-18 16:55:39,858 ler32.o adler32.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:39,942 ler32.o adler32.c install_environment.STDOUT DEBUG 2017-11-18 16:55:39,984 c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:40,045 c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:40,150 libtool -o libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o inftrees.o trees.o zutilgcc -O3 -DHAVE_HIDDEN -ogcc -O3 -DHAVE_HIDDEN -I. -c -gcc -O3 -DHAVE_HIDDEN -o minigzip minigcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/adgcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c install_environment.STDOUT DEBUG 2017-11-18 16:55:40,583 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:40,663 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:40,868 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c install_environment.STDOUT DEBUG 2017-11-18 16:55:41,004 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:41,071 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:41,071 inflate.c:1507:61: warning: shifting a negative signed value is undefined [-Wshift-negative-value] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:41,071 if (strm == Z_NULL || strm->state == Z_NULL) return -1L << 16; tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:41,071 ~~~ ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:41,586 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:41,586 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 16:55:41,758 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:41,792 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:42,308 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c install_environment.STDOUT DEBUG 2017-11-18 16:55:42,323 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:42,409 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:42,409 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c install_environment.STDOUT DEBUG 2017-11-18 16:55:42,443 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:42,513 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:42,513 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c install_environment.STDOUT DEBUG 2017-11-18 16:55:42,613 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:42,613 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:42,822 gcc -O3 -fPIC -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c install_environment.STDOUT DEBUG 2017-11-18 16:55:42,876 gcc -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_HIDDEN -o libz.1.2.8.dylilate.lo infback.lo inffast.lo izutil.lo compress.lo uncompr.lo gzclose install_environment.STDOUT DEBUG 2017-11-18 16:55:42,909 ln -s libz.1.2.8.dylib libz.dylib install_environment.STDOUT DEBUG 2017-11-18 16:55:42,919 gcc -O3 -DHAVE_HIDDEN -o examplesh example.o -L. libz.1.2.8.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:42,924 gcc -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_HIDDEN -o libz.1.2.8.dylilate.lo infback.lo inffast.lo izutil.lo compress.lo uncompr.lo gzclose tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:42,924 2_8/411985b46ae8/lib/libz.1.dylib -compatibility_version 1 -current_version 1.2.8 -O3 -fPIC -DHAVE_b adler32.lo crc32.lo defnflate.lo inftrees.lo trees.lo .lo gzlib.lo gzread.lo gzwrite.lo -lc rm -f libz.dylib libz.1.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:42,924 ln -s libz.1.2.8.dylib libz.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:42,925 ln -s libz.1.2.8.dylib libz.1.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:42,925 gcc -O3 -DHAVE_HIDDEN -o examplesh example.o -L. libz.1.2.8.dylib 127.0.0.1 - - [18/Nov/2017:16:55:42 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:43,027 gcc -O3 -DHAVE_HIDDEN -o minigzipsh minigzip.o -L. libz.1.2.8.dylib install_environment.STDOUT DEBUG 2017-11-18 16:55:43,068 cp libz.a /galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/libchmod 644 /galaxydir/galacp libz.1.2.8.dylib /galaxydir/chmod 755 /galaxydir/galaxy/database/decp zlib.3 /galaxydir/galaxy/database/dependenciere/man/man3/zlib.3 install_environment.STDOUT DEBUG 2017-11-18 16:55:43,069 axy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib/pkgconfig install_environment.STDOUT DEBUG 2017-11-18 16:55:43,074 abase/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib/pkgconfig/zlib.pc install_environment.STDOUT DEBUG 2017-11-18 16:55:43,085 abase/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/include install_environment.STDOUT DEBUG 2017-11-18 16:55:43,092 s/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/include/zlib.h /galaxydir/galaxy/database/dependencconf.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:43,230 xy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib/libz.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:43,230 galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:43,230 pendencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib/libz.1.2.8.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:43,230 s/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/share/man/man3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:43,230 cp libz.a /galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/libchmod 644 /galaxydir/galacp libz.1.2.8.dylib /galaxydir/chmod 755 /galaxydir/galaxy/database/decp zlib.3 /galaxydir/galaxy/database/dependenciere/man/man3/zlib.3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:43,230 axy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib/pkgconfig tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:43,230 abase/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib/pkgconfig/zlib.pc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:43,230 abase/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/include tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:43,230 s/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/include/zlib.h /galaxydir/galaxy/database/dependencconf.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:zlib DEBUG 2017-11-18 16:55:43,231 chmod 644 /galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/shacp zlib.pc /galaxydir/galchmod 644 /galaxydir/galaxy/datcp zlib.h zconf.h /galaxydir/galaxy/datchmod 644 /galaxydir/galaxy/database/dependencieies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/include/z tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 16:55:43,375 Changing status for tool dependency zlib from Installing to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:55:43,375 Updating an existing record for version 1.2.8 of tool dependency zlib for revision 411985b46ae8 of repository package_zlib_1_2_8 by updating the status from Installing to Installed. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 16:55:43,409 Tool dependency zlib version 1.2.8 has been installed in /galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:55:46,039 Creating a new record for version 1.0.6 of tool dependency bzlib for revision af4887e1f595 of repository package_bzlib_1_0. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:55:46,114 Updating an existing record for version 1.0.6 of tool dependency bzlib for revision af4887e1f595 of repository package_bzlib_1_0 by updating the status from Never installed to Installing. 127.0.0.1 - - [18/Nov/2017:16:55:45 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 16:55:46,159 Proceeding with install and compile recipe for tool dependency bzlib. tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 16:55:46,159 Attempting to download via url: http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 16:55:48,070 Successfully downloaded from url: http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:48,070 + make && make install PREFIX=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib install_environment.STDOUT DEBUG 2017-11-18 16:55:48,100 If compilation produces errors, or a large number of warnings, install_environment.STDOUT DEBUG 2017-11-18 16:55:48,100 handle so-called 'large files' -- files of size 2GB or more. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:48,289 please read README.COMPILATION.PROBLEMS -- you might be able to tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:48,289 adjust the flags in this Makefile to improve matters. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:48,390 Also in README.COMPILATION.PROBLEMS are some hints that may help tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:48,390 If compilation produces errors, or a large number of warnings, tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:48,390 if your build produces an executable which is unable to correctly tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:48,492 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:48,492 handle so-called 'large files' -- files of size 2GB or more. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:48,800 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c install_environment.STDOUT DEBUG 2017-11-18 16:55:48,960 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:49,004 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c install_environment.STDOUT DEBUG 2017-11-18 16:55:49,053 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:49,106 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:49,106 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 127.0.0.1 - - [18/Nov/2017:16:55:49 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:49,723 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c install_environment.STDOUT DEBUG 2017-11-18 16:55:50,631 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:50,648 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c install_environment.STDOUT DEBUG 2017-11-18 16:55:51,019 ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o install_environment.STDOUT DEBUG 2017-11-18 16:55:51,041 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzip2.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,055 rm -f libbz2.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,055 ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,056 ranlib libbz2.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,056 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzip2.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,467 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2 bzip2.o -L. -lbz2 install_environment.STDOUT DEBUG 2017-11-18 16:55:51,481 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzip2recover.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,568 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzip2recover.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,568 bzip2recover.c:375:59: warning: length modifier 'L' results in undefined behavior or no effect with 'u' conversion specifier [-Wformat] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,568 fprintf ( stderr, " block %d runs from " MaybeUInt64_FMT tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,568 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,568 bzip2recover.c:40:29: note: expanded from macro 'MaybeUInt64_FMT' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,568 # define MaybeUInt64_FMT "%Lu" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,568 ~^~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,569 bzip2recover.c:375:59: note: did you mean to use 'll'? tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,569 bzip2recover.c:40:29: note: expanded from macro 'MaybeUInt64_FMT' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,569 # define MaybeUInt64_FMT "%Lu" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,569 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,569 bzip2recover.c:376:41: warning: length modifier 'L' results in undefined behavior or no effect with 'u' conversion specifier [-Wformat] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,569 " to " MaybeUInt64_FMT " (incomplete)\n", tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,569 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,569 bzip2recover.c:40:29: note: expanded from macro 'MaybeUInt64_FMT' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,569 # define MaybeUInt64_FMT "%Lu" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,569 ~^~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,570 bzip2recover.c:376:41: note: did you mean to use 'll'? tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,570 bzip2recover.c:40:29: note: expanded from macro 'MaybeUInt64_FMT' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,570 # define MaybeUInt64_FMT "%Lu" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,570 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,570 bzip2recover.c:397:56: warning: length modifier 'L' results in undefined behavior or no effect with 'u' conversion specifier [-Wformat] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,570 fprintf ( stderr, " block %d runs from " MaybeUInt64_FMT tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,570 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,570 bzip2recover.c:40:29: note: expanded from macro 'MaybeUInt64_FMT' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,570 # define MaybeUInt64_FMT "%Lu" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,570 ~^~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,570 bzip2recover.c:397:56: note: did you mean to use 'll'? tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,571 bzip2recover.c:40:29: note: expanded from macro 'MaybeUInt64_FMT' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,571 # define MaybeUInt64_FMT "%Lu" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,571 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,571 bzip2recover.c:398:38: warning: length modifier 'L' results in undefined behavior or no effect with 'u' conversion specifier [-Wformat] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,571 " to " MaybeUInt64_FMT "\n", tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,571 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,571 bzip2recover.c:40:29: note: expanded from macro 'MaybeUInt64_FMT' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,571 # define MaybeUInt64_FMT "%Lu" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,571 ~^~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,571 bzip2recover.c:398:38: note: did you mean to use 'll'? tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,571 bzip2recover.c:40:29: note: expanded from macro 'MaybeUInt64_FMT' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,571 # define MaybeUInt64_FMT "%Lu" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,572 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,675 gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2recover bzip2recover.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,676 4 warnings generated. install_environment.STDOUT DEBUG 2017-11-18 16:55:51,691 install_environment.STDOUT DEBUG 2017-11-18 16:55:51,709 ./bzip2 -2 < sample2.ref > sample2.rb2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,776 Doing 6 tests (3 compress, 3 uncompress) ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,776 If there's a problem, things might stop at this point. install_environment.STDOUT DEBUG 2017-11-18 16:55:51,787 ./bzip2 -d < sample1.bz2 > sample1.tst install_environment.STDOUT DEBUG 2017-11-18 16:55:51,819 ./bzip2 -ds < sample3.bz2 > sample3.tst install_environment.STDOUT DEBUG 2017-11-18 16:55:51,838 cmp sample2.bz2 sample2.rb2 install_environment.STDOUT DEBUG 2017-11-18 16:55:51,844 cmp sample1.tst sample1.ref install_environment.STDOUT DEBUG 2017-11-18 16:55:51,855 cmp sample3.tst sample3.ref install_environment.STDOUT DEBUG 2017-11-18 16:55:51,861 If you got this far and the 'cmp's didn't complain, it looks install_environment.STDOUT DEBUG 2017-11-18 16:55:51,861 install_environment.STDOUT DEBUG 2017-11-18 16:55:51,861 /usr/local/include, type install_environment.STDOUT DEBUG 2017-11-18 16:55:51,861 make install install_environment.STDOUT DEBUG 2017-11-18 16:55:51,861 To install somewhere else, eg, /xxx/yyy/{bin,lib,man,include}, type install_environment.STDOUT DEBUG 2017-11-18 16:55:51,862 make install PREFIX=/xxx/yyy install_environment.STDOUT DEBUG 2017-11-18 16:55:51,862 install_environment.STDOUT DEBUG 2017-11-18 16:55:51,862 If you are (justifiably) paranoid and want to see what 'make install' install_environment.STDOUT DEBUG 2017-11-18 16:55:51,862 is going to do, you can first do install_environment.STDOUT DEBUG 2017-11-18 16:55:51,862 install_environment.STDOUT DEBUG 2017-11-18 16:55:51,862 make -n install or install_environment.STDOUT DEBUG 2017-11-18 16:55:51,862 make -n install PREFIX=/xxx/yyy respectively. install_environment.STDOUT DEBUG 2017-11-18 16:55:51,862 install_environment.STDOUT DEBUG 2017-11-18 16:55:51,862 The -n instructs make to show the commands it would execute, but install_environment.STDOUT DEBUG 2017-11-18 16:55:51,862 not actually execute them. install_environment.STDOUT DEBUG 2017-11-18 16:55:51,862 install_environment.STDOUT DEBUG 2017-11-18 16:55:51,862 Instructions for use are in the preformatted manual page, in the file install_environment.STDOUT DEBUG 2017-11-18 16:55:51,862 bzip2.txt. For more detailed documentation, read the full manual. install_environment.STDOUT DEBUG 2017-11-18 16:55:51,863 It is available in Postscript form (manual.ps), PDF form (manual.pdf), install_environment.STDOUT DEBUG 2017-11-18 16:55:51,863 and HTML form (manual.html). install_environment.STDOUT DEBUG 2017-11-18 16:55:51,863 install_environment.STDOUT DEBUG 2017-11-18 16:55:51,863 You can also do "bzip2 --help" to see some helpful information. install_environment.STDOUT DEBUG 2017-11-18 16:55:51,863 "bzip2 -L" displays the software license. install_environment.STDOUT DEBUG 2017-11-18 16:55:51,863 install_environment.STDOUT DEBUG 2017-11-18 16:55:51,879 if ( test ! -d /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f591_0/af4887e1f595/bzlib/biif ( test ! -d /galaxydir/galaxgalaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib ; fi install_environment.STDOUT DEBUG 2017-11-18 16:55:51,884 /galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/man ) ; then mkdi/dependencies/bzlib/1.0.6ib/man ; fi install_environment.STDOUT DEBUG 2017-11-18 16:55:51,895 encies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/man/man1 ) ; then mkdir -p /galaxydir/ga/af4887e1f595/bzlib/man/mif ( test ! -d /galaxydir/galax-p /galaxydir/galaxy/database/dependencge_bzlib_1_0/af4887e1f595/bzlib/include ; fi install_environment.STDOUT DEBUG 2017-11-18 16:55:51,901 atabase/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzip2 install_environment.STDOUT DEBUG 2017-11-18 16:55:51,928 cp -f bzip2 /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bcp -f bzip2 /galaxydir/gacp -f bzip2recover /galaxydir/gchmod a+x /galaxydir/galaxy/database/dechmod a+x /galaxydir/galaxy/database/dependenciechmod a+x /galaxydir/galaxy/database/dependencies/bzlib/1.0.chmod a+x /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bcp -f bzip2.1 /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887chmod a+r /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/man/man1/bzip2.cp -f bzlib.h /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include install_environment.STDOUT DEBUG 2017-11-18 16:55:51,930 ib/include/bzlib.h install_environment.STDOUT DEBUG 2017-11-18 16:55:51,932 /galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib install_environment.STDOUT DEBUG 2017-11-18 16:55:51,935 abase/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib/libbz2.a install_environment.STDOUT DEBUG 2017-11-18 16:55:51,938 /dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzgrep install_environment.STDOUT DEBUG 2017-11-18 16:55:51,945 /bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzgrep /galaxydir/galaxy/database/dependenn/bzegrep install_environment.STDOUT DEBUG 2017-11-18 16:55:51,958 lib_1_0/af4887e1f595/bzlib/bin/bzgrep /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/packagchmod a+x /galaxydir/galacp -f bzmore /galaxydir/galaxy/ln -s -f /galaxydir/galaxy/database/dep/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/less install_environment.STDOUT DEBUG 2017-11-18 16:55:51,960 abase/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzmore install_environment.STDOUT DEBUG 2017-11-18 16:55:51,962 /dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzdiff install_environment.STDOUT DEBUG 2017-11-18 16:55:51,964 /bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzdiff /galaxydir/galaxy/database/dependenn/bzcmp install_environment.STDOUT DEBUG 2017-11-18 16:55:51,966 zlib_1_0/af4887e1f595/bzlib/bin/bzdiff install_environment.STDOUT DEBUG 2017-11-18 16:55:51,968 ge_bzlib_1_0/af4887e1f595/bzlib/man/man1 install_environment.STDOUT DEBUG 2017-11-18 16:55:51,972 .1 install_environment.STDOUT DEBUG 2017-11-18 16:55:51,982 chmod a+r /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlecho ".so man1/bzgrep.1" an1/bzegrep.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,983 ./bzip2 -1 < sample1.ref > sample1.rb2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,983 ./bzip2 -2 < sample2.ref > sample2.rb2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,983 ./bzip2 -3 < sample3.ref > sample3.rb2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,983 ./bzip2 -d < sample1.bz2 > sample1.tst tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,983 ./bzip2 -d < sample2.bz2 > sample2.tst tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,983 ./bzip2 -ds < sample3.bz2 > sample3.tst tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,983 cmp sample1.bz2 sample1.rb2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,983 cmp sample2.bz2 sample2.rb2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,983 cmp sample3.bz2 sample3.rb2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,984 cmp sample1.tst sample1.ref tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,984 cmp sample2.tst sample2.ref tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:51,984 cmp sample3.tst sample3.ref install_environment.STDOUT DEBUG 2017-11-18 16:55:51,990 > /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/man/mecho ".so man1/bzmore.1" an1/bzless.1 install_environment.STDOUT DEBUG 2017-11-18 16:55:51,999 > /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/man/m tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,085 If you got this far and the 'cmp's didn't complain, it looks tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,085 like you're in business. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,186 To install in /usr/local/bin, /usr/local/lib, /usr/local/man and tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,187 /usr/local/include, type tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,287 make install tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,392 To install somewhere else, eg, /xxx/yyy/{bin,lib,man,include}, type tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,393 make install PREFIX=/xxx/yyy 127.0.0.1 - - [18/Nov/2017:16:55:52 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,497 If you are (justifiably) paranoid and want to see what 'make install' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,497 is going to do, you can first do tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,598 make -n install or tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,598 make -n install PREFIX=/xxx/yyy respectively. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,703 The -n instructs make to show the commands it would execute, but tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,703 not actually execute them. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,804 Instructions for use are in the preformatted manual page, in the file tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,804 bzip2.txt. For more detailed documentation, read the full manual. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,804 It is available in Postscript form (manual.ps), PDF form (manual.pdf), tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,804 and HTML form (manual.html). tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,908 You can also do "bzip2 --help" to see some helpful information. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:52,908 "bzip2 -L" displays the software license. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,115 5/bzlib/bin ) ; then mkdir -p /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_n ; fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,115 if ( test ! -d /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f591_0/af4887e1f595/bzlib/biif ( test ! -d /galaxydir/galaxgalaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib ; fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,115 /galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/man ) ; then mkdi/dependencies/bzlib/1.0.6ib/man ; fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,115 y/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib ) ; then mkdir -p /if ( test ! -d /galaxydirr -p /galaxydir/galaxy/database/iuc/package_bzlib_1_0/af4887e1f595/bzlif ( test ! -d /galaxydir/galaxy/database/dependlaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0an1 ; fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,115 encies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/man/man1 ) ; then mkdir -p /galaxydir/ga/af4887e1f595/bzlib/man/mif ( test ! -d /galaxydir/galax-p /galaxydir/galaxy/database/dependencge_bzlib_1_0/af4887e1f595/bzlib/include ; fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,116 atabase/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzip2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,116 y/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include ) ; then mkdir ies/bzlib/1.0.6/iuc/packacp -f bzip2 /galaxydir/galaxy/dzlib/bin/bunzip2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,116 laxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzcat tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,116 alaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzip2recover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,116 pendencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzip2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,117 s/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bunzip2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,117 6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzcat tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,117 zlib_1_0/af4887e1f595/bzlib/bin/bzip2recover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,117 e1f595/bzlib/man/man1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,118 1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,118 cp -f bzip2 /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bcp -f bzip2 /galaxydir/gacp -f bzip2recover /galaxydir/gchmod a+x /galaxydir/galaxy/database/dechmod a+x /galaxydir/galaxy/database/dependenciechmod a+x /galaxydir/galaxy/database/dependencies/bzlib/1.0.chmod a+x /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bcp -f bzip2.1 /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887chmod a+r /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/man/man1/bzip2.cp -f bzlib.h /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,118 ib/include/bzlib.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,118 /galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,118 abase/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib/libbz2.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,119 /dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzgrep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,119 /bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzgrep /galaxydir/galaxy/database/dependenn/bzegrep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,119 chmod a+r /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlcp -f libbz2.a /galaxydirchmod a+r /galaxydir/galaxy/datcp -f bzgrep /galaxydir/galaxy/databaseln -s -f /galaxydir/galaxy/database/dependenciescies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/biln -s -f /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bze_bzlib_1_0/af4887e1f595/bzlib/bin/bzfgrep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,119 xy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzgrep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,119 database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzmore tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,120 lib_1_0/af4887e1f595/bzlib/bin/bzgrep /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/packagchmod a+x /galaxydir/galacp -f bzmore /galaxydir/galaxy/ln -s -f /galaxydir/galaxy/database/dep/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/less tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,120 abase/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzmore tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,120 /dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzdiff tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,120 /bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzdiff /galaxydir/galaxy/database/dependenn/bzcmp tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,120 zlib_1_0/af4887e1f595/bzlib/bin/bzdiff tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,121 ge_bzlib_1_0/af4887e1f595/bzlib/man/man1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,121 .1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,121 endencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin/bzmore /galaxydir/galaxy/databaseaf4887e1f595/bzlib/bin/bzchmod a+x /galaxydir/galaxy/datcp -f bzdiff /galaxydir/galaxy/databaseln -s -f /galaxydir/galaxy/database/dependenciescies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bichmod a+x /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bcp -f bzgrep.1 bzmore.1 bzdiff.1 /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/packachmod a+r /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/man/man1/bzgrepchmod a+r /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/man/man1/bzmore.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,121 ib/man/man1/bzdiff.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,121 chmod a+r /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlecho ".so man1/bzgrep.1" an1/bzegrep.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,122 > /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/man/mecho ".so man1/bzgrep.1" an1/bzfgrep.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,122 > /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/man/mecho ".so man1/bzmore.1" an1/bzless.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,122 > /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/man/mecho ".so man1/bzdiff.1" an1/bzcmp.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:bzlib DEBUG 2017-11-18 16:55:53,122 > /galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/man/m tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 16:55:53,239 Changing status for tool dependency bzlib from Installing to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:55:53,240 Updating an existing record for version 1.0.6 of tool dependency bzlib for revision af4887e1f595 of repository package_bzlib_1_0 by updating the status from Installing to Installed. 127.0.0.1 - - [18/Nov/2017:16:55:55 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:55:55,806 Creating a new record for version 2.4 of tool dependency libtool for revision 7f67694b167c of repository package_libtool_2_4. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:55:55,861 Updating an existing record for version 2.4 of tool dependency libtool for revision 7f67694b167c of repository package_libtool_2_4 by updating the status from Never installed to Installing. tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 16:55:55,885 Attempting to download via url: ftp://ftp.gnu.org/gnu/libtool/libtool-2.4.tar.gz tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 16:55:57,182 Successfully downloaded from url: ftp://ftp.gnu.org/gnu/libtool/libtool-2.4.tar.gz tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:57,183 + ./configure --prefix=/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c && make && make install install_environment.STDOUT DEBUG 2017-11-18 16:55:57,499 ## Configuring libtool 2.4 ## tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:57,499 ## ----------------------- ## tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:57,500 ## ----------------------- ## tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:57,500 ## Configuring libtool 2.4 ## install_environment.STDOUT DEBUG 2017-11-18 16:55:57,521 checking for a BSD-compatible install... /usr/bin/install -c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:57,603 checking for a BSD-compatible install... /usr/bin/install -c install_environment.STDOUT DEBUG 2017-11-18 16:55:58,555 checking for a thread-safe mkdir -p... libltdl/config/install-sh -c -d install_environment.STDOUT DEBUG 2017-11-18 16:55:58,556 checking for mawk... no install_environment.STDOUT DEBUG 2017-11-18 16:55:58,557 checking for awk... awk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,632 checking whether build environment is sane... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,632 checking for a thread-safe mkdir -p... libltdl/config/install-sh -c -d tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,633 checking for gawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,633 checking for mawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,633 checking for nawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,633 checking for awk... awk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,633 checking whether make sets $(MAKE)... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:58,768 checking build system type... x86_64-apple-darwin15.6.0 install_environment.STDOUT DEBUG 2017-11-18 16:55:58,769 configure: autobuild project... GNU Libtool install_environment.STDOUT DEBUG 2017-11-18 16:55:58,773 configure: autobuild hostname... CFM5081985.fda.gov install_environment.STDOUT DEBUG 2017-11-18 16:55:58,777 checking for gcc... gcc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,838 checking build system type... x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,838 checking host system type... x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,838 configure: autobuild project... GNU Libtool tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,838 configure: autobuild revision... 2.4 () tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,838 configure: autobuild mode... default tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,839 configure: autobuild hostname... CFM5081985.fda.gov tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,839 configure: autobuild timestamp... 20171118T215558Z tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:58,839 checking for gcc... gcc 127.0.0.1 - - [18/Nov/2017:16:55:58 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:55:58,974 checking for C compiler default output file name... a.out tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:59,045 checking whether the C compiler works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:59,046 checking for C compiler default output file name... a.out tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:59,046 checking for suffix of executables... install_environment.STDOUT DEBUG 2017-11-18 16:55:59,095 checking whether we are cross compiling... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:59,147 checking whether we are cross compiling... no install_environment.STDOUT DEBUG 2017-11-18 16:55:59,192 checking whether we are using the GNU C compiler... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:59,252 checking for suffix of object files... o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:59,252 checking whether we are using the GNU C compiler... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:59,252 checking whether gcc accepts -g... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:59,308 checking for gcc option to accept ISO C89... none needed tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:59,353 checking for gcc option to accept ISO C89... none needed tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:59,353 checking for style of include used by make... GNU install_environment.STDOUT DEBUG 2017-11-18 16:55:59,441 checking dependency style of gcc... gcc3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:59,456 checking dependency style of gcc... gcc3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:59,659 checking whether gcc and cc understand -c and -o together... yes install_environment.STDOUT DEBUG 2017-11-18 16:55:59,682 checking how to run the C preprocessor... gcc -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:59,761 checking how to run the C preprocessor... gcc -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:55:59,865 checking how to print strings... printf install_environment.STDOUT DEBUG 2017-11-18 16:55:59,997 checking for a sed that does not truncate output... /usr/bin/sed tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,075 checking for a sed that does not truncate output... /usr/bin/sed install_environment.STDOUT DEBUG 2017-11-18 16:56:00,188 checking for egrep... /usr/bin/grep -E install_environment.STDOUT DEBUG 2017-11-18 16:56:00,218 checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld install_environment.STDOUT DEBUG 2017-11-18 16:56:00,239 checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,279 checking for grep that handles long lines and -e... /usr/bin/grep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,279 checking for egrep... /usr/bin/grep -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,279 checking for fgrep... /usr/bin/grep -F tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,279 checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,279 checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,280 checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B install_environment.STDOUT DEBUG 2017-11-18 16:56:00,304 checking whether ln -s works... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:00,316 checking whether the shell understands some XSI constructs... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:00,328 checking how to convert x86_64-apple-darwin15.6.0 file names to x86_64-apple-darwin15.6.0 format... checking how to convert xchecking for /Library/Developerchecking for objdump... no install_environment.STDOUT DEBUG 2017-11-18 16:56:00,330 checking for dlltool... no install_environment.STDOUT DEBUG 2017-11-18 16:56:00,332 checking for ar... ar tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,380 checking the name lister (/usr/bin/nm -B) interface... BSD nm tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,380 checking whether ln -s works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,380 checking the maximum length of command line arguments... 196608 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,380 checking whether the shell understands some XSI constructs... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,380 checking whether the shell understands "+="... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,380 func_convert_file_noop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,381 86_64-apple-darwin15.6.0 file names to toolchain format... func_convert_file_noop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,381 /CommandLineTools/usr/bin/ld option to reload object files... -r tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,381 checking how to convert x86_64-apple-darwin15.6.0 file names to x86_64-apple-darwin15.6.0 format... checking how to convert xchecking for /Library/Developerchecking for objdump... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,381 checking how to recognize dependent libraries... pass_all tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,381 checking for dlltool... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,381 checking how to associate runtime and link libraries... printf %s\n tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,381 checking for ar... ar install_environment.STDOUT DEBUG 2017-11-18 16:56:00,390 checking for strip... strip tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,482 checking for archiver @FILE support... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,482 checking for ranlib... ranlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,482 checking for strip... strip install_environment.STDOUT DEBUG 2017-11-18 16:56:00,617 checking for sysroot... no install_environment.STDOUT DEBUG 2017-11-18 16:56:00,628 checking if : is a manifest tool... no install_environment.STDOUT DEBUG 2017-11-18 16:56:00,631 checking for nmedit... nmedit install_environment.STDOUT DEBUG 2017-11-18 16:56:00,633 checking for otool... otool tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,685 checking command to parse /usr/bin/nm -B output from gcc object... ok tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,685 checking for sysroot... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,686 checking for mt... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,686 checking if : is a manifest tool... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,686 checking for dsymutil... dsymutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,686 checking for nmedit... nmedit tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,686 checking for lipo... lipo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,686 checking for otool... otool tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,686 checking for otool64... no install_environment.STDOUT DEBUG 2017-11-18 16:56:00,696 checking for -single_module linker flag... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,788 checking for -single_module linker flag... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,788 checking for -exported_symbols_list linker flag... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:00,887 checking for -force_load linker flag... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:00,888 checking for -force_load linker flag... no install_environment.STDOUT DEBUG 2017-11-18 16:56:01,182 checking for sys/types.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:01,199 checking for ANSI C header files... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:01,199 checking for sys/types.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:01,302 checking for sys/stat.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:01,321 checking for stdlib.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:01,407 checking for stdlib.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:01,408 checking for string.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:01,465 checking for memory.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:01,513 checking for memory.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:01,616 checking for strings.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:01,634 checking for inttypes.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:01,719 checking for inttypes.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:01,719 checking for stdint.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:01,785 checking for unistd.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:01,820 checking for unistd.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:01,881 checking for objdir... .libs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:01,924 checking for dlfcn.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:01,924 checking for objdir... .libs 127.0.0.1 - - [18/Nov/2017:16:56:01 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:56:02,078 checking for gcc option to produce PIC... -fno-common -DPIC tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,128 checking if gcc supports -fno-rtti -fno-exceptions... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,128 checking for gcc option to produce PIC... -fno-common -DPIC install_environment.STDOUT DEBUG 2017-11-18 16:56:02,187 checking if gcc static flag -static works... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,233 checking if gcc PIC flag -fno-common -DPIC works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,233 checking if gcc static flag -static works... no install_environment.STDOUT DEBUG 2017-11-18 16:56:02,259 checking if gcc supports -c -o file.o... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 16:56:02,318 checking dynamic linker characteristics... darwin15.6.0 dyld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,333 checking if gcc supports -c -o file.o... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,334 checking if gcc supports -c -o file.o... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,334 checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,335 checking dynamic linker characteristics... darwin15.6.0 dyld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,335 checking how to hardcode library paths into programs... immediate install_environment.STDOUT DEBUG 2017-11-18 16:56:02,389 checking for dlopen in -ldl... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,436 checking for dlopen in -ldl... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,541 checking whether a program can dlopen itself... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:02,561 checking whether a statically linked program can dlopen itself... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:02,568 checking if libtool supports shared libraries... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:02,569 checking whether to build static libraries... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:02,575 checking which variable specifies run-time module search path... DYLD_LIBRARY_PATH tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,645 checking whether a statically linked program can dlopen itself... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,645 checking whether stripping libraries is possible... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,646 checking if libtool supports shared libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,646 checking whether to build shared libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,646 checking whether to build static libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,646 checking which extension is used for runtime loadable modules... .so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,646 checking which variable specifies run-time module search path... DYLD_LIBRARY_PATH tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,646 checking for the default library search path... /usr/local/lib /lib /usr/lib install_environment.STDOUT DEBUG 2017-11-18 16:56:02,660 checking for library containing dlopen... none required tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,750 checking for library containing dlopen... none required tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,750 checking for dlerror... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:02,811 checking for shl_load... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,853 checking for shl_load... no install_environment.STDOUT DEBUG 2017-11-18 16:56:02,943 checking for dld_link in -ldld... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,953 checking for shl_load in -ldld... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:02,954 checking for dld_link in -ldld... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,055 checking for _ prefix in compiled symbols... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:03,089 checking whether we have to add an underscore for dlsym... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,156 checking whether we have to add an underscore for dlsym... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,156 checking whether deplibs are loaded by dlopen... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:03,161 checking for argz.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,260 checking for argz.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,260 checking for error_t... no install_environment.STDOUT DEBUG 2017-11-18 16:56:03,291 checking for argz_add... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,364 checking for argz_add... no install_environment.STDOUT DEBUG 2017-11-18 16:56:03,456 checking for argz_count... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,465 checking for argz_append... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,465 checking for argz_count... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,571 checking for argz_create_sep... no install_environment.STDOUT DEBUG 2017-11-18 16:56:03,629 checking for argz_insert... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,671 checking for argz_insert... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,776 checking for argz_next... no install_environment.STDOUT DEBUG 2017-11-18 16:56:03,803 checking for argz_stringify... no install_environment.STDOUT DEBUG 2017-11-18 16:56:03,810 checking for unistd.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,882 checking for argz_stringify... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,882 checking whether libtool supports -dlopen/-dlpreopen... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,882 checking for unistd.h... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 16:56:03,976 checking for sys/dl.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,982 checking for dl.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:03,983 checking for sys/dl.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:04,086 checking for dld.h... no install_environment.STDOUT DEBUG 2017-11-18 16:56:04,148 checking for mach-o/dyld.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:04,187 checking for mach-o/dyld.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:04,293 checking for dirent.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:04,308 checking for closedir... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:04,393 checking for closedir... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:04,481 checking for readdir... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:04,493 checking for opendir... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:04,493 checking for readdir... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:04,594 checking for strlcat... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:04,671 checking for strlcpy... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:04,695 checking for strlcpy... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:04,696 checking for g++... g++ install_environment.STDOUT DEBUG 2017-11-18 16:56:04,880 checking whether we are using the GNU C++ compiler... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:04,903 checking whether we are using the GNU C++ compiler... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,007 checking whether g++ accepts -g... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:05,043 checking dependency style of g++... gcc3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,112 checking dependency style of g++... gcc3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,313 checking how to run the C++ preprocessor... g++ -E 127.0.0.1 - - [18/Nov/2017:16:56:05 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:56:05,565 checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,621 checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,621 checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,621 raries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,725 o produce PIC... -fno-common -DPIC tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,826 ommon -DPIC works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,826 ks... no install_environment.STDOUT DEBUG 2017-11-18 16:56:05,912 checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libchecking for g++ option tchecking if g++ PIC flag -fno-cchecking if g++ static flag -static worchecking if g++ supports -c -o file.o... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:05,918 checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libchecking dynamic linker cchecking how to hardcode librarchecking for g77... no install_environment.STDOUT DEBUG 2017-11-18 16:56:05,919 checking for f77... no install_environment.STDOUT DEBUG 2017-11-18 16:56:05,921 checking for pgf77... no install_environment.STDOUT DEBUG 2017-11-18 16:56:05,923 checking for fort77... no install_environment.STDOUT DEBUG 2017-11-18 16:56:05,925 checking for af77... no install_environment.STDOUT DEBUG 2017-11-18 16:56:05,926 checking for f90... no install_environment.STDOUT DEBUG 2017-11-18 16:56:05,928 checking for pghpf... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,928 checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libchecking for g++ option tchecking if g++ PIC flag -fno-cchecking if g++ static flag -static worchecking if g++ supports -c -o file.o... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,928 checking if g++ supports -c -o file.o... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,928 raries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,929 haracteristics... darwin15.6.0 dyld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,929 y paths into programs... immediate tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,929 checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libchecking dynamic linker cchecking how to hardcode librarchecking for g77... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,929 checking for xlf... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,929 checking for f77... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,929 checking for frt... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,929 checking for pgf77... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,930 checking for cf77... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,930 checking for fort77... no install_environment.STDOUT DEBUG 2017-11-18 16:56:05,930 checking for gfortran... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,930 checking for fl32... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,930 checking for af77... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,930 checking for xlf90... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,930 checking for f90... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,931 checking for pgf90... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,931 checking for pghpf... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,931 checking for epcf90... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,931 checking for gfortran... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:05,931 checking for g95... no install_environment.STDOUT DEBUG 2017-11-18 16:56:05,931 checking for xlf95... no install_environment.STDOUT DEBUG 2017-11-18 16:56:05,933 checking for fort... no install_environment.STDOUT DEBUG 2017-11-18 16:56:05,935 checking for ifc... no install_environment.STDOUT DEBUG 2017-11-18 16:56:05,936 checking for pgfortran... no install_environment.STDOUT DEBUG 2017-11-18 16:56:05,938 checking for lf95... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,031 checking for xlf95... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,032 checking for f95... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,032 checking for fort... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,032 checking for ifort... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,032 checking for ifc... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,032 checking for efc... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,032 checking for pgfortran... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,033 checking for pgf95... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,033 checking for lf95... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,033 checking for ftn... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,069 checking whether we are using the GNU Fortran 77 compiler... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,130 checking for gfortran... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,131 checking for xlf95... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,133 checking for fort... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,134 checking whether we are using the GNU Fortran 77 compiler... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,134 checking whether accepts -g... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,134 checking for gfortran... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,134 checking for g95... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,134 checking for xlf95... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,134 checking for f95... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,134 checking for ifc... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,135 checking for fort... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,135 checking for ifort... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,135 checking for ifc... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,136 checking for pgfortran... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,137 checking for lf95... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,139 checking for xlf90... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,140 checking for pgf90... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,142 checking for epcf90... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,144 checking for xlf... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,146 checking for frt... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,147 checking for cf77... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,149 checking for fl32... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,239 checking for efc... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,240 checking for pgfortran... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,240 checking for pgf95... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,240 checking for lf95... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,240 checking for ftn... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,240 checking for xlf90... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,240 checking for f90... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,240 checking for pgf90... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,240 checking for pghpf... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,240 checking for epcf90... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,240 checking for g77... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,240 checking for xlf... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,241 checking for f77... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,241 checking for frt... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,241 checking for pgf77... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,241 checking for cf77... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,241 checking for fort77... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,241 checking for fl32... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,241 checking for af77... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,280 checking whether we are using the GNU Fortran compiler... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,340 checking for gcj... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,345 checking whether we are using the GNU Fortran compiler... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,345 checking whether accepts -g... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,345 checking for gcj... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,448 checking for windres... no install_environment.STDOUT DEBUG 2017-11-18 16:56:06,547 checking whether make supports order-only prerequisites... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,549 checking whether make supports order-only prerequisites... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:06,653 configure: creating ./config.status 127.0.0.1 - - [18/Nov/2017:16:56:08 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:56:08,984 config.status: creating Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,013 config.status: creating Makefile install_environment.STDOUT DEBUG 2017-11-18 16:56:09,061 config.status: executing tests/atconfig commands tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,115 config.status: creating config.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,115 config.status: executing tests/atconfig commands tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,115 config.status: executing depfiles commands install_environment.STDOUT DEBUG 2017-11-18 16:56:09,212 config.status: executing libtool commands tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,216 config.status: executing libtool commands tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,627 rm -f libtoolize.tmp libtoolize tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,628 $2" ;; *) TIMESTAMP="" ;; esac; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,628 bin/grep -E,g' -e 's,@FGREP\@,/usr/bin/grep -F,g' -e 's,@GREP\@,/usr/bin/grep,g' -e 's,@LN_S\@,ln -s,g' -e 's,@MACRO_VERSION\@,2.4,g' -e 's,@PACKAGE\@,libtool,g' -e 's,@PACKAGE_BUGREPORT\@,bug-libtool@gnu.org,g' -e 's,@PACKAGE_URL\@,http://www.gnu.org/software/libtool/,g' -e 's,@PACKAGE_NAME\@,GNU Libtool,g' -e 's,@PACKAGE_STRING\@,GNU Libtool 2.4,g' -e 's,@PACKAGE_TARNAME\@,libtool,g' -e 's,@PACKAGE_VERSION\@,2.4,g' -e 's,@SED\@,/usr/bin/sed,g' -e 's,@VERSION\@,2.4,g' -e 's,@aclocaldir\@,/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/aclocal,g' -e 's,@datadir\@,/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share,g' -e 's,@pkgdatadir\@,/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/libtool,g' -e 's,@host_triplet\@,x86_64-apple-darwin15.6.0,g' -e 's,@prefix\@,/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c,g' -e "s,@TIMESTAMP\@,$TIMESTAMP,g" \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,628 -e 's,@aclocal_DATA\@,m4/argz.m4 m4/libtool.m4 m4/ltdl.m4 m4/ltoptions.m4 m4/ltsugar.m4 m4/ltversion.m4 m4/lt~obsolete.m4,g' \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,628 -e "s,@pkgltdl_files\@,libltdl/COPYING.LIB libltdl/README libltdl/Makefile.inc libltdl/Makefile.am libltdl/configure.ac libltdl/aclocal.m4 libltdl/Makefile.in libltdl/config-h.in libltdl/configure libltdl/argz_.h libltdl/argz.c libltdl/loaders/dld_link.c libltdl/loaders/dlopen.c libltdl/loaders/dyld.c libltdl/loaders/load_add_on.c libltdl/loaders/loadlibrary.c libltdl/loaders/shl_load.c libltdl/lt__dirent.c libltdl/lt__strl.c libltdl/libltdl/lt__alloc.h libltdl/libltdl/lt__dirent.h libltdl/libltdl/lt__glibc.h libltdl/libltdl/lt__private.h libltdl/libltdl/lt__strl.h libltdl/libltdl/lt_dlloader.h libltdl/libltdl/lt_error.h libltdl/libltdl/lt_system.h libltdl/libltdl/slist.h libltdl/loaders/preopen.c libltdl/lt__alloc.c libltdl/lt_dlloader.c libltdl/lt_error.c libltdl/ltdl.c libltdl/ltdl.h libltdl/slist.c,g" \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,628 -e "s,@pkgconfig_files\@,config/compile config/config.guess config/config.sub config/depcomp config/install-sh config/missing config/ltmain.sh,g" \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,628 ./libtoolize.in > libtoolize.tmp install_environment.STDOUT DEBUG 2017-11-18 16:56:09,679 set dummy `/bin/sh ./libltdl/config/mkstamp .`; shift; case 2.4 in *[acegikmoqsuwy]) TIMESTAMP=" $1 sed -e 's,@EGREP\@,/usr/chmod a-w libtoolize.tmp tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,732 chmod a+x libtoolize.tmp tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,732 set dummy `/bin/sh ./libltdl/config/mkstamp .`; shift; case 2.4 in *[acegikmoqsuwy]) TIMESTAMP=" $1 sed -e 's,@EGREP\@,/usr/chmod a-w libtoolize.tmp tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,732 mv -f libtoolize.tmp libtoolize tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,732 -d . libltdl/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,732 tdl/argz.h-t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,733 z.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,733 /bin/make all-recursive install_environment.STDOUT DEBUG 2017-11-18 16:56:09,743 /bin/sh /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdUscPyu/libtool-2.4/libltdl/config/install-sh cp ./libltdl/argz_.h liblmv libltdl/argz.h-t libltdl/arg/Library/Developer/CommandLineTools/usr/bin/sh ./libtool --tag=CC --mode=compile gccltdl -I./libltdl/libltdl -g -O2 -MT libltdl/loaders/libltdMD -MP -MF libltdl/loaders/.deps/libltdl_libltdl_la-preopen.Tpo -c -o libltreopen.lo `test -f 'libltdl/loaders/preopen.c' || echo './'`libltdl/loaders/preopen.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,835 /bin/sh /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdUscPyu/libtool-2.4/libltdl/config/install-sh cp ./libltdl/argz_.h liblmv libltdl/argz.h-t libltdl/arg/Library/Developer/CommandLineTools/usr/bin/sh ./libtool --tag=CC --mode=compile gccltdl -I./libltdl/libltdl -g -O2 -MT libltdl/loaders/libltdMD -MP -MF libltdl/loaders/.deps/libltdl_libltdl_la-preopen.Tpo -c -o libltreopen.lo `test -f 'libltdl/loaders/preopen.c' || echo './'`libltdl/loaders/preopen.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,835 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdl -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libl_libltdl_la-preopen.lo -dl/loaders/libltdl_libltdl_la-plibtool: compile: gcc -DHAVE_CONFIG_H ibltdl -g -O2 -MT libltdl/loaders/libltdl_libltdMF libltdl/loaders/.deps/libltdl_libltdl_la-preopen.Tpo -c lcommon -DPIC -o libltdl/loaders/.libs/libltdl_libltdl_la-preopen.o install_environment.STDOUT DEBUG 2017-11-18 16:56:09,890 -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/ll_la-preopen.lo -MD -MP -ibltdl/loaders/preopen.c -fno-libtool: compile: gcc -DHAVE_CONFIG_H ibltdl -g -O2 -MT libltdl/loaders/libltdl_libltdMF libltdl/loaders/.deps/libltdl_libltdl_la-preopen.Tpo -c lltdl/loaders/libltdl_libltdl_la-preopen.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:09,937 -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/ll_la-preopen.lo -MD -MP -ibltdl/loaders/preopen.c -fno-libtool: compile: gcc -DHAVE_CONFIG_H ibltdl -g -O2 -MT libltdl/loaders/libltdl_libltdMF libltdl/loaders/.deps/libltdl_libltdl_la-preopen.Tpo -c lltdl/loaders/libltdl_libltdl_la-preopen.o >/dev/null 2>&1 install_environment.STDOUT DEBUG 2017-11-18 16:56:09,994 ltdl_la-preopen.Tpo libltdl/loaders/.deps/libltdl_libltdl_la-preopen.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,039 ltdl_la-preopen.Tpo libltdl/loaders/.deps/libltdl_libltdl_la-preopen.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,040 -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/ll_la-preopen.lo -MD -MP -ibltdl/loaders/preopen.c -o libmv -f libltdl/loaders/.deps/libltdl_lib/bin/sh ./libtool --tag=CC --mode=compile gccltdl -I./libltdl/libltdl -g -O2 -MT libltdl/libltdl_libltd -MF libltdl/.deps/libltdl_libltdl_la-lt__alloc.Tpo -c -o libltdl/libltdl_l 'libltdl/lt__alloc.c' || echo './'`libltdl/lt__alloc.c install_environment.STDOUT DEBUG 2017-11-18 16:56:10,060 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdl -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libl_la-lt__alloc.lo -MD -MPibltdl_la-lt__alloc.lo `test -flibtool: compile: gcc -DHAVE_CONFIG_H ibltdl -g -O2 -MT libltdl/libltdl_libltdl_la-lt__alloc.lo -MD -MP -MF libltdl/.deps/libltdl_libltdl_la-lt__alloc.Tpo -c libltdl/lt__alloc.c -fno-common -DPIC -o libltdl/.libs/libltdl_libltdl_la-lt__alloc.o install_environment.STDOUT DEBUG 2017-11-18 16:56:10,133 HAVE_CONFIG_H -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl libltdl/libltdl_libltdl_ps/libltdl_libltdl_la-lt__allocibltdl_la-lt__alloc.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,142 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdl -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libl_la-lt__alloc.lo -MD -MPibltdl_la-lt__alloc.lo `test -flibtool: compile: gcc -DHAVE_CONFIG_H ibltdl -g -O2 -MT libltdl/libltdl_libltdl_la-lt__alloc.lo -MD -MP -MF libltdl/.deps/libltdl_libltdl_la-lt__alloc.Tpo -c libltdl/lt__alloc.c -fno-common -DPIC -o libltdl/.libs/libltdl_libltdl_la-lt__alloc.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,143 HAVE_CONFIG_H -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl libltdl/libltdl_libltdl_ps/libltdl_libltdl_la-lt__allocibltdl_la-lt__alloc.o >/dev/null 2>&1 install_environment.STDOUT DEBUG 2017-11-18 16:56:10,203 /.deps/libltdl_libltdl_la-lt__alloc.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,247 /.deps/libltdl_libltdl_la-lt__alloc.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,247 -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/llibtool: compile: gcc -D -I./libltdl/libltdl -g -O2 -MTla-lt__alloc.lo -MD -MP -MF libltdl/.de.Tpo -c libltdl/lt__alloc.c -o libltdl/libltdl_lmv -f libltdl/.deps/libltdl_libltdl_la-lt__alloc.Tpo libltdl/bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTD-g -O2 -MT libltdl/libltdl_libltdl_la-lt_dlloader.lo -MD -MP -MF libltdl/.deps/libltdl_libltdl libltdl/libltdl_libltdl_la-lt_dlloader.lo `test -f 'libltdl/lt_dlloader.c' || echo './'`libltdl/lt_dlloader.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,247 ONFIG_H -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./ldl_libltdl_la-lt_dlloader-lt_dlloader.Tpo -c libltdl/lt_dl_la-lt_dlloader.o install_environment.STDOUT DEBUG 2017-11-18 16:56:10,321 LOPEN=libltdl -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/libltdl _la-lt_dlloader.Tpo -c -olibtool: compile: gcc -DHAVE_Cibltdl/libltdl -g -O2 -MT libltdl/liblt.lo -MD -MP -MF libltdl/.deps/libltdl_libltdl_ladlloader.c -fno-common -DPIC -o libltdl/.libs/libltdl_libltlibtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_bltdl_la-lt_dlloader.lo -MD -MP -MF libltdl/.deps/libltdl_libltdl_la-lt_dlloader.Tpo -c libltdl/libltdl_libltdl_la-lt_dlloader.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,352 LOPEN=libltdl -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/libltdl _la-lt_dlloader.Tpo -c -olibtool: compile: gcc -DHAVE_Cibltdl/libltdl -g -O2 -MT libltdl/liblt.lo -MD -MP -MF libltdl/.deps/libltdl_libltdl_ladlloader.c -fno-common -DPIC -o libltdl/.libs/libltdl_libltlibtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_bltdl_la-lt_dlloader.lo -MD -MP -MF libltdl/.deps/libltdl_libltdl_la-lt_dlloader.Tpo -c libltdl/libltdl_libltdl_la-lt_dlloader.o >/dev/null 2>&1 install_environment.STDOUT DEBUG 2017-11-18 16:56:10,410 ltdl_la-lt_dlloader.Tpo libltdl/.deps/libltdl_libltdl_la-lt_dlloader.Plo install_environment.STDOUT DEBUG 2017-11-18 16:56:10,413 mpile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdl -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdibltdl/libltdl_libltdl_la_error.Tpo -c -o libltdl/libltd/lt_error.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,454 ltdl_la-lt_dlloader.Tpo libltdl/.deps/libltdl_libltdl_la-lt_dlloader.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,455 mpile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdl -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdibltdl/libltdl_libltdl_la_error.Tpo -c -o libltdl/libltd/lt_error.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,455 H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/libltdl -g -O2 -MT libltdl/libltdl_lil/lt_dlloader.c -o libltdmv -f libltdl/.deps/libltdl_lib/bin/sh ./libtool --tag=CC --mode=col -I./libltdl -I./libltdl/libltdl -g -O2 -MT l-lt_error.lo -MD -MP -MF libltdl/.deps/libltdl_libltdl_la-ltl_libltdl_la-lt_error.lo `test -f 'libltdl/lt_error.c' || echo './'`libltdllibtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_H=<config.h>" -DLTDo -MD -MP -MF libltdl/.deps/libltdl_libltdl_la-lt_error.Tpo -c libltdl/lt_error.c -fno-common -DPIC -o libltdl/.libs/or.o install_environment.STDOUT DEBUG 2017-11-18 16:56:10,527 L -I. -I. -Ilibltdl -I./libltdl -I./libltdl/libltdl -g -O2 -MT libltdl/libltdl_libltdl_la-lt_error.llibltdl_libltdl_la-lt_errlibtool: compile: gcc -DHAVE_Cibltdl/libltdl -g -O2 -MT libltdl/libltdl_libltdl_la-lt_error.lo -MD -MP -MF libltdl/.deps/libltdl_libltdl_la-lt_error.Tpo -c libltdl/lt_error.c -o libltdl/libltdl_libltdl_la-lt_error.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,559 L -I. -I. -Ilibltdl -I./libltdl -I./libltdl/libltdl -g -O2 -MT libltdl/libltdl_libltdl_la-lt_error.llibltdl_libltdl_la-lt_errlibtool: compile: gcc -DHAVE_Cibltdl/libltdl -g -O2 -MT libltdl/libltdl_libltdl_la-lt_error.lo -MD -MP -MF libltdl/.deps/libltdl_libltdl_la-lt_error.Tpo -c libltdl/lt_error.c -o libltdl/libltdl_libltdl_la-lt_error.o >/dev/null 2>&1 install_environment.STDOUT DEBUG 2017-11-18 16:56:10,600 dl_libltdl_la-lt_error.Tpo libltdl/.deps/libltdl_libltdl_la-lt_error.Plo install_environment.STDOUT DEBUG 2017-11-18 16:56:10,603 -mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdl -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. dl -g -O2 -MT libltdl/leps/libltdl_libltdl_la-ltdl.Tpoltdl.c' || echo './'`libltdl/ltdl.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,664 dl_libltdl_la-lt_error.Tpo libltdl/.deps/libltdl_libltdl_la-lt_error.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,664 -mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdl -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. dl -g -O2 -MT libltdl/leps/libltdl_libltdl_la-ltdl.Tpoltdl.c' || echo './'`libltdl/ltdl.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:10,664 ONFIG_H -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./lmv -f libltdl/.deps/liblt/bin/sh ./libtool --tag=CC --Ilibltdl -I./libltdl -I./libltdl/libltibltdl_libltdl_la-ltdl.lo -MD -MP -MF libltdl/.d -c -o libltdl/libltdl_libltdl_la-ltdl.lo `test -f 'libltdl/libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_bltdl_la-ltdl.lo -MD -MP -MF libltdl/.deps/libltdl_libltdl_la-ltdl.Tpo -c libltdl/ltdl.c -fno.libs/libltdl_libltdl_la-ltdl.o install_environment.STDOUT DEBUG 2017-11-18 16:56:10,983 H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/libltdl -g -O2 -MT libltdl/libltdl_li-common -DPIC -o libltdl/libtool: compile: gcc -DHAVE_Cibltdl/libltdl -g -O2 -MT libltdl/liblt -MP -MF libltdl/.deps/libltdl_libltdl_la-ltdl.T/libltdl_libltdl_la-ltdl.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:11,079 H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/libltdl -g -O2 -MT libltdl/libltdl_li-common -DPIC -o libltdl/libtool: compile: gcc -DHAVE_Cibltdl/libltdl -g -O2 -MT libltdl/liblt -MP -MF libltdl/.deps/libltdl_libltdl_la-ltdl.T/libltdl_libltdl_la-ltdl.o >/dev/null 2>&1 install_environment.STDOUT DEBUG 2017-11-18 16:56:11,341 ltdl.Tpo libltdl/.deps/libltdl_libltdl_la-ltdl.Plo install_environment.STDOUT DEBUG 2017-11-18 16:56:11,385 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdl -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libl_la-slist.lo -MD -MP -MFa-slist.lo `test -f 'libltdl/sllibtool: compile: gcc -DHAVE_CONFIG_H ibltdl -g -O2 -MT libltdl/libltdl_libltdl_la-sli/.deps/libltdl_libltdl_la-slist.Tpo -c libltdl/slist.c -fnolibltdl_libltdl_la-slist.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:11,388 ltdl.Tpo libltdl/.deps/libltdl_libltdl_la-ltdl.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:11,388 ONFIG_H -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./ldl_libltdl_la-ltdl.lo -MDpo -c libltdl/ltdl.c -o libltdlmv -f libltdl/.deps/libltdl_libltdl_la-/bin/sh ./libtool --tag=CC --mode=compile gccltdl -I./libltdl/libltdl -g -O2 -MT libltdl/libltdl_libltd libltdl/.deps/libltdl_libltdl_la-slist.Tpo -c -o libltdl/libltdl_libltdl_list.c' || echo './'`libltdl/slist.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:11,388 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdl -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libl_la-slist.lo -MD -MP -MFa-slist.lo `test -f 'libltdl/sllibtool: compile: gcc -DHAVE_CONFIG_H ibltdl -g -O2 -MT libltdl/libltdl_libltdl_la-sli/.deps/libltdl_libltdl_la-slist.Tpo -c libltdl/slist.c -fnolibltdl_libltdl_la-slist.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:11,492 -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/lst.lo -MD -MP -MF libltdl-common -DPIC -o libltdl/.libs/libtool: compile: gcc -DHAVE_CONFIG_H ibltdl -g -O2 -MT libltdl/libltdl_libltdl_la-sli/.deps/libltdl_libltdl_la-slist.Tpo -c libltdl/slist.c -o lio >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:11,594 slist.Tpo libltdl/.deps/libltdl_libltdl_la-slist.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:11,594 depbase=`echo libltdl/loaders/dlopen.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:11,595 /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/libltdl -g -O2 -MT libltdl/loaders/dlopen.lo -MD -MP -MF $depbase.Tpo -c -o libltdl/loaders/dlopen.lo libltdl/loaders/dlopen.c &&\ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:11,595 mv -f $depbase.Tpo $depbase.Plo install_environment.STDOUT DEBUG 2017-11-18 16:56:11,629 -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/lst.lo -MD -MP -MF libltdlbltdl/libltdl_libltdl_la-slist.mv -f libltdl/.deps/libltdl_libltdl_la-ibltdl -I./libltdl/libltdl -g -O2 -MT libltdl/loaders/dlopen.lo -MD -MP -MF libltdl/loaders/.deps/dlopen.Tpo -c libltdl/loaders/dlopen.c -fno-common -DPIC -o libltdl/loaders/.libs/dlopen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:11,699 -I. -DLTDLOPEN=libltdl "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/lst.lo -MD -MP -MF libltdlbltdl/libltdl_libltdl_la-slist.mv -f libltdl/.deps/libltdl_libltdl_la-ibltdl -I./libltdl/libltdl -g -O2 -MT libltdl/loaders/dlopen.lo -MD -MP -MF libltdl/loaders/.deps/dlopen.Tpo -c libltdl/loaders/dlopen.c -fno-common -DPIC -o libltdl/loaders/.libs/dlopen.o 127.0.0.1 - - [18/Nov/2017:16:56:11 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:56:11,707 libtool: compile: gcc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./ll -g -O2 -MT libltdl/loaddl/loaders/.deps/dlopen.Tpo -c ders/dlopen.o >/dev/null 2>&1 install_environment.STDOUT DEBUG 2017-11-18 16:56:11,796 -O2 -module -avoid-version -o libltdl/dlopen.la libltdl/loaders/dlopen.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:11,804 libtool: compile: gcc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./ll -g -O2 -MT libltdl/loaddl/loaders/.deps/dlopen.Tpo -c ders/dlopen.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:11,805 -O2 -module -avoid-version -o libltdl/dlopen.la libltdl/loaders/dlopen.lo install_environment.STDOUT DEBUG 2017-11-18 16:56:11,904 /.libs/dlopen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:11,905 /.libs/dlopen.o install_environment.STDOUT DEBUG 2017-11-18 16:56:11,936 libtool: link: ( cd "libltdl/.libs" && rm -f "dlopen.la" && ln -s "../dlopen.la" "dlopen.la" ) install_environment.STDOUT DEBUG 2017-11-18 16:56:11,987 /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLT_CONFIG_H='<config.h>' -DLibltdl -I./libltdl/libltd.lo -MD -MP -MF libltdl/.deps/a-common -DPIC -o libltdl/.libs/argz.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,006 libtool: compile: gcc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/libltders/dlopen.lo -MD -MP -MF libltlibltdl/loaders/dlopen.c -o libltdl/loa/bin/sh ./libtool --tag=CC --mode=link gcc -glibtool: link: ar cru libltdl/.libs/dlopen.a libltdl/loaderslibtool: link: ranlib libltdl/.libs/dlopen.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,006 libtool: link: ( cd "libltdl/.libs" && rm -f "dlopen.la" && ln -s "../dlopen.la" "dlopen.la" ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,006 depbase=`echo libltdl/argz.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,006 TDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/libltdl -g -O2 -MT libltdl/argz.lo -MD -MP -MF $depbase.Tpo -c -o libltdl/argz.lo libltdl/argz.c &&\ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,007 mv -f $depbase.Tpo $depbase.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,007 /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLT_CONFIG_H='<config.h>' -DLibltdl -I./libltdl/libltd.lo -MD -MP -MF libltdl/.deps/a-common -DPIC -o libltdl/.libs/argz.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,111 libtool: compile: gcc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./ll -g -O2 -MT libltdl/argzrgz.Tpo -c libltdl/argz.c -fnolibtool: compile: gcc -DHAVE_CONFIG_H ibltdl/argz.lo -MD -MP -MF libltdl/.deps/argz.Tpbltdl/argz.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,216 mode=link gcc -g -O2 -no-undefined -version-info 10:0:3 -dlpreopen libltdl/dlopen.la -o libltdl/lbase/dependencies/libtoolbltdl/loaders/libltdl_libltdl_l/libltdl_libltdl_la-lt_dlloader.lo libldl/libltdl_libltdl_la-slist.lo libltdl/argz.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,321 nmT tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,321 c") install_environment.STDOUT DEBUG 2017-11-18 16:56:12,327 -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/libltdl -g -O2 -MT lo -c libltdl/argz.c -o li/bin/sh ./libtool --tag=CC --ibltdl.la -rpath /galaxydir/galaxy/data/2.4/iuc/package_libtool_2_4/7f67694b167c/lib lia-preopen.lo libltdl/libltdl_libltdl_la-lt__alloc.lo libltdltdl/libltdl_libltdl_la-lt_error.lo libltdl/libltdl_libltdl_la-ltdl.lo libltlibtool: link: rm -f libltdl/.libs/libltdl.nm libltdl/.libs/libltdl.nmS libltdl/.libs/libltdl.libtool: link: (cd libltdl/.libs && gcc -g -O2 -c -fno-builtin -fno-rtti -fno-exceptions -fno-common -DPIC "libltdlS.libtool: link: rm -f "libltdl/.libs/libltdlS.c" "libltdl/.libs/libltdl.nm" "libltdl/.libs/libltdl.nmS" "libltdl/.libs/libltdl.nmT" install_environment.STDOUT DEBUG 2017-11-18 16:56:12,408 olshed-mtdUscPyu/libtool-2.4/libltdl/.libs/dlopen.a") tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,424 -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl/libltdl -g -O2 -MT lo -c libltdl/argz.c -o li/bin/sh ./libtool --tag=CC --ibltdl.la -rpath /galaxydir/galaxy/data/2.4/iuc/package_libtool_2_4/7f67694b167c/lib lia-preopen.lo libltdl/libltdl_libltdl_la-lt__alloc.lo libltdltdl/libltdl_libltdl_la-lt_error.lo libltdl/libltdl_libltdl_la-ltdl.lo libltlibtool: link: rm -f libltdl/.libs/libltdl.nm libltdl/.libs/libltdl.nmS libltdl/.libs/libltdl.libtool: link: (cd libltdl/.libs && gcc -g -O2 -c -fno-builtin -fno-rtti -fno-exceptions -fno-common -DPIC "libltdlS.libtool: link: rm -f "libltdl/.libs/libltdlS.c" "libltdl/.libs/libltdl.nm" "libltdl/.libs/libltdl.nmS" "libltdl/.libs/libltdl.nmT" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,425 olshed-mtdUscPyu/libtool-2.4/libltdl/.libs/dlopen.a") install_environment.STDOUT DEBUG 2017-11-18 16:56:12,465 iclib -o libltdl/.libs/libltdl.7.dylib libltdl/loaders/.libs/libltdl_libltdl_la-preopen.o libltdl/loc.o libltdl/.libs/libltbs/libltdl_libltdl_la-lt_error.l/.libs/libltdl_libltdl_la-slist.o liblltdl.lax/dlopen.a/dlopen.o -O2 -install_nam2_4/7f67694b167c/lib/libltdl.7.dylib -compatibility_version libtool: link: dsymutil libltdl/.libs/libltdl.7.dylib || : install_environment.STDOUT DEBUG 2017-11-18 16:56:12,489 b") tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,526 libtool: link: (cd libltdl/.libs/libltdl.lax/dlopen.a && ar x "/galaxydir/galaxy/database/tmp/tmp-tolibtool: link: gcc -dynam.libs/libltdl_libltdl_la-lt__aldl_libltdl_la-lt_dlloader.o libltdl/.lio libltdl/.libs/libltdl_libltdl_la-ltdl.o libltdtdl/.libs/argz.o libltdl/.libs/libltdlS.o libltdl/.libs/libe /galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_11 -current_version 11.0 -Wl,-single_module tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,527 iclib -o libltdl/.libs/libltdl.7.dylib libltdl/loaders/.libs/libltdl_libltdl_la-preopen.o libltdl/loc.o libltdl/.libs/libltbs/libltdl_libltdl_la-lt_error.l/.libs/libltdl_libltdl_la-slist.o liblltdl.lax/dlopen.a/dlopen.o -O2 -install_nam2_4/7f67694b167c/lib/libltdl.7.dylib -compatibility_version libtool: link: dsymutil libltdl/.libs/libltdl.7.dylib || : tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,527 b") install_environment.STDOUT DEBUG 2017-11-18 16:56:12,537 l/.libs/libltdl.lax/lt1-dlopen.a && ar x "/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdUscPyu/libt) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,627 l/.libs/libltdl.lax/lt1-dlopen.a && ar x "/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdUscPyu/libt) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,628 libtool: link: (cd "libltdl/.libs" && rm -f "libltdl.dylib" && ln -s "libltdl.7.dylib" "libltdl.dylilibtool: link: (cd libltdool-2.4/libltdl/.libs/dlopen.a"libtool: link: ar cru libltdl/.libs/liblibltdl_libltdl_la-lt_dlloader.o libltdl/libltdlbltdl/libltdl_libltdl_la-ltdl.o libltdl/libltdl_libltdl_la-slibs/libltdlS.o libltdl/.libs/libltdl.lax/lt1-dlopen.a/dlopen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,628 ltdl.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,628 libltdl/.libs/libltdl.lax tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,628 ln -s "../libltdl.la" "libltdl.la" ) install_environment.STDOUT DEBUG 2017-11-18 16:56:12,661 ltdl.a libltdl/loaders/libltdl_libltdl_la-preopen.o libltdl/libltdl_libltdl_la-lt__alloc.o libltdl/_libltdl_la-lt_error.o lilist.o libltdl/argz.o libltdl/.libtool: link: ranlib libltdl/.libs/liblibtool: link: rm -fr libltdl/.libs/libltdl.lax libtool: link: ( cd "libltdl/.libs" && rm -f "libltdl.la" &&/Library/Developer/CommandLineTools/usr/bin/make install-recursive tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,733 ltdl.a libltdl/loaders/libltdl_libltdl_la-preopen.o libltdl/libltdl_libltdl_la-lt__alloc.o libltdl/_libltdl_la-lt_error.o lilist.o libltdl/argz.o libltdl/.libtool: link: ranlib libltdl/.libs/liblibtool: link: rm -fr libltdl/.libs/libltdl.lax libtool: link: ( cd "libltdl/.libs" && rm -f "libltdl.la" &&/Library/Developer/CommandLineTools/usr/bin/make install-recursive install_environment.STDOUT DEBUG 2017-11-18 16:56:12,734 n" || libltdl/config/install-sh -c -d "/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/packa7c/bin" install_environment.STDOUT DEBUG 2017-11-18 16:56:12,798 libtool '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/btest -z "/galaxydir/galaxall-sh -c -d "/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/lib" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,835 n" || libltdl/config/install-sh -c -d "/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/packa7c/bin" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,835 test -z "/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/bige_libtool_2_4/7f67694b16 /usr/bin/install -c libtoolizein' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,835 libtool '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/btest -z "/galaxydir/galaxall-sh -c -d "/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/lib" install_environment.STDOUT DEBUG 2017-11-18 16:56:12,838 de=install /usr/bin/install -c libltdl/libltdl.la '/galaxydir/galaxy/database/dependencies/libtool67694b167c/lib' install_environment.STDOUT DEBUG 2017-11-18 16:56:12,873 ibltdl/.libs/libltdl.7.dylib /galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtoollibtool: install: (cd /ga -f libltdl.7.dylib libltdl.dylib && ln -s libltdl.7.dylib libltdl.dyllibtool: install: /usr/bin/install -c libltdl/.l167c/lib/libltdl.la install_environment.STDOUT DEBUG 2017-11-18 16:56:12,876 n/install -c libltdl/.libs/libltdl.a /galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/packageibltdl.a install_environment.STDOUT DEBUG 2017-11-18 16:56:12,883 galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/lib/libltdl.a install_environment.STDOUT DEBUG 2017-11-18 16:56:12,886 ase/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/lib/libltdl.a install_environment.STDOUT DEBUG 2017-11-18 16:56:12,935 uc/package_libtool_2_4/7f67694b167c/share/libtool/* tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,938 de=install /usr/bin/install -c libltdl/libltdl.la '/galaxydir/galaxy/database/dependencies/libtool67694b167c/lib' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,938 y/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/lib" || libltdl/config/inst /bin/sh ./libtool --mo/2.4/iuc/package_libtool_2_4/7flibtool: install: /usr/bin/install -c l_2_4/7f67694b167c/lib/libltdl.7.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,939 laxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/lib && { ln -sib || { rm -f libltdl.dylib; }; }) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,939 ibltdl/.libs/libltdl.7.dylib /galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtoollibtool: install: (cd /ga -f libltdl.7.dylib libltdl.dylib && ln -s libltdl.7.dylib libltdl.dyllibtool: install: /usr/bin/install -c libltdl/.l167c/lib/libltdl.la tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,939 n/install -c libltdl/.libs/libltdl.a /galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/packageibltdl.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,939 galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/lib/libltdl.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,939 ase/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/lib/libltdl.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:12,939 uc/package_libtool_2_4/7f67694b167c/share/libtool/* install_environment.STDOUT DEBUG 2017-11-18 16:56:12,987 ibltdl/config/install-sh -d /galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_ /usr/bin/install -c -m 6_4/7f67694b167c/share/aclocal/a /usr/bin/install -c -m 644 './libltdl/167c/share/aclocal/libtool.m4' install_environment.STDOUT DEBUG 2017-11-18 16:56:12,997 44 './libltdl/m4/ltdl.m4' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2tdl.m4' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,011 m4/ltoptions.m4' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f6769ol/2.4/iuc/package_libtooaclocal/ltsugar.m4' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,018 libltdl/m4/ltversion.m4' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_m4' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,034 olete.m4' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c//bin/sh /galaxydir/galaxybase/dependencies/libtool/2.4/i67694b167c/share/libtool tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,042 ibs/libltdl.lai /galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694blibtool: install: /usr/bi_libtool_2_4/7f67694b167c/lib/llibtool: install: chmod 644 /galaxydir/libtool: install: ranlib /galaxydir/galaxy/databrm -rf /galaxydir/galaxy/database/dependencies/libtool/2.4/i/bin/sh /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdUscPyu/libtool-2.4/l2_4/7f67694b167c/share/aclocal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,042 44 './libltdl/m4/argz.m4' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2rgz.m4' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,042 ibltdl/config/install-sh -d /galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_ /usr/bin/install -c -m 6_4/7f67694b167c/share/aclocal/a /usr/bin/install -c -m 644 './libltdl/167c/share/aclocal/libtool.m4' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,042 44 './libltdl/m4/ltdl.m4' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2tdl.m4' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,042 m4/libtool.m4' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b /usr/bin/install -c -m 6_4/7f67694b167c/share/aclocal/l /usr/bin/install -c -m 644 './libltdl/4b167c/share/aclocal/ltoptions.m4' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,043 m4/ltoptions.m4' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f6769ol/2.4/iuc/package_libtooaclocal/ltsugar.m4' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,043 libltdl/m4/ltversion.m4' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_m4' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,043 /usr/bin/install -c -m 644 './libltdl/m4/ltsugar.m4' '/galaxydir/galaxy/database/dependencies/libtol_2_4/7f67694b167c/share/ /usr/bin/install -c -m 644 './4/7f67694b167c/share/aclocal/ltversion. /usr/bin/install -c -m 644 './libltdl/m4/lt~obsshare/aclocal/lt~obsolete.m4' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,043 olete.m4' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c//bin/sh /galaxydir/galaxybase/dependencies/libtool/2.4/i67694b167c/share/libtool install_environment.STDOUT DEBUG 2017-11-18 16:56:13,105 ase/tmp/tmp-toolshed-mtdUscPyu/libtool-2.4/libltdl/config/install-sh -d /galaxydir/galaxy/database/dtool_2_4/7f67694b167c/sha /usr/bin/install -c './libltdl4b167c/share/libtool/config/compile' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,108 ibltdl/config/config.guess' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool/config/config.guess' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,119 config.sub' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167 /usr/bin/install -c './l7f67694b167c/share/libtool/conf /usr/bin/install -c './libltdl/config/c/share/libtool/config/install-sh' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,122 ibltdl/config/missing' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/ig/missing' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,130 ltmain.sh' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/bin/sh /galaxydir/galaxybase/dependencies/libtool/2.4/i67694b167c/share/libtool/libltdl tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,144 /database/tmp/tmp-toolshed-mtdUscPyu/libtool-2.4/libltdl/config/install-sh -d /galaxydir/galaxy/datauc/package_libtool_2_4/7f/bin/sh /galaxydir/galaxy/databependencies/libtool/2.4/iuc/package_libre/libtool/config tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,144 ase/tmp/tmp-toolshed-mtdUscPyu/libtool-2.4/libltdl/config/install-sh -d /galaxydir/galaxy/database/dtool_2_4/7f67694b167c/sha /usr/bin/install -c './libltdl4b167c/share/libtool/config/compile' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,144 ibltdl/config/config.guess' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool/config/config.guess' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,144 /config/compile' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f6769 /usr/bin/install -c './l_2_4/7f67694b167c/share/libtool /usr/bin/install -c './libltdl/config/c/share/libtool/config/config.sub' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,144 ibltdl/config/depcomp' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/ig/depcomp' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,145 config.sub' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167 /usr/bin/install -c './l7f67694b167c/share/libtool/conf /usr/bin/install -c './libltdl/config/c/share/libtool/config/install-sh' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,145 ibltdl/config/missing' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/ig/missing' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,145 install-sh' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167 /usr/bin/install -c './l7f67694b167c/share/libtool/conf /usr/bin/install -c './libltdl/config//share/libtool/config/ltmain.sh' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,145 ltmain.sh' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/bin/sh /galaxydir/galaxybase/dependencies/libtool/2.4/i67694b167c/share/libtool/libltdl install_environment.STDOUT DEBUG 2017-11-18 16:56:13,211 ase/tmp/tmp-toolshed-mtdUscPyu/libtool-2.4/libltdl/config/install-sh -d /galaxydir/galaxy/database/dtool_2_4/7f67694b167c/sha/bin/sh /galaxydir/galaxy/databependencies/libtool/2.4/iuc/package_libre/libtool/libltdl/loaders tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,250 /database/tmp/tmp-toolshed-mtdUscPyu/libtool-2.4/libltdl/config/install-sh -d /galaxydir/galaxy/datauc/package_libtool_2_4/7f/bin/sh /galaxydir/galaxy/databependencies/libtool/2.4/iuc/package_libre/libtool/libltdl/libltdl tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,250 ase/tmp/tmp-toolshed-mtdUscPyu/libtool-2.4/libltdl/config/install-sh -d /galaxydir/galaxy/database/dtool_2_4/7f67694b167c/sha/bin/sh /galaxydir/galaxy/databependencies/libtool/2.4/iuc/package_libre/libtool/libltdl/loaders install_environment.STDOUT DEBUG 2017-11-18 16:56:13,257 libltdl/COPYING.LIB' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7fG.LIB' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,272 /galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/libto /usr/bin/install -c -m 6_2_4/7f67694b167c/share/libtool /usr/bin/install -c -m 644 './libltdl/7c/share/libtool/libltdl/Makefile.am' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,276 44 './libltdl/configure.ac' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool/libltdl/configure.ac' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,289 aclocal.m4' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167 /usr/bin/install -c -m 62_4/7f67694b167c/share/libtool/ /usr/bin/install -c -m 644 './libltdl/7c/share/libtool/libltdl/config-h.in' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,293 44 './libltdl/configure' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_bltdl/configure' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,307 argz_.h' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/s /usr/bin/install -c -m 6f67694b167c/share/libtool/liblt /usr/bin/install -c -m 644 './libltdl/7694b167c/share/libtool/libltdl/loaders/dld_link /usr/bin/install -c -m 644 './libltdl/loaders/dlopen.c' '/g/libltdl/loaders/dlopen.c' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,314 44 './libltdl/loaders/dyld.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool/libltdl/loaders/dyld.c /usr/bin/install -c -m 644 './ool_2_4/7f67694b167c/share/libtool/libl' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,324 libltdl/loaders/loadlibrary.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libttdl/loaders/loadlibrary.c /usr/bin/install -c -m 644 './_2_4/7f67694b167c/share/libtool/libltdl /usr/bin/install -c -m 644 './libltdl/lt__diren/libtool/libltdl/lt__dirent.c' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,329 44 './libltdl/lt__strl.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2ibltdl/lt__strl.c' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,333 libltdl/lt__alloc.h' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7foc.h' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,341 '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/lib /usr/bin/install -c -m 6libtool_2_4/7f67694b167c/share/t__glibc.h' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,350 libltdl/COPYING.LIB' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7fG.LIB' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,351 ase/tmp/tmp-toolshed-mtdUscPyu/libtool-2.4/libltdl/config/install-sh -d /galaxydir/galaxy/database/dtool_2_4/7f67694b167c/sha /usr/bin/install -c -m 644 './67694b167c/share/libtool/libltdl/COPYIN /usr/bin/install -c -m 644 './libltdl/README' 'ol/libltdl/README' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,351 44 './libltdl/Makefile.inc' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool/libltdl/Makefile.inc' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,351 /galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/libto /usr/bin/install -c -m 6_2_4/7f67694b167c/share/libtool /usr/bin/install -c -m 644 './libltdl/7c/share/libtool/libltdl/Makefile.am' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,351 44 './libltdl/configure.ac' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool/libltdl/configure.ac' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,351 Makefile.am' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b16 /usr/bin/install -c -m 6_2_4/7f67694b167c/share/libtool /usr/bin/install -c -m 644 './libltdl/c/share/libtool/libltdl/aclocal.m4' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,351 44 './libltdl/Makefile.in' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_libltdl/Makefile.in' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,351 aclocal.m4' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167 /usr/bin/install -c -m 62_4/7f67694b167c/share/libtool/ /usr/bin/install -c -m 644 './libltdl/7c/share/libtool/libltdl/config-h.in' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,352 44 './libltdl/configure' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_bltdl/configure' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,352 config-h.in' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b16 /usr/bin/install -c -m 64/7f67694b167c/share/libtool/li /usr/bin/install -c -m 644 './libltdl/hare/libtool/libltdl/argz_.h' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,352 44 './libltdl/argz.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7dl/argz.c' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,352 loaders/dld_link.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f6.c' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,352 argz_.h' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/s /usr/bin/install -c -m 6f67694b167c/share/libtool/liblt /usr/bin/install -c -m 644 './libltdl/7694b167c/share/libtool/libltdl/loaders/dld_link /usr/bin/install -c -m 644 './libltdl/loaders/dlopen.c' '/g/libltdl/loaders/dlopen.c' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,352 alaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/libtool /usr/bin/install -c -m 6ol_2_4/7f67694b167c/share/libto' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,352 44 './libltdl/loaders/dyld.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool/libltdl/loaders/dyld.c /usr/bin/install -c -m 644 './ool_2_4/7f67694b167c/share/libtool/libl' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,352 libltdl/loaders/load_add_on.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libttdl/loaders/load_add_on.c /usr/bin/install -c -m 644 './ool_2_4/7f67694b167c/share/libtool/libl' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,352 libltdl/loaders/shl_load.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool/loaders/shl_load.c' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,352 libltdl/loaders/loadlibrary.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libttdl/loaders/loadlibrary.c /usr/bin/install -c -m 644 './_2_4/7f67694b167c/share/libtool/libltdl /usr/bin/install -c -m 644 './libltdl/lt__diren/libtool/libltdl/lt__dirent.c' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,352 44 './libltdl/lt__strl.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2ibltdl/lt__strl.c' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,353 libltdl/lt__alloc.h' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7foc.h' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,353 t.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share /usr/bin/install -c -m 6_4/7f67694b167c/share/libtool/l /usr/bin/install -c -m 644 './libltdl/67694b167c/share/libtool/libltdl/libltdl/lt__all /usr/bin/install -c -m 644 './libltdl/libltdl/lt__dirent.h'tool/libltdl/libltdl/lt__dirent.h' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,353 '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/lib /usr/bin/install -c -m 6libtool_2_4/7f67694b167c/share/t__glibc.h' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,353 44 './libltdl/libltdl/lt__glibc.h' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool/libltdl/libltdl/l /usr/bin/install -c -m 644 './ool_2_4/7f67694b167c/share/libtool/libl' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,353 libltdl/libltdl/lt__strl.h' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool/libltdl/lt__strl.h' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,353 t_dlloader.h' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/libtool/libltdl/libltdl/lt_dlloader.h' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,355 libltdl/libltdl/lt__private.h' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libttdl/libltdl/lt__private.h /usr/bin/install -c -m 644 './_2_4/7f67694b167c/share/libtool/libltdl /usr/bin/install -c -m 644 './libltdl/libltdl/llibtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/libtoor.h' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,357 libltdl/libltdl/lt_system.h' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool/libltdl/lt_system.h' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,365 list.h' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/shibtool/2.4/iuc/package_li/2.4/iuc/package_libtool_2_4/7flibltdl/lt__alloc.c' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,368 libltdl/lt_dlloader.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/lloader.c' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,377 c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/l /usr/bin/install -c -m 6f67694b167c/share/libtool/liblt /usr/bin/install -c -m 644 './libltdl/are/libtool/libltdl/ltdl.h' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,380 44 './libltdl/slist.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/tdl/slist.c' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,384 pendencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/libtool/libltdl/configure install_environment.STDOUT DEBUG 2017-11-18 16:56:13,435 /libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/include" || libltdl/config/install-sh -c -d "/galaibtool_2_4/7f67694b167c/i /usr/bin/install -c -m 644 libc/include' install_environment.STDOUT DEBUG 2017-11-18 16:56:13,439 y/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/info" || libltdl/conf/galaxy/database/dependen4/7f67694b167c/share/info" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,454 libltdl/libltdl/lt__private.h' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libttdl/libltdl/lt__private.h /usr/bin/install -c -m 644 './_2_4/7f67694b167c/share/libtool/libltdl /usr/bin/install -c -m 644 './libltdl/libltdl/llibtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/libtoor.h' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,454 libltdl/libltdl/lt_system.h' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool/libltdl/lt_system.h' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,454 /usr/bin/install -c -m 644 './libltdl/libltdl/lt_error.h' '/galaxydir/galaxy/database/dependencies/ol/libltdl/libltdl/lt_err /usr/bin/install -c -m 644 './l_2_4/7f67694b167c/share/libtool/libltd /usr/bin/install -c -m 644 './libltdl/libltdl/sare/libtool/libltdl/libltdl/slist.h' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,455 /usr/bin/install -c -m 644 './libltdl/loaders/preopen.c' '/galaxydir/galaxy/database/dependencies/lbtool_2_4/7f67694b167c/share/libtool/libltdl/loaders/preopen.c' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,455 list.h' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/shibtool/2.4/iuc/package_li/2.4/iuc/package_libtool_2_4/7flibltdl/lt__alloc.c' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,455 libltdl/lt_dlloader.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/lloader.c' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,455 /usr/bin/install -c -m 644 './libltdl/lt__alloc.c' '/galaxydir/galaxy/database/dependencies/libtool67694b167c/share/libtool/ /usr/bin/install -c -m 644 './7f67694b167c/share/libtool/libltdl/lt_d /usr/bin/install -c -m 644 './libltdl/lt_error.ibtool/libltdl/lt_error.c' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,455 44 './libltdl/ltdl.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7dl/ltdl.c' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,455 c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/l /usr/bin/install -c -m 6f67694b167c/share/libtool/liblt /usr/bin/install -c -m 644 './libltdl/are/libtool/libltdl/ltdl.h' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,455 44 './libltdl/slist.c' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/tdl/slist.c' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,455 pendencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/libtool/libltdl/configure tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,455 ltdl.h' '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/sh /usr/bin/install -c -m 67f67694b167c/share/libtool/liblchmod a+x /galaxydir/galaxy/database/detest -z "/galaxydir/galaxy/database/dependenciesxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_lnclude" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,455 /libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/include" || libltdl/config/install-sh -c -d "/galaibtool_2_4/7f67694b167c/i /usr/bin/install -c -m 644 libc/include' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,456 y/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/info" || libltdl/conf/galaxy/database/dependen4/7f67694b167c/share/info" install_environment.STDOUT DEBUG 2017-11-18 16:56:13,522 /doc/libtool.info-1 ./doc/libtool.info-2 '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/pa install-info --info-dir=' '/galaxydir/galaxy/database/duc/package_libtool_2_4/7f67694b167c/shatest -z "/galaxydir/galaxy/database/dependenciesd "/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/include/libltdl" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,563 ltdl/ltdl.h '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167test -z "/galaxydir/galaxig/install-sh -c -d "/galaxydircies/libtool/2.4/iuc/package_libtool_2_ /usr/bin/install -c -m 644 ./doc/libtool.info .ckage_libtool_2_4/7f67694b167c/share/info' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,563 '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/infoependencies/libtool/2.4/ire/info/libtool.info' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,563 /doc/libtool.info-1 ./doc/libtool.info-2 '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/pa install-info --info-dir=' '/galaxydir/galaxy/database/duc/package_libtool_2_4/7f67694b167c/shatest -z "/galaxydir/galaxy/database/dependenciesd "/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/include/libltdl" install_environment.STDOUT DEBUG 2017-11-18 16:56:13,626 44 libltdl/libltdl/lt_system.h libltdl/libltdl/lt_error.h libltdl/libltdl/lt_dlloader.h '/galaxydir/btool/2.4/iuc/package_libtest -z "/galaxydir/galaxy/data/install-sh -c -d "/galaxydir/galaxy/daol/2.4/iuc/package_libtool_2_4/7f67694b167c/shar /usr/bin/install -c -m 644 ./doc/libtool.1 ./doc/libtoolizean/man1' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,666 /libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/include/libltdl" || libltdl/config/install-sh -c - /usr/bin/install -c -m 6galaxy/database/dependencies/litool_2_4/7f67694b167c/include/libltdl' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,666 base/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/man/man1" || libltdl/configtabase/dependencies/libtoe/man/man1" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,667 44 libltdl/libltdl/lt_system.h libltdl/libltdl/lt_error.h libltdl/libltdl/lt_dlloader.h '/galaxydir/btool/2.4/iuc/package_libtest -z "/galaxydir/galaxy/data/install-sh -c -d "/galaxydir/galaxy/daol/2.4/iuc/package_libtool_2_4/7f67694b167c/shar /usr/bin/install -c -m 644 ./doc/libtool.1 ./doc/libtoolizean/man1' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:libtool DEBUG 2017-11-18 16:56:13,667 .1 '/galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c/share/m tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 16:56:13,835 Changing status for tool dependency libtool from Installing to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:56:13,835 Updating an existing record for version 2.4 of tool dependency libtool for revision 7f67694b167c of repository package_libtool_2_4 by updating the status from Installing to Installed. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 16:56:13,881 Tool dependency libtool version 2.4 has been installed in /galaxydir/galaxy/database/dependencies/libtool/2.4/iuc/package_libtool_2_4/7f67694b167c. 127.0.0.1 - - [18/Nov/2017:16:56:14 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:56:16,455 Creating a new record for version 3.8.3 of tool dependency sqlite for revision c8a5c11cc921 of repository package_sqlite_3_8_3. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:56:16,510 Updating an existing record for version 3.8.3 of tool dependency sqlite for revision c8a5c11cc921 of repository package_sqlite_3_8_3 by updating the status from Never installed to Installing. tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 16:56:16,534 Attempting to download via url: https://github.com/bgruening/download_store/raw/master/sqlite/sqlite-autoconf-3080300.tar.gz 127.0.0.1 - - [18/Nov/2017:16:56:17 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 16:56:18,259 Successfully downloaded from url: https://github.com/bgruening/download_store/raw/master/sqlite/sqlite-autoconf-3080300.tar.gz tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:18,259 + ./configure --prefix=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921 && make && make install tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:18,478 checking for a BSD-compatible install... /usr/bin/install -c install_environment.STDOUT DEBUG 2017-11-18 16:56:19,484 checking whether build environment is sane... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:19,506 checking for gawk... no install_environment.STDOUT DEBUG 2017-11-18 16:56:19,507 checking for nawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:19,524 checking whether build environment is sane... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:19,524 checking for a thread-safe mkdir -p... ./install-sh -c -d tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:19,524 checking for gawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:19,524 checking for mawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:19,525 checking for nawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:19,525 checking for awk... awk install_environment.STDOUT DEBUG 2017-11-18 16:56:19,532 checking whether make sets $(MAKE)... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:19,571 checking for gcc... gcc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:19,625 checking whether make sets $(MAKE)... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:19,625 checking for style of include used by make... GNU tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:19,625 checking for gcc... gcc install_environment.STDOUT DEBUG 2017-11-18 16:56:19,755 checking for C compiler default output file name... a.out tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:19,830 checking whether the C compiler works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:19,831 checking for C compiler default output file name... a.out tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:19,831 checking for suffix of executables... install_environment.STDOUT DEBUG 2017-11-18 16:56:19,867 checking whether we are cross compiling... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:19,933 checking whether we are cross compiling... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:19,933 checking for suffix of object files... o install_environment.STDOUT DEBUG 2017-11-18 16:56:19,958 checking whether we are using the GNU C compiler... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,034 checking whether we are using the GNU C compiler... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,035 checking whether gcc accepts -g... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:20,072 checking for gcc option to accept ISO C89... none needed tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,136 checking for gcc option to accept ISO C89... none needed install_environment.STDOUT DEBUG 2017-11-18 16:56:20,184 checking for special C compiler options needed for large files... no install_environment.STDOUT DEBUG 2017-11-18 16:56:20,233 checking for gcc... (cached) gcc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,238 checking dependency style of gcc... gcc3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,238 checking for special C compiler options needed for large files... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,238 checking for _FILE_OFFSET_BITS value needed for large files... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,238 checking for gcc... (cached) gcc install_environment.STDOUT DEBUG 2017-11-18 16:56:20,368 checking whether gcc accepts -g... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 16:56:20,369 checking dependency style of gcc... (cached) gcc3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,443 checking whether we are using the GNU C compiler... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,444 checking whether gcc accepts -g... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,444 checking for gcc option to accept ISO C89... (cached) none needed tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,444 checking dependency style of gcc... (cached) gcc3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,444 checking for ranlib... ranlib install_environment.STDOUT DEBUG 2017-11-18 16:56:20,500 checking build system type... x86_64-apple-darwin15.6.0 install_environment.STDOUT DEBUG 2017-11-18 16:56:20,504 checking how to print strings... printf tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,544 checking build system type... x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,545 checking host system type... x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,545 checking how to print strings... printf tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,751 checking for a sed that does not truncate output... /usr/bin/sed install_environment.STDOUT DEBUG 2017-11-18 16:56:20,890 checking for grep that handles long lines and -e... /usr/bin/grep install_environment.STDOUT DEBUG 2017-11-18 16:56:20,896 checking for fgrep... /usr/bin/grep -F install_environment.STDOUT DEBUG 2017-11-18 16:56:20,932 checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,954 checking for grep that handles long lines and -e... /usr/bin/grep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,954 checking for egrep... /usr/bin/grep -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,955 checking for fgrep... /usr/bin/grep -F tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,955 checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,955 checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:20,955 checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B install_environment.STDOUT DEBUG 2017-11-18 16:56:21,010 checking the name lister (/usr/bin/nm -B) interface... BSD nm install_environment.STDOUT DEBUG 2017-11-18 16:56:21,021 checking the maximum length of command line arguments... 196608 install_environment.STDOUT DEBUG 2017-11-18 16:56:21,025 checking whether the shell understands "+="... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:21,034 func_convert_file_noop install_environment.STDOUT DEBUG 2017-11-18 16:56:21,035 86_64-apple-darwin15.6.0 file names to toolchain format... func_convert_file_noop install_environment.STDOUT DEBUG 2017-11-18 16:56:21,035 /CommandLineTools/usr/bin/ld option to reload object files... -r install_environment.STDOUT DEBUG 2017-11-18 16:56:21,037 checking how to recognize dependent libraries... pass_all install_environment.STDOUT DEBUG 2017-11-18 16:56:21,039 checking how to associate runtime and link libraries... printf %s\n tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,058 checking the name lister (/usr/bin/nm -B) interface... BSD nm tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,059 checking whether ln -s works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,059 checking the maximum length of command line arguments... 196608 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,059 checking whether the shell understands some XSI constructs... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,059 checking whether the shell understands "+="... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,059 func_convert_file_noop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,059 86_64-apple-darwin15.6.0 file names to toolchain format... func_convert_file_noop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,059 /CommandLineTools/usr/bin/ld option to reload object files... -r tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,059 checking how to convert x86_64-apple-darwin15.6.0 file names to x86_64-apple-darwin15.6.0 format... checking how to convert xchecking for /Library/Developerchecking for objdump... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,060 checking how to recognize dependent libraries... pass_all tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,060 checking for dlltool... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,060 checking how to associate runtime and link libraries... printf %s\n tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,060 checking for ar... ar install_environment.STDOUT DEBUG 2017-11-18 16:56:21,099 checking for archiver @FILE support... no install_environment.STDOUT DEBUG 2017-11-18 16:56:21,103 checking for ranlib... (cached) ranlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,162 checking for archiver @FILE support... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,174 checking for strip... strip tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,174 checking for ranlib... (cached) ranlib 127.0.0.1 - - [18/Nov/2017:16:56:21 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:56:21,413 checking for sysroot... no install_environment.STDOUT DEBUG 2017-11-18 16:56:21,433 checking if : is a manifest tool... no install_environment.STDOUT DEBUG 2017-11-18 16:56:21,438 checking for nmedit... nmedit install_environment.STDOUT DEBUG 2017-11-18 16:56:21,440 checking for otool... otool tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,486 checking command to parse /usr/bin/nm -B output from gcc object... ok tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,486 checking for sysroot... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,486 checking for mt... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,487 checking if : is a manifest tool... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,487 checking for dsymutil... dsymutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,487 checking for nmedit... nmedit tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,487 checking for lipo... lipo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,487 checking for otool... otool tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,487 checking for otool64... no install_environment.STDOUT DEBUG 2017-11-18 16:56:21,535 checking for -single_module linker flag... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,588 checking for -single_module linker flag... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,689 checking for -exported_symbols_list linker flag... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:21,805 checking for -force_load linker flag... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,893 checking for -force_load linker flag... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:21,993 checking how to run the C preprocessor... gcc -E install_environment.STDOUT DEBUG 2017-11-18 16:56:22,270 checking for ANSI C header files... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:22,302 checking for ANSI C header files... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:22,403 checking for sys/types.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:22,426 checking for sys/stat.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:22,506 checking for sys/stat.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:22,506 checking for stdlib.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:22,592 checking for string.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:22,609 checking for string.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:22,712 checking for memory.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:22,741 checking for strings.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:22,816 checking for strings.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:22,894 checking for stdint.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:22,917 checking for inttypes.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:22,917 checking for stdint.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,021 checking for unistd.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:23,037 checking for dlfcn.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,123 checking for dlfcn.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,124 checking for objdir... .libs install_environment.STDOUT DEBUG 2017-11-18 16:56:23,223 checking if gcc supports -fno-rtti -fno-exceptions... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,226 checking if gcc supports -fno-rtti -fno-exceptions... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,227 checking for gcc option to produce PIC... -fno-common -DPIC install_environment.STDOUT DEBUG 2017-11-18 16:56:23,279 checking if gcc PIC flag -fno-common -DPIC works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,330 checking if gcc PIC flag -fno-common -DPIC works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,331 checking if gcc static flag -static works... no install_environment.STDOUT DEBUG 2017-11-18 16:56:23,399 checking if gcc supports -c -o file.o... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,436 checking if gcc supports -c -o file.o... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,436 checking if gcc supports -c -o file.o... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,439 raries... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:23,461 checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libchecking dynamic linker cchecking how to hardcode librarchecking whether stripping libraries ischecking if libtool supports shared libraries...checking whether to build shared libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,540 haracteristics... darwin15.6.0 dyld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,541 y paths into programs... immediate tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,541 possible... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,541 yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,541 checking whether to build static libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,541 checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libchecking dynamic linker cchecking how to hardcode librarchecking whether stripping libraries ischecking if libtool supports shared libraries...checking whether to build shared libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,541 checking for fdatasync... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:23,623 checking for usleep... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,642 checking for usleep... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,747 checking for fullfsync... no install_environment.STDOUT DEBUG 2017-11-18 16:56:23,777 checking for localtime_r... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,850 checking for localtime_r... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:23,942 checking whether strerror_r is declared... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,955 checking for gmtime_r... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:23,955 checking whether strerror_r is declared... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:24,060 checking for strerror_r... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:24,090 checking whether strerror_r returns char *... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:24,162 checking whether strerror_r returns char *... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:24,266 checking for library containing tgetent... -lcurses install_environment.STDOUT DEBUG 2017-11-18 16:56:24,378 checking for library containing readline... -lreadline tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:24,471 checking for library containing readline... -lreadline tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:24,472 checking for readline... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:24,544 checking for library containing pthread_create... none required tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:24,578 checking for library containing pthread_create... none required 127.0.0.1 - - [18/Nov/2017:16:56:24 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:56:24,629 checking for whether to support dynamic extensions... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:24,680 checking for library containing dlopen... none required tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:24,680 checking for whether to support dynamic extensions... yes install_environment.STDOUT DEBUG 2017-11-18 16:56:24,762 configure: creating ./config.status tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:24,785 checking for posix_fallocate... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:24,785 configure: creating ./config.status install_environment.STDOUT DEBUG 2017-11-18 16:56:25,696 config.status: creating sqlite3.pc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:25,704 config.status: creating Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:25,705 config.status: creating sqlite3.pc install_environment.STDOUT DEBUG 2017-11-18 16:56:25,781 config.status: executing libtool commands tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:25,810 config.status: executing depfiles commands tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:25,810 config.status: executing libtool commands tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:26,111 /bin/sh ./libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"sqlite\" -DPACKAGE_TARNAME=\"sqliteqlite.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"sqlite\" -DVERSION=\"3.8.3\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_FDATASYNC=1 -DHAVE_USLEEP=1 -DHAVE_LOCALTIME_R=1 -DHAVE_GMTIME_R=1 -DHAVE_DECL_STRERROR_R=1 -DHAVE_STRERROR_R=1 -DHAVE_READLINE=1 -I. -D_REENTRANT=1 -DSQLITE_THREADSAFE=1 -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g -O2 -MT sqlite3.lo -MD -MP -MF .deps/sqlite3.Tpo -c -o sqlite3.lo sqlite3.c install_environment.STDOUT DEBUG 2017-11-18 16:56:26,139 \" -DPACKAGE_VERSION=\"3.8.3\" -DPACKAGE_STRING=\"sqlite\ 3.8.3\" -DPACKAGE_BUGREPORT=\"http://www.s8.3\" "-DPACKAGE_STRING=\AVE_USLEEP=1 -DHAVE_LOCALTIME_R=1 -DHAVE_GMTIME_R=1 -DHAVE_DECL_STRERROR_R=1 -DHAVE_STRERROR_R=1 -DHAVE_READLINE=1 -I. -D_REENTRANT=1 -DSQLITE_THREADSAFE=1 -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g -O2 -MT sqlite3.lo -MD -MP -MF .deps/sqlite3.Tpo -c sqlite3.c -fno-common -DPIC -o .libs/sqlite3.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:26,212 \" -DPACKAGE_VERSION=\"3.8.3\" -DPACKAGE_STRING=\"sqlite\ 3.8.3\" -DPACKAGE_BUGREPORT=\"http://www.s8.3\" "-DPACKAGE_STRING=\AVE_USLEEP=1 -DHAVE_LOCALTIME_R=1 -DHAVE_GMTIME_R=1 -DHAVE_DECL_STRERROR_R=1 -DHAVE_STRERROR_R=1 -DHAVE_READLINE=1 -I. -D_REENTRANT=1 -DSQLITE_THREADSAFE=1 -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g -O2 -MT sqlite3.lo -MD -MP -MF .deps/sqlite3.Tpo -c sqlite3.c -fno-common -DPIC -o .libs/sqlite3.o 127.0.0.1 - - [18/Nov/2017:16:56:27 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:56:30 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:56:33 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:56:37 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:56:40 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:56:43 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:56:46 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:56:49 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:56:52 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:56:56 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:56:56,317 libtool: compile: gcc -DPACKAGE_NAME=\"sqlite\" -DPACKAGE_TARNAME=\"sqlite\" -DPACKAGE_VERSION=\"3."sqlite 3.8.3\"" -DPACKAGE_BUGREPORT=\"http://www.sqlite.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"sqlite\" -DVERSION=\"3.8.3\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_FDATASYNC=1 -DHlibtool: compile: gcc -DPACKAGE_NAME=\"sqlite\" -DPACKAGE_TARNAME=\"sqlite\" -DPACKAGE_VERSION=\"3.8.3\" "-DPACKAGE_Sqlite3.lo -MD -MP -MF .deps/sqlite3.Tpo -c sqlite3.c -o sqlite3.o >/dev/null 2>&1 127.0.0.1 - - [18/Nov/2017:16:56:59 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:57:02 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:57:05 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:57:08 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:57:11 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:57:15 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:57:18 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:57:21 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:57:24 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:57:26,130 TRING=\"sqlite 3.8.3\"" -DPACKAGE_BUGREPORT=\"http://www.sqlite.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"sqlite\" -DVERSION=\"3.8.3\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_FDATASYNC=1 -DHAVE_USLEEP=1 -DHAVE_LOCALTIME_R=1 -DHAVE_GMTIME_R=1 -DHAVE_DECL_STRERROR_R=1 -DHAVE_STRERROR_R=1 -DHAVE_READLINE=1 -I. -D_REENTRANT=1 -DSQLITE_THREADSAFE=1 -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g -O2 -MT s/bin/sh ./libtool --tag=CC --mode=link gcc -D_REENTRANT=1 -DSQLITE_THREADSAFE=1 -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g -O2 -no-undefined c/package_sqlite_3_8_3/c8a5c11cc921/lib sqlite3.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:26,204 mv -f .deps/sqlite3.Tpo .deps/sqlite3.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:26,204 TRING=\"sqlite 3.8.3\"" -DPACKAGE_BUGREPORT=\"http://www.sqlite.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"sqlite\" -DVERSION=\"3.8.3\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_FDATASYNC=1 -DHAVE_USLEEP=1 -DHAVE_LOCALTIME_R=1 -DHAVE_GMTIME_R=1 -DHAVE_DECL_STRERROR_R=1 -DHAVE_STRERROR_R=1 -DHAVE_READLINE=1 -I. -D_REENTRANT=1 -DSQLITE_THREADSAFE=1 -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g -O2 -MT s/bin/sh ./libtool --tag=CC --mode=link gcc -D_REENTRANT=1 -DSQLITE_THREADSAFE=1 -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g -O2 -no-undefined c/package_sqlite_3_8_3/c8a5c11cc921/lib sqlite3.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:26,306 -version-info 8:6:8 -o libsqlite3.la -rpath /galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iulibtool: link: gcc -dynamse/dependencies/sqlite/3.8.3/iua5c11cc921/lib/libsqlite3.0.dylib -comprsion 9.6 -Wl,-single_module tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:26,306 bsqlite3.dylib" && ln -s "libsqlite3.0.dylib" "libsqlite3.dylib") install_environment.STDOUT DEBUG 2017-11-18 16:57:26,355 iclib -o .libs/libsqlite3.0.dylib .libs/sqlite3.o -O2 -install_name /galaxydir/galaxy/databac/package_sqlite_3_8_3/c8atibility_version 9 -current_velibtool: link: (cd ".libs" && rm -f "lilibtool: link: ar cru .libs/libsqlite3.a sqlitelibtool: link: ranlib .libs/libsqlite3.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:26,409 3.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:26,409 iclib -o .libs/libsqlite3.0.dylib .libs/sqlite3.o -O2 -install_name /galaxydir/galaxy/databac/package_sqlite_3_8_3/c8atibility_version 9 -current_velibtool: link: (cd ".libs" && rm -f "lilibtool: link: ar cru .libs/libsqlite3.a sqlitelibtool: link: ranlib .libs/libsqlite3.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:26,409 libtool: link: ( cd ".libs" && rm -f "libsqlite3.la" && ln -s "../libsqlite3.la" "libsqlite3.la" ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:26,409 ING=\"sqlite\ 3.8.3\" -DPACKAGE_BUGREPORT=\"http://www.sqlite.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"s\" -DSTDC_HEADERS=1 -DHAV_H=1 -DHAVE_STDLIB_H=1 -DHAVE_SNGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_FDATASYNC=1 -DHAVE_USLEEP=1 -DHAVE_LOCALTIME_R=1 -DHAVE_GMTIME_R=1 -DHAVE_DECL_STRERROR_R=1 -DHAVE_STRERROR_R=1 -DHAVE_READLINE=1 -I. -D_REENTRANT=1 -DSQLITE_THREADSAFE=1 -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g -O2 -MT shell.o -MD -MP -MF .deps/shell.Tpo -c -o shell.o shell.c install_environment.STDOUT DEBUG 2017-11-18 16:57:27,262 gcc -DPACKAGE_NAME=\"sqlite\" -DPACKAGE_TARNAME=\"sqlite\" -DPACKAGE_VERSION=\"3.8.3\" -DPACKAGE_STRqlite\" -DVERSION=\"3.8.3E_SYS_TYPES_H=1 -DHAVE_SYS_STATTRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRI/bin/sh ./libtool --tag=CC --mode=link gcc -D_ell.o ./libsqlite3.la -lreadline -lcurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,333 mv -f .deps/shell.Tpo .deps/shell.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,333 gcc -DPACKAGE_NAME=\"sqlite\" -DPACKAGE_TARNAME=\"sqlite\" -DPACKAGE_VERSION=\"3.8.3\" -DPACKAGE_STRqlite\" -DVERSION=\"3.8.3E_SYS_TYPES_H=1 -DHAVE_SYS_STATTRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRI/bin/sh ./libtool --tag=CC --mode=link gcc -D_ell.o ./libsqlite3.la -lreadline -lcurses install_environment.STDOUT DEBUG 2017-11-18 16:57:27,384 NTRANT=1 -DSQLITE_THREADSAFE=1 -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g -O2 -o .libs/sqlite3 sh -lreadline -lcurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,434 NTRANT=1 -DSQLITE_THREADSAFE=1 -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g -O2 -o .libs/sqlite3 sh -lreadline -lcurses install_environment.STDOUT DEBUG 2017-11-18 16:57:27,499 database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,536 database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,537 REENTRANT=1 -DSQLITE_THREADSAFE=1 -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_RTREE -g -O2 -o sqlite3 shlibtool: link: gcc -D_REEell.o ./.libs/libsqlite3.dylib ./install-sh -c -d '/galaxydir/galaxy/ /bin/sh ./libtool --mode=install /usr/bin/ins_3/c8a5c11cc921/lib' install_environment.STDOUT DEBUG 2017-11-18 16:57:27,555 tall -c libsqlite3.la '/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8es/sqlite/3.8.3/iuc/packa921/lib/libsqlite3.0.dylib install_environment.STDOUT DEBUG 2017-11-18 16:57:27,564 r/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib && { ln -s -f { rm -f libsqlite3.dylib }) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,641 tall -c libsqlite3.la '/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8es/sqlite/3.8.3/iuc/packa921/lib/libsqlite3.0.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,641 r/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib && { ln -s -f { rm -f libsqlite3.dylib }) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,641 libtool: install: /usr/bin/install -c .libs/libsqlite3.0.dylib /galaxydir/galaxy/database/dependencige_sqlite_3_8_3/c8a5c11cclibtool: install: (cd /galaxydilibsqlite3.0.dylib libsqlite3.dylib || && ln -s libsqlite3.0.dylib libsqlite3.dylib; };libtool: install: /usr/bin/install -c .libs/libsqlite3.lai /ite3.la tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,641 n/install -c .libs/libsqlite3.a /galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlqlite3.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,641 galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib/libsqlite3.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,641 ase/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib/libsqlite3.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,642 /sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/bin' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,745 r/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/bin' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,745 lite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/bin/sqlite3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,745 e' install_environment.STDOUT DEBUG 2017-11-18 16:57:27,772 galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib/libsqllibtool: install: /usr/biite_3_8_3/c8a5c11cc921/lib/libslibtool: install: chmod 644 /galaxydir/libtool: install: ranlib /galaxydir/galaxy/datab ./install-sh -c -d '/galaxydir/galaxy/database/dependencies /bin/sh ./libtool --mode=install /usr/bin/install -c sqlite3 '/galaxydilibtool: install: /usr/bin/install -c .libs/sqlite3 /galaxydir/galaxy/database/dependencies/sq ./install-sh -c -d '/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/includ /usr/bin/install -c -m 644 sqlite3.h sqlite3ext.h '/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/incl ./install-sh -c -d '/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/share/man/man1' install_environment.STDOUT DEBUG 2017-11-18 16:57:27,822 age_sqlite_3_8_3/c8a5c11cc921/share/man/man1' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,850 ude' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,851 galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib/libsqllibtool: install: /usr/biite_3_8_3/c8a5c11cc921/lib/libslibtool: install: chmod 644 /galaxydir/libtool: install: ranlib /galaxydir/galaxy/datab ./install-sh -c -d '/galaxydir/galaxy/database/dependencies /bin/sh ./libtool --mode=install /usr/bin/install -c sqlite3 '/galaxydilibtool: install: /usr/bin/install -c .libs/sqlite3 /galaxydir/galaxy/database/dependencies/sq ./install-sh -c -d '/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/includ /usr/bin/install -c -m 644 sqlite3.h sqlite3ext.h '/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/incl ./install-sh -c -d '/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/share/man/man1' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,851 age_sqlite_3_8_3/c8a5c11cc921/share/man/man1' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,851 /usr/bin/install -c -m 644 sqlite3.1 '/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/pack ./install-sh -c -d '/gal' install_environment.STDOUT DEBUG 2017-11-18 16:57:27,880 axydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib/pkgconfig /usr/bin/install -c -m 6cc921/lib/pkgconfig' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:27,954 axydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib/pkgconfig /usr/bin/install -c -m 6cc921/lib/pkgconfig' 127.0.0.1 - - [18/Nov/2017:16:57:27 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:sqlite DEBUG 2017-11-18 16:57:28,057 44 sqlite3.pc '/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11 tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 16:57:28,190 Changing status for tool dependency sqlite from Installing to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:57:28,190 Updating an existing record for version 3.8.3 of tool dependency sqlite for revision c8a5c11cc921 of repository package_sqlite_3_8_3 by updating the status from Installing to Installed. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 16:57:28,223 Tool dependency sqlite version 3.8.3 has been installed in /galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:57:30,928 Creating a new record for version 3.10.2 of tool dependency atlas for revision 98c017ec230d of repository package_atlas_3_10. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:57:31,016 Updating an existing record for version 3.10.2 of tool dependency atlas for revision 98c017ec230d of repository package_atlas_3_10 by updating the status from Never installed to Installing. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 16:57:31,061 Changing status for tool dependency atlas from Installing to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:57:31,061 Updating an existing record for version 3.10.2 of tool dependency atlas for revision 98c017ec230d of repository package_atlas_3_10 by updating the status from Installing to Installed. 127.0.0.1 - - [18/Nov/2017:16:57:30 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:57:33,760 Creating a new record for version 6.0 of tool dependency ncurses for revision 0efde9889efd of repository package_ncurses_6_0. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:57:33,817 Updating an existing record for version 6.0 of tool dependency ncurses for revision 0efde9889efd of repository package_ncurses_6_0 by updating the status from Never installed to Installing. tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 16:57:33,840 Attempting to download via url: https://depot.galaxyproject.org/software/ncurses/ncurses_6.0_src_all.tar.gz 127.0.0.1 - - [18/Nov/2017:16:57:34 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 16:57:36,163 Successfully downloaded from url: https://depot.galaxyproject.org/software/ncurses/ncurses_6.0_src_all.tar.gz tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,163 + ./configure --prefix=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd --with-shared --enable-symlinks && make && make install install_environment.STDOUT DEBUG 2017-11-18 16:57:36,403 Configuring NCURSES 6.0 ABI 6 (Sat Nov 18 16:57:36 EST 2017) install_environment.STDOUT DEBUG 2017-11-18 16:57:36,435 checking for package patch date... 20150725 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,478 checking for egrep... grep -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,478 Configuring NCURSES 6.0 ABI 6 (Sat Nov 18 16:57:36 EST 2017) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,478 checking for package version... 6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,479 checking for package patch date... 20150725 install_environment.STDOUT DEBUG 2017-11-18 16:57:36,634 checking host system type... x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,685 checking build system type... x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,685 checking host system type... x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,685 checking target system type... x86_64-apple-darwin15.6.0 install_environment.STDOUT DEBUG 2017-11-18 16:57:36,700 Configuring for darwin15.6.0 install_environment.STDOUT DEBUG 2017-11-18 16:57:36,701 efde9889efd install_environment.STDOUT DEBUG 2017-11-18 16:57:36,705 o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,786 Configuring for darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,786 efde9889efd tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,787 o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,787 checking for prefix... /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0checking for gnatgcc... nchecking for gcc... gcc install_environment.STDOUT DEBUG 2017-11-18 16:57:36,873 checking for C compiler default output... a.out install_environment.STDOUT DEBUG 2017-11-18 16:57:36,883 checking whether we are cross compiling... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,889 checking for C compiler default output... a.out tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,889 checking whether the C compiler works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,889 checking whether we are cross compiling... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:36,991 checking for executable suffix... install_environment.STDOUT DEBUG 2017-11-18 16:57:36,996 checking for object suffix... o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:37,092 checking for object suffix... o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:37,093 checking whether we are using the GNU C compiler... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:37,107 checking whether gcc accepts -g... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:37,195 checking whether gcc accepts -g... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:37,195 checking version of gcc... 8.0.0 install_environment.STDOUT DEBUG 2017-11-18 16:57:37,286 checking for gcc option to accept ANSI C... none needed tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:37,299 checking for gcc option to accept ANSI C... none needed tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:37,299 checking $CC variable... ok install_environment.STDOUT DEBUG 2017-11-18 16:57:37,401 checking how to run the C preprocessor... gcc -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:37,403 checking how to run the C preprocessor... gcc -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:37,616 checking whether gcc needs -traditional... no install_environment.STDOUT DEBUG 2017-11-18 16:57:37,725 checking whether gcc understands -c and -o together... yes 127.0.0.1 - - [18/Nov/2017:16:57:37 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:57:37,727 checking if you want to ensure bool is consistent with C++... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:37,822 checking whether gcc understands -c and -o together... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:37,822 checking for ldconfig... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:37,822 checking if you want to ensure bool is consistent with C++... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:37,822 checking for g++... g++ install_environment.STDOUT DEBUG 2017-11-18 16:57:37,882 checking whether we are using the GNU C++ compiler... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:37,923 checking whether we are using the GNU C++ compiler... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,027 checking whether g++ accepts -g... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:38,264 checking if g++ works... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:38,292 checking version of /usr/bin/g++... 8.0.0 install_environment.STDOUT DEBUG 2017-11-18 16:57:38,293 checking if you want to build with Ada95... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:38,294 checking if you want to install manpages... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:38,295 checking if you want to build test-programs... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:38,310 checking for mawk... no install_environment.STDOUT DEBUG 2017-11-18 16:57:38,312 checking for nawk... no install_environment.STDOUT DEBUG 2017-11-18 16:57:38,315 checking for egrep... (cached) grep -E install_environment.STDOUT DEBUG 2017-11-18 16:57:38,326 checking for tdlint... no install_environment.STDOUT DEBUG 2017-11-18 16:57:38,328 checking for alint... no install_environment.STDOUT DEBUG 2017-11-18 16:57:38,330 checking for lclint... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,330 checking if g++ works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,330 checking for g++... /usr/bin/g++ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,330 checking version of /usr/bin/g++... 8.0.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,331 checking if you want to build C++ binding and demo... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,331 checking if you want to build with Ada95... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,331 checking if you want to install terminal database... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,331 checking if you want to install manpages... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,331 checking if you want to build programs such as tic... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,331 checking if you want to build test-programs... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,332 checking if you wish to install curses.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,332 checking for mawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,332 checking for gawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,332 checking for nawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,332 checking for awk... awk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,332 checking for egrep... (cached) grep -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,332 checking for a BSD compatible install... /usr/bin/install -c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,332 checking for tdlint... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,332 checking for lint... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,332 checking for alint... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,333 checking for splint... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,333 checking for lclint... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,333 checking whether ln -s works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,333 Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 install_environment.STDOUT DEBUG 2017-11-18 16:57:38,341 checking if ln -s -f options work... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:38,394 checking if you want to use pkg-config... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:38,397 checking if we should install .pc files... no install_environment.STDOUT DEBUG 2017-11-18 16:57:38,412 checking if filesystem supports mixed-case filenames... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,433 checking if ln -s -f options work... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,434 checking for long file names... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,434 checking if you want to use pkg-config... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,434 checking for pkg-config... none tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,434 checking if we should install .pc files... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,434 checking if we should assume mixed-case filenames... auto tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,434 checking if filesystem supports mixed-case filenames... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,434 configure: WARNING: pkg-config is not installed install_environment.STDOUT DEBUG 2017-11-18 16:57:38,439 checking for exctags... no install_environment.STDOUT DEBUG 2017-11-18 16:57:38,443 checking for exetags... no install_environment.STDOUT DEBUG 2017-11-18 16:57:38,445 checking for ctags... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:38,479 checking for ranlib... ranlib install_environment.STDOUT DEBUG 2017-11-18 16:57:38,482 checking for ar... ar install_environment.STDOUT DEBUG 2017-11-18 16:57:38,484 checking for ar... (cached) ar tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,535 checking whether make sets ${MAKE}... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,535 checking for exctags... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,535 checking for ctags... ctags tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,535 checking for exetags... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,535 checking for etags... etags tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,535 checking for ctags... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,535 checking for makeflags variable... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,535 checking for ranlib... ranlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,536 checking for ld... ld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,536 checking for ar... ar tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,536 checking for nm... nm tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,536 checking for ar... (cached) ar install_environment.STDOUT DEBUG 2017-11-18 16:57:38,556 checking if you have specified an install-prefix... install_environment.STDOUT DEBUG 2017-11-18 16:57:38,559 checking if you want to build libraries with libtool... no install_environment.STDOUT DEBUG 2017-11-18 16:57:38,561 checking if you want to build static libraries... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:38,562 checking if you want to build profiling libraries... no install_environment.STDOUT DEBUG 2017-11-18 16:57:38,563 checking for specified models... shared normal debug install_environment.STDOUT DEBUG 2017-11-18 16:57:38,571 checking if you want to have a library-prefix... auto install_environment.STDOUT DEBUG 2017-11-18 16:57:38,572 checking if you want to build a separate terminfo library... no install_environment.STDOUT DEBUG 2017-11-18 16:57:38,573 checking if you want to link with the GPM mouse library... maybe install_environment.STDOUT DEBUG 2017-11-18 16:57:38,625 checking for default loader flags... install_environment.STDOUT DEBUG 2017-11-18 16:57:38,626 checking if shared libraries should be relinked during install... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:38,627 checking if release/abi version should be used for shared libs... auto tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,637 checking for options to update archives... -curv tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,637 checking if you have specified an install-prefix... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,637 checking if libtool -version-number should be used... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,637 checking if you want to build libraries with libtool... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,637 checking if you want to build shared libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,638 checking if you want to build static libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,638 checking if you want to build debug libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,638 checking if you want to build profiling libraries... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,638 checking if you want to build C++ shared libraries... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,638 checking for specified models... shared normal debug tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,638 checking for default model... shared tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,638 checking if you want to have a library-prefix... auto tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,638 checking for PATH separator... : tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,638 checking if you want to build a separate terminfo library... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,638 checking if you want to build a separate tic library... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,638 checking if you want to link with the GPM mouse library... maybe tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,638 checking for gpm.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,639 checking for default loader flags... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,639 checking if rpath option should be used... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,639 checking if shared libraries should be relinked during install... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,639 checking for an rpath option... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,639 checking if release/abi version should be used for shared libs... auto tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,742 checking which gcc option to use... -fPIC install_environment.STDOUT DEBUG 2017-11-18 16:57:38,789 checking if ld -search_paths_first works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,843 checking if ld -search_paths_first works... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:38,863 checking if versioned-symbols file should be used... no install_environment.STDOUT DEBUG 2017-11-18 16:57:38,864 checking if rpath-hack should be disabled... no install_environment.STDOUT DEBUG 2017-11-18 16:57:38,865 checking if you wish to append extra suffix to header/library paths... install_environment.STDOUT DEBUG 2017-11-18 16:57:38,866 checking if external terminfo-database is used... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:38,867 checking whether to use hashed database instead of directory/tree... no install_environment.STDOUT DEBUG 2017-11-18 16:57:38,873 checking if you want modern xterm or antique... xterm-new install_environment.STDOUT DEBUG 2017-11-18 16:57:38,878 checking for list of terminfo directories... /galaxydir/galaxy/database/dependencies/ncurses/6.0/iucchecking for default term889efd/share/terminfo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,947 checking if CFLAGS option -no-cpp-precomp works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,947 checking if versioned-symbols file should be used... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,948 checking if you want to disable library suffixes... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,948 checking if rpath-hack should be disabled... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,948 checking for updated LDFLAGS... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,948 checking if you wish to append extra suffix to header/library paths... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,948 checking if you wish to install ncurses overwriting curses... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,948 checking if external terminfo-database is used... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,948 checking which terminfo source-file will be installed... ${top_srcdir}/misc/terminfo.src tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,948 checking whether to use hashed database instead of directory/tree... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,948 checking for list of fallback descriptions... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,949 checking if you want modern xterm or antique... xterm-new tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,949 checking if xterm backspace sends BS or DEL... BS tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,949 /package_ncurses_6_0/0efde9889efd/share/terminfo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:38,949 checking for list of terminfo directories... /galaxydir/galaxy/database/dependencies/ncurses/6.0/iucchecking for default term889efd/share/terminfo install_environment.STDOUT DEBUG 2017-11-18 16:57:38,987 on selected... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:39,020 selected... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:39,020 upport... no install_environment.STDOUT DEBUG 2017-11-18 16:57:39,045 checking if you want to use restricted environment when running as root... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,053 on selected... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,053 selected... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,054 upport... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,054 info directory... /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9checking if big-core optichecking if big-strings option checking if you want termcap-fallback schecking if ~/.terminfo is wanted... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,054 checking if you want to use restricted environment when running as root... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,156 checking for remove... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:39,258 checking for unlink... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,261 checking for unlink... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,468 checking if link/symlink functions work... link symlink install_environment.STDOUT DEBUG 2017-11-18 16:57:39,471 checking if tic should use symbolic links... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:39,476 checking if tputs should process BSD-style prefix padding... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,572 checking if tic should use symbolic links... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,572 checking if you want broken-linker support code... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,572 checking if tputs should process BSD-style prefix padding... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,572 checking if SIGWINCH is defined... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:39,636 checking for nl_langinfo and CODESET... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:39,644 checking whether to enable _LP64 definition in curses.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,675 checking for nl_langinfo and CODESET... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,675 checking if you want wide-character code... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,676 checking whether to enable _LP64 definition in curses.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,676 checking for special C compiler options needed for large files... no install_environment.STDOUT DEBUG 2017-11-18 16:57:39,698 checking for _FILE_OFFSET_BITS value needed for large files... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,779 checking for _FILE_OFFSET_BITS value needed for large files... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,779 checking for _LARGE_FILES value needed for large files... no install_environment.STDOUT DEBUG 2017-11-18 16:57:39,834 checking for _LARGEFILE_SOURCE value needed for large files... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,881 checking for _LARGEFILE_SOURCE value needed for large files... no install_environment.STDOUT DEBUG 2017-11-18 16:57:39,980 checking whether to use struct dirent64... no install_environment.STDOUT DEBUG 2017-11-18 16:57:39,981 checking for type of bool... auto install_environment.STDOUT DEBUG 2017-11-18 16:57:39,982 checking for type of chtype... uint32_t install_environment.STDOUT DEBUG 2017-11-18 16:57:39,983 checking for type of mmask_t... uint32_t install_environment.STDOUT DEBUG 2017-11-18 16:57:39,984 checking for type of tparm args... intptr_t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,985 checking for fseeko... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,987 checking whether to use struct dirent64... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,987 checking if you want tparm not to use X/Open fixed-parameter list... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,987 checking for type of bool... auto tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,988 checking for alternate terminal capabilities file... Caps tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,988 checking for type of chtype... uint32_t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,989 checking for type of ospeed... short tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,989 checking for type of mmask_t... uint32_t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,989 checking for size CCHARW_MAX... 5 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,989 checking for type of tparm args... intptr_t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:39,989 checking if RCS identifiers should be compiled-in... no install_environment.STDOUT DEBUG 2017-11-18 16:57:40,468 checking format of man-pages... normal install_environment.STDOUT DEBUG 2017-11-18 16:57:40,469 checking if manpage aliases will be installed... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:40,470 checking for manpage tbl... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:40,498 checking format of man-pages... normal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:40,498 checking for manpage renaming... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:40,498 checking if manpage aliases will be installed... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:40,498 checking if manpage symlinks should be used... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:40,498 checking for manpage tbl... no install_environment.STDOUT DEBUG 2017-11-18 16:57:40,774 checking if you want to build with SCREEN extensions... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:40,778 checking for extended use of const keyword... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:40,779 checking if you want to use extended mouse encoding... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:40,784 checking if you want $NCURSES_NO_PADDING code... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:40,803 checking if you want to build with function extensions... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:40,805 checking if you want to build with SCREEN extensions... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:40,806 checking if you want to build with terminal-driver... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:40,806 checking for extended use of const keyword... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:40,806 checking if you want to use extended colors... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:40,806 checking if you want to use extended mouse encoding... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:40,806 checking if you want to use extended putwin/screendump... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:40,806 checking if you want $NCURSES_NO_PADDING code... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:40,807 configure: WARNING: This option applies only to wide-character library 127.0.0.1 - - [18/Nov/2017:16:57:40 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:41,121 checking for ANSI C header files... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:41,164 checking for sys/types.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:41,225 checking for sys/types.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:41,326 checking for sys/stat.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:41,338 checking for stdlib.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:41,426 checking for stdlib.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:41,525 checking for memory.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:41,526 checking for string.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:41,527 checking for memory.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:41,629 checking for strings.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:41,695 checking for inttypes.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:41,733 checking for inttypes.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:41,835 checking for stdint.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:41,868 checking for unistd.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:41,936 checking for unistd.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,039 checking for signed char... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:42,070 checking size of signed char... 1 install_environment.STDOUT DEBUG 2017-11-18 16:57:42,084 checking if you want SIGWINCH handler... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:42,088 checking if you want all development code... no install_environment.STDOUT DEBUG 2017-11-18 16:57:42,089 checking if you want limited support for xmc... no install_environment.STDOUT DEBUG 2017-11-18 16:57:42,094 checking if you want hashmap scrolling-optimization code... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:42,100 checking if you want interop bindings... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:42,104 checking if you want reentrant code... no install_environment.STDOUT DEBUG 2017-11-18 16:57:42,108 checking if you want wgetch-events code... no install_environment.STDOUT DEBUG 2017-11-18 16:57:42,109 checking if you want to see compiler warnings... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,140 checking size of signed char... 1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,140 checking if you want to use signed Boolean array in term.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,141 checking if you want SIGWINCH handler... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,141 checking if you want user-definable terminal capabilities like termcap... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,141 checking if you want all development code... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,141 checking if you want hard-tabs code... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,141 checking if you want limited support for xmc... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,141 checking if you do not want to assume colors are white-on-black... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,141 checking if you want hashmap scrolling-optimization code... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,141 checking if you want colorfgbg code... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,141 checking if you want interop bindings... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,141 checking if you want to link with the pthread library... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,141 checking if you want reentrant code... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,141 checking if you want experimental safe-sprintf code... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,141 checking if you want wgetch-events code... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,142 checking if you want to see long compiling messages... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,142 checking if you want to see compiler warnings... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,142 configure: checking for gcc __attribute__ directives... install_environment.STDOUT DEBUG 2017-11-18 16:57:42,164 ... scanf tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,244 ... scanf tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,244 ... printf install_environment.STDOUT DEBUG 2017-11-18 16:57:42,293 ... unused tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,349 ... unused install_environment.STDOUT DEBUG 2017-11-18 16:57:42,368 checking if you want to work around bogus compiler/loader warnings... no install_environment.STDOUT DEBUG 2017-11-18 16:57:42,371 checking if you want to use dmalloc for testing... no install_environment.STDOUT DEBUG 2017-11-18 16:57:42,373 checking if you want to use valgrind for testing... no install_environment.STDOUT DEBUG 2017-11-18 16:57:42,385 checking whether to add trace feature to all models... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,450 ... noreturn tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,450 checking if you want to work around bogus compiler/loader warnings... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,450 checking if you want to enable runtime assertions... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,450 checking if you want to use dmalloc for testing... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,450 checking if you want to use dbmalloc for testing... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,450 checking if you want to use valgrind for testing... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,450 checking if you want to perform memory-leak testing... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,450 checking whether to add trace feature to all models... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,451 checking if we want to use GNAT projects... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:42,456 checking for gettimeofday... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:42,544 checking for ANSI C header files... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,554 checking for gettimeofday... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,554 checking if -lm needed for math functions... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,554 checking for ANSI C header files... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,658 checking for dirent.h that defines DIR... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:42,676 checking for opendir in -ldir... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,763 checking for opendir in -ldir... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,763 checking whether time.h and sys/time.h may both be included... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:42,816 checking for regcomp... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,864 checking for regcomp... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:42,964 checking for regular-expression headers... regex.h install_environment.STDOUT DEBUG 2017-11-18 16:57:42,967 checking for fcntl.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:43,068 checking for fcntl.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:43,068 checking for getopt.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:43,108 checking for limits.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:43,169 checking for limits.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:43,169 checking for locale.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:43,236 checking for math.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:43,270 checking for math.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:43,363 checking for sys/bsdtypes.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:43,375 checking for poll.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:43,375 checking for sys/bsdtypes.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:43,478 checking for sys/ioctl.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:43,494 checking for sys/param.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:43,579 checking for sys/param.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:43,579 checking for sys/poll.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:43,651 checking for sys/select.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:43,683 checking for sys/select.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:43,784 checking for sys/time.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:43,870 checking for sys/times.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:43,885 checking for sys/times.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:43,990 checking for ttyent.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:44,036 checking for unistd.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:44,091 checking for unistd.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:44,192 checking for wctype.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:44,207 checking for unistd.h... (cached) yes 127.0.0.1 - - [18/Nov/2017:16:57:43 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:44,297 checking for unistd.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:44,297 checking for getopt.h... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 16:57:44,513 checking for header declaring getopt variables... unistd.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:44,603 checking for header declaring getopt variables... unistd.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:44,706 checking if sys/time.h works with sys/select.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:44,722 checking for an ANSI C-conforming const... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:44,809 checking for an ANSI C-conforming const... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:44,810 checking for inline... inline install_environment.STDOUT DEBUG 2017-11-18 16:57:44,864 checking if gcc supports options to tune inlining... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:44,912 checking if gcc supports options to tune inlining... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:45,014 checking for signal global datatype... volatile sig_atomic_t install_environment.STDOUT DEBUG 2017-11-18 16:57:45,049 checking if unsigned literals are legal... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:45,116 checking if unsigned literals are legal... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:45,218 checking if external errno is declared... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:45,265 checking if external errno exists... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:45,322 checking if external errno exists... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:45,630 checking if data-only library module links... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:45,723 checking for getcwd... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:45,730 checking for getcwd... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:45,931 checking for getegid... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:46,016 checking for geteuid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:46,032 checking for geteuid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:46,237 checking for getopt... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:46,294 checking for getttynam... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:46,337 checking for getttynam... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:46,443 checking for issetugid... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:46,539 checking for poll... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:46,547 checking for poll... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:46,648 checking for putenv... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:46,658 checking for remove... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:46,752 checking for remove... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:46,855 checking for select... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:46,864 checking for setbuf... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:46,959 checking for setbuf... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:47,058 checking for setenv... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:47,062 checking for setbuffer... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:47,062 checking for setenv... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:47,167 checking for setvbuf... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:47,265 checking for sigaction... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:47,268 checking for sigaction... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:47,470 checking for sigvec... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:47,498 checking for strdup... yes 127.0.0.1 - - [18/Nov/2017:16:57:47 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:47,572 checking for strdup... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:47,672 checking for strstr... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:47,716 checking for tcgetpgrp... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:47,775 checking for tcgetpgrp... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:47,876 checking for times... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:47,920 checking for vsnprintf... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:47,978 checking for vsnprintf... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:48,083 checking for isascii... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:48,099 checking whether sigaction needs _POSIX_SOURCE... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:48,186 checking whether sigaction needs _POSIX_SOURCE... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:49,015 checking if nanosleep really works... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:49,017 checking for termio.h... no install_environment.STDOUT DEBUG 2017-11-18 16:57:49,106 checking for unistd.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:49,116 checking for termio.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:49,116 checking for termios.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:49,116 checking for unistd.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:49,216 checking whether termios.h needs _POSIX_SOURCE... no install_environment.STDOUT DEBUG 2017-11-18 16:57:49,257 checking for tcgetattr... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:49,319 checking for tcgetattr... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:49,420 checking for vsscanf function or workaround... vsscanf install_environment.STDOUT DEBUG 2017-11-18 16:57:49,453 checking for working mkstemp... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:49,524 checking for working mkstemp... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:49,627 checking whether setvbuf arguments are reversed... no install_environment.STDOUT DEBUG 2017-11-18 16:57:49,629 checking for intptr_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:49,733 checking for intptr_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:49,733 checking for ssize_t... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:49,750 checking for type sigaction_t... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:49,837 checking for type sigaction_t... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:49,837 checking declaration of size-change... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:49,881 checking for memmove... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:49,938 checking for memmove... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:50,038 checking if poll really works... no install_environment.STDOUT DEBUG 2017-11-18 16:57:50,058 checking for va_copy... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:50,139 checking for va_copy... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:50,139 checking for __va_copy... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:50,211 checking for pid_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:50,241 checking for pid_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:50,241 checking for unistd.h... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 16:57:50,288 checking for vfork.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:50,342 checking for vfork.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:50,446 checking for fork... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:50,476 checking for vfork... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:50,487 checking for working vfork... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:50,546 checking for vfork... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:50,547 checking for working fork... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:50,547 checking for working vfork... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:50,647 checking for openpty in -lutil... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:50,778 checking for openpty header... util.h 127.0.0.1 - - [18/Nov/2017:16:57:50 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:50,850 checking for openpty header... util.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:50,953 checking if we should include stdbool.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:50,995 checking for builtin bool type... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:51,056 checking for builtin bool type... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:51,159 checking for library stdc++... no install_environment.STDOUT DEBUG 2017-11-18 16:57:51,162 checking whether /usr/bin/g++ understands -c and -o together... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:51,264 checking whether /usr/bin/g++ understands -c and -o together... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:51,366 checking how to run the C++ preprocessor... /usr/bin/g++ -E install_environment.STDOUT DEBUG 2017-11-18 16:57:51,500 checking for typeinfo... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:51,569 checking for typeinfo... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:51,772 checking for iostream... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:52,181 checking if iostream uses std-namespace... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,183 checking if iostream uses std-namespace... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:52,256 checking for builtin bool type... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,285 checking if we should include stdbool.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,285 checking for builtin bool type... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,389 checking for size of bool... unsigned char install_environment.STDOUT DEBUG 2017-11-18 16:57:52,426 checking for special defines needed for etip.h... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,490 checking for special defines needed for etip.h... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,490 checking if /usr/bin/g++ accepts parameter initialization... no install_environment.STDOUT DEBUG 2017-11-18 16:57:52,563 checking if /usr/bin/g++ accepts static_cast... yes install_environment.STDOUT DEBUG 2017-11-18 16:57:52,579 checking for library subsets... ticlib+termlib+ext_tinfo+base+ext_funcs install_environment.STDOUT DEBUG 2017-11-18 16:57:52,580 checking default library-dependency suffix... .dylib install_environment.STDOUT DEBUG 2017-11-18 16:57:52,581 checking c++ library-dependency suffix... .a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,594 checking if /usr/bin/g++ accepts static_cast... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,594 checking for gnatmake... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,594 checking for library subsets... ticlib+termlib+ext_tinfo+base+ext_funcs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,595 checking default library suffix... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,595 checking default library-dependency suffix... .dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,595 checking default object directory... obj_s tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,595 checking c++ library-dependency suffix... .a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,595 checking where we will install curses.h... ${prefix}/include/ncurses install_environment.STDOUT DEBUG 2017-11-18 16:57:52,675 checking for src modules... ncurses progs panel menu form tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,696 checking for src modules... ncurses progs panel menu form install_environment.STDOUT DEBUG 2017-11-18 16:57:52,708 checking for defines to add to ncurses6-config script... -D_DARWIN_C_SOURCE install_environment.STDOUT DEBUG 2017-11-18 16:57:52,757 configure: creating ./config.status tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,797 checking for tic... /usr/bin/tic tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,797 checking for defines to add to ncurses6-config script... -D_DARWIN_C_SOURCE tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,797 package: ncurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:52,797 configure: creating ./config.status install_environment.STDOUT DEBUG 2017-11-18 16:57:53,193 config.status: creating include/curses.head tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:53,206 config.status: creating include/MKterm.h.awk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:53,208 config.status: creating include/curses.head tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:53,309 config.status: creating include/ncurses_dll.h install_environment.STDOUT DEBUG 2017-11-18 16:57:53,353 config.status: creating include/termcap.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:53,410 config.status: creating include/termcap.h install_environment.STDOUT DEBUG 2017-11-18 16:57:53,483 config.status: creating man/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:53,513 config.status: creating include/unctrl.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:53,513 config.status: creating man/Makefile install_environment.STDOUT DEBUG 2017-11-18 16:57:53,610 config.status: creating ncurses/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:53,614 config.status: creating include/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:53,614 config.status: creating ncurses/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:53,715 config.status: creating progs/Makefile install_environment.STDOUT DEBUG 2017-11-18 16:57:53,796 config.status: creating panel/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:53,825 config.status: creating panel/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:53,926 config.status: creating menu/Makefile install_environment.STDOUT DEBUG 2017-11-18 16:57:53,969 config.status: creating form/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,027 config.status: creating form/Makefile 127.0.0.1 - - [18/Nov/2017:16:57:53 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,129 config.status: creating test/Makefile install_environment.STDOUT DEBUG 2017-11-18 16:57:54,150 config.status: creating misc/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,232 config.status: creating misc/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,233 config.status: creating c++/Makefile install_environment.STDOUT DEBUG 2017-11-18 16:57:54,309 config.status: creating misc/run_tic.sh tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,336 config.status: creating misc/run_tic.sh tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,437 config.status: creating misc/ncurses-config install_environment.STDOUT DEBUG 2017-11-18 16:57:54,457 config.status: creating man/ncurses6-config.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,541 config.status: creating man/ncurses6-config.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,541 config.status: creating Makefile install_environment.STDOUT DEBUG 2017-11-18 16:57:54,583 config.status: creating include/ncurses_cfg.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,643 config.status: creating include/ncurses_cfg.h install_environment.STDOUT DEBUG 2017-11-18 16:57:54,725 Appending rules for normal model (ncurses: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,746 Appending rules for shared model (ncurses: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,746 Appending rules for normal model (ncurses: ticlib+termlib+ext_tinfo+base+ext_funcs) install_environment.STDOUT DEBUG 2017-11-18 16:57:54,783 Appending rules for shared model (progs: ticlib+termlib+ext_tinfo+base+ext_funcs) install_environment.STDOUT DEBUG 2017-11-18 16:57:54,812 Appending rules for debug model (progs: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,847 Appending rules for debug model (ncurses: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,847 Appending rules for shared model (progs: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,848 Appending rules for normal model (progs: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,848 Appending rules for debug model (progs: ticlib+termlib+ext_tinfo+base+ext_funcs) install_environment.STDOUT DEBUG 2017-11-18 16:57:54,865 Appending rules for normal model (panel: ticlib+termlib+ext_tinfo+base+ext_funcs) install_environment.STDOUT DEBUG 2017-11-18 16:57:54,911 Appending rules for shared model (menu: ticlib+termlib+ext_tinfo+base+ext_funcs) install_environment.STDOUT DEBUG 2017-11-18 16:57:54,938 Appending rules for debug model (menu: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,950 Appending rules for shared model (panel: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,950 Appending rules for normal model (panel: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,950 Appending rules for debug model (panel: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,950 Appending rules for shared model (menu: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,950 Appending rules for normal model (menu: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:54,951 Appending rules for debug model (menu: ticlib+termlib+ext_tinfo+base+ext_funcs) install_environment.STDOUT DEBUG 2017-11-18 16:57:54,995 Appending rules for normal model (form: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,051 Appending rules for shared model (form: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,051 Appending rules for normal model (form: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,052 Appending rules for debug model (form: ticlib+termlib+ext_tinfo+base+ext_funcs) install_environment.STDOUT DEBUG 2017-11-18 16:57:55,063 Appending rules for shared model (test: ticlib+termlib+ext_tinfo+base+ext_funcs) install_environment.STDOUT DEBUG 2017-11-18 16:57:55,092 Appending rules for debug model (test: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,152 Appending rules for shared model (test: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,152 Appending rules for normal model (test: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,152 Appending rules for debug model (test: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,152 Appending rules for shared model (c++: ticlib+termlib+ext_tinfo+base+ext_funcs) install_environment.STDOUT DEBUG 2017-11-18 16:57:55,156 Appending rules for debug model (c++: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,253 Appending rules for debug model (c++: ticlib+termlib+ext_tinfo+base+ext_funcs) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,358 creating headers.sh install_environment.STDOUT DEBUG 2017-11-18 16:57:55,385 install_environment.STDOUT DEBUG 2017-11-18 16:57:55,389 install_environment.STDOUT DEBUG 2017-11-18 16:57:55,396 xterm terminfo: xterm-new install_environment.STDOUT DEBUG 2017-11-18 16:57:55,404 bin directory: /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0 lib directory: /gefde9889efd/include/ncurses install_environment.STDOUT DEBUG 2017-11-18 16:57:55,407 alaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man install_environment.STDOUT DEBUG 2017-11-18 16:57:55,409 ir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/terminfo install_environment.STDOUT DEBUG 2017-11-18 16:57:55,413 ** Include-directory is not in a standard location install_environment.STDOUT DEBUG 2017-11-18 16:57:55,496 database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib" all install_environment.STDOUT DEBUG 2017-11-18 16:57:55,503 info.head ./../include/Caps ./terminfo.tail >terminfo.5 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,563 ** Configuration summary for NCURSES 6.0 20150725: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,664 extended funcs: yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,664 xterm terminfo: xterm-new install_environment.STDOUT DEBUG 2017-11-18 16:57:55,737 r/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/ncurs9efd/lib" all install_environment.STDOUT DEBUG 2017-11-18 16:57:55,751 AWK=awk sh ./MKkey_defs.sh ./Caps >>curses.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,766 efde9889efd/bin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,766 alaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,766 bin directory: /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0 lib directory: /gefde9889efd/include/ncurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,766 alaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,766 ir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/terminfo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,766 include directory: /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0 man directory: /g terminfo directory: /galaxyd tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,767 ** Include-directory is not in a standard location tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,767 database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib" all tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,767 info.head ./../include/Caps ./terminfo.tail >terminfo.5 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,767 r/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/ncurs9efd/lib" all tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,768 cd man && /Library/Developer/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/sh ./MKterminfo.sh ./termcd include && /Library/Developees/6.0/iuc/package_ncurses_6_0/0efde988cat curses.head >curses.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,768 AWK=awk sh ./MKkey_defs.sh ./Caps >>curses.h install_environment.STDOUT DEBUG 2017-11-18 16:57:55,885 cat ./curses.tail >>curses.h install_environment.STDOUT DEBUG 2017-11-18 16:57:55,905 AWK=awk sh ./MKncurses_def.sh ./ncurses_defs >ncurses_def.h install_environment.STDOUT DEBUG 2017-11-18 16:57:55,943 touch config.h install_environment.STDOUT DEBUG 2017-11-18 16:57:55,958 sh ./edit_cfg.sh ../include/ncurses_cfg.h term.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,972 sh -c 'if test "chtype" = "cchar_t" ; then cat ./curses.wide >>curses.h ; fi' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,972 cat ./curses.tail >>curses.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,972 sh ./MKhashsize.sh ./Caps >hashsize.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,973 AWK=awk sh ./MKncurses_def.sh ./ncurses_defs >ncurses_def.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,973 AWK=awk sh ./MKparametrized.sh ./Caps >parametrized.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,973 touch config.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,973 awk -f MKterm.h.awk ./Caps > term.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,973 sh ./edit_cfg.sh ../include/ncurses_cfg.h term.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:55,973 ** edit: HAVE_TCGETATTR 1 install_environment.STDOUT DEBUG 2017-11-18 16:57:56,004 ** edit: HAVE_TERMIOS_H 1 install_environment.STDOUT DEBUG 2017-11-18 16:57:56,055 ** edit: BROKEN_LINKER 0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:56,074 ** edit: HAVE_TERMIOS_H 1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:56,074 ** edit: HAVE_TERMIO_H 0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:56,074 ** edit: BROKEN_LINKER 0 install_environment.STDOUT DEBUG 2017-11-18 16:57:56,076 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib" all install_environment.STDOUT DEBUG 2017-11-18 16:57:56,094 k bigstrings=1 ./../include/Caps >codes.c install_environment.STDOUT DEBUG 2017-11-18 16:57:56,112 H -DUSE_BUILD_CC -I../ncurses -I. -I../include -I./../include -DHAVE_CONFIG_H -I. -I../include -D_recomp --param max-inlinech_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:56,175 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib" all tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:56,175 k bigstrings=1 ./../include/Caps >codes.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:56,175 H -DUSE_BUILD_CC -I../ncurses -I. -I../include -I./../include -DHAVE_CONFIG_H -I. -I../include -D_recomp --param max-inlinech_paths_first install_environment.STDOUT DEBUG 2017-11-18 16:57:56,273 clude/Caps > comp_captab.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:56,279 clude/Caps > comp_captab.c install_environment.STDOUT DEBUG 2017-11-18 16:57:56,341 RWIN_C_SOURCE -DNDEBUG > expanded.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:56,385 RWIN_C_SOURCE -DNDEBUG > expanded.c install_environment.STDOUT DEBUG 2017-11-18 16:57:56,429 urses_6_0/0efde9889efd/share/terminfo ../misc/terminfo.src /usr/bin/tic >fallback.c install_environment.STDOUT DEBUG 2017-11-18 16:57:56,457 include/curses.h >lib_gen.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:56,488 urses_6_0/0efde9889efd/share/terminfo ../misc/terminfo.src /usr/bin/tic >fallback.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:56,488 include/curses.h >lib_gen.c install_environment.STDOUT DEBUG 2017-11-18 16:57:56,679 awk -f ./base/MKkeyname.awk bigstrings=1 keys.list > lib_keyname.c install_environment.STDOUT DEBUG 2017-11-18 16:57:56,687 wk" implemented <../include/curses.h >link_test.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:56,696 cd ncurses && /Library/Developer/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galawk -f ./tinfo/MKcodes.awgcc -o make_hash -DHAVE_CONFIG_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-p-insns-single=1200 ./tinfo/make_hash.c -Wl,-searsh -e ./tinfo/MKcaptab.sh awk 1 ./tinfo/MKcaptab.awk ./../insh -e ./tty/MKexpanded.sh "gcc -E" -DHAVE_CONFIG_H -I. -I../include -D_DAsh -e ./tinfo/MKfallback.sh /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncsh -e ./base/MKlib_gen.sh "gcc -E -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG" "awk" generated <../AWK=awk sh ./tinfo/MKkeys_list.sh ../include/Caps | sort >keys.list tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:56,696 awk -f ./base/MKkeyname.awk bigstrings=1 keys.list > lib_keyname.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:56,696 wk" implemented <../include/curses.h >link_test.c install_environment.STDOUT DEBUG 2017-11-18 16:57:56,920 k bigstrings=1 ./../include/Caps >names.c install_environment.STDOUT DEBUG 2017-11-18 16:57:56,940 wk bigstrings=1 >unctrl.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,007 k bigstrings=1 ./../include/Caps >names.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,007 wk bigstrings=1 >unctrl.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,007 sh -e ./base/MKlib_gen.sh "gcc -E -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG" "aawk -f ./tinfo/MKnames.awecho | awk -f ./base/MKunctrl.agcc -o make_keys -DHAVE_CONFIG_H -DUSE__SOURCE -DNDEBUG -O2 -no-cpp-precomp --param ma0 ./tinfo/make_keys.c -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,110 ytry.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,110 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../l.o install_environment.STDOUT DEBUG 2017-11-18 16:57:57,207 BUILD_CC -I../ncurses -I. -I../include -I./../include -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_Cx-inline-insns-single=120./make_keys keys.list > init_kegcc -DHAVE_CONFIG_H -I. -I../include ncurses/./tty/hardscroll.c -o ../obj_s/hardscrolgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -D.c -o ../obj_s/hashmap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,214 BUILD_CC -I../ncurses -I. -I../include -I./../include -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_Cx-inline-insns-single=120./make_keys keys.list > init_kegcc -DHAVE_CONFIG_H -I. -I../include ncurses/./tty/hardscroll.c -o ../obj_s/hardscrolgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -D.c -o ../obj_s/hashmap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,214 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:57:57 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,319 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:57:57,496 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./b_addch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,524 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./b_addch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,524 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:57:57,594 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../tr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,628 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../tr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,630 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,735 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/./tty/hashmapnline-insns-single=1200 -ase/lib_addch.c -o ../obj_s/libgcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_addstr.c -o ../obj_s/lib_addsgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dep.c -o ../obj_s/lib_beep.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,735 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:57:57,831 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/./base/lib_benline-insns-single=1200 -ase/lib_bkgd.c -o ../obj_s/lib_gcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_box.c -o ../obj_s/lib_box.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,840 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./bbkgd.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,840 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/./base/lib_benline-insns-single=1200 -ase/lib_bkgd.c -o ../obj_s/lib_gcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_box.c -o ../obj_s/lib_box.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,840 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,944 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/li_chgat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,944 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:57,945 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,048 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami./obj_s/lib_clear.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,049 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:57:58,052 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -b_chgat.c -o ../obj_s/libgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_clear.c -o .gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_clearok.c -o ../obj_s/lib_clearok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,153 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -b_chgat.c -o ../obj_s/libgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_clear.c -o .gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_clearok.c -o ../obj_s/lib_clearok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,153 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_clrbot.c -o ../obj_s/lib_clrbot.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,153 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,153 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:57:58,187 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_clreol.c -o ../obj_s/lib_clreol.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,257 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_clreol.c -o ../obj_s/lib_clreol.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,258 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,360 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_color.c -o ../obj_s/lib_color.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,361 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,465 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./blib_colorset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,465 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:57:58,494 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -ase/lib_colorset.c -o ../obj_s/gcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_delch.c -o ../obj_s/lib_delch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,566 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -ase/lib_colorset.c -o ../obj_s/gcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_delch.c -o ../obj_s/lib_delch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,566 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,667 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_delwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,667 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami/obj_s/lib_echo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,667 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,667 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:57:58,713 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -b_delwin.c -o ../obj_s/ligcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_echo.c -o ..gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_endwin.c -o ../obj_s/lib_endwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,772 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -b_delwin.c -o ../obj_s/ligcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_echo.c -o ..gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_endwin.c -o ../obj_s/lib_endwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,773 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,874 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_erase.c -o ../obj_s/lib_erase.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,874 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./base/lib_flash.c -o ../obj_s/lib_flash.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,874 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,978 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic -c ../ncurses/lib_gen.c -o ../obj_s/lib_gen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,978 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:58,978 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:57:59,110 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -dynaminline-insns-single=1200 -dynamic -c ../c -o ../obj_s/lib_getch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,189 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -dynaminline-insns-single=1200 -dynamic -c ../c -o ../obj_s/lib_getch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,189 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:57:59,237 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami../obj_s/lib_getstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,294 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami../obj_s/lib_getstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,294 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,396 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-incurses/./base/lib_getch.gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_getstr.c -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_hline.c -o ../obj_s/lib_hline.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,397 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,497 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./base/lib_immedok.c -o ../obj_s/lib_immedok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,497 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic -c ../ncurses/./base/lib_inchstr.c -o ../obj_s/lib_inchstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,497 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,498 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:57:59,542 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.nline-insns-single=1200 -nline-insns-single=1200 -dynaminline-insns-single=1200 -dynamic -c ../r.c -o ../obj_s/lib_initscr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,600 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.nline-insns-single=1200 -nline-insns-single=1200 -dynaminline-insns-single=1200 -dynamic -c ../r.c -o ../obj_s/lib_initscr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,601 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:57:59,618 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami./obj_s/lib_insch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,704 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami./obj_s/lib_insch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,705 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-incurses/./base/lib_initscgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_insch.c -o .gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_insdel.c -o ../obj_s/lib_insdel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,705 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,809 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./bib_insnstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,809 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,809 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:57:59,902 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.nline-insns-single=1200 -ase/lib_insnstr.c -o ../obj_s/lgcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_instr.c -o ../obj_s/lib_instrgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dendwin.c -o ../obj_s/lib_isendwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,913 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,913 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.nline-insns-single=1200 -ase/lib_insnstr.c -o ../obj_s/lgcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_instr.c -o ../obj_s/lib_instrgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dendwin.c -o ../obj_s/lib_isendwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:57:59,913 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,014 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/./base/lib_isgcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/liib_leaveok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,014 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,014 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,116 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami./obj_s/lib_mouse.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,116 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:00,235 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -b_leaveok.c -o ../obj_s/lgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_mouse.c -o .gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_move.c -o ../obj_s/lib_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,321 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -b_leaveok.c -o ../obj_s/lgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_mouse.c -o .gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_move.c -o ../obj_s/lib_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,323 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tty/libmvcur.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,323 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,323 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:00 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,532 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami./obj_s/lib_mvwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,532 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:00,580 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -_mvcur.c -o ../obj_s/lib_gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_mvwin.c -o .gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_newterm.c -o ../obj_s/lib_newterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,633 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -_mvcur.c -o ../obj_s/lib_gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_mvwin.c -o .gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_newterm.c -o ../obj_s/lib_newterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,633 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,738 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_newwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,738 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,839 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamibj_s/lib_nl.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,839 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:00,849 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -b_newwin.c -o ../obj_s/ligcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_nl.c -o ../ogcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_overlay.c -o ../obj_s/lib_overlay.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,942 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -b_newwin.c -o ../obj_s/ligcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_nl.c -o ../ogcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_overlay.c -o ../obj_s/lib_overlay.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:00,942 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,045 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_pad.c -o ../obj_s/lib_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,045 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:01,144 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -ase/lib_printw.c -o ../obj_s/ligcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_redrawln.c -o ../obj_s/lib_redrawln.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,146 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./bb_printw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,147 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -ase/lib_printw.c -o ../obj_s/ligcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_redrawln.c -o ../obj_s/lib_redrawln.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,147 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,250 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_refresh.c -o ../obj_s/lib_refresh.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,250 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,250 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,352 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./base/lib_restart.c -o ../obj_s/lib_restart.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,352 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,453 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic -c ../ncurses/./base/lib_scanw.c -o ../obj_s/lib_scanw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,453 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:01,457 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -dynaminline-insns-single=1200 -dynamic -c ../.c -o ../obj_s/lib_screen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,555 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -dynaminline-insns-single=1200 -dynamic -c ../.c -o ../obj_s/lib_screen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,555 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:01,658 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami../obj_s/lib_scroll.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,759 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami../obj_s/lib_scroll.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,759 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:01,856 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_scrreg.c -o ../obj_s/lib_scrreg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,863 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-incurses/./base/lib_screengcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_scroll.c -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_scrollok.c -o ../obj_s/lib_scrollok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,864 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_scrreg.c -o ../obj_s/lib_scrreg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,864 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,969 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_set_term.c -o ../obj_s/lib_set_term.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,969 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:01,969 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,071 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./blk.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,071 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,173 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../slkatr_set.o install_environment.STDOUT DEBUG 2017-11-18 16:58:02,232 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -ase/lib_slk.c -o ../obj_s/lib_sgcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_slkatr_set.c -o ../obj_s/lib_gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dkatrof.c -o ../obj_s/lib_slkatrof.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,276 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -ase/lib_slk.c -o ../obj_s/lib_sgcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_slkatr_set.c -o ../obj_s/lib_gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dkatrof.c -o ../obj_s/lib_slkatrof.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,276 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,276 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,377 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/./base/lib_slgcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_slkatron.c -o ../obj_s/lib_slkatron.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,377 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./base/lib_slkatrset.c -o ../obj_s/lib_slkatrset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,377 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,481 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami ../obj_s/lib_slkattr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,481 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,481 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:02,510 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_slkattr.c -ogcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_slkclear.c -o ../obj_s/lib_slkclear.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,581 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_slkattr.c -ogcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_slkclear.c -o ../obj_s/lib_slkclear.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,581 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lilib_slkcolor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,581 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:02,646 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -b_slkcolor.c -o ../obj_s/gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_slkinit.c -o ../obj_s/lib_slkinit.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,686 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -b_slkcolor.c -o ../obj_s/gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_slkinit.c -o ../obj_s/lib_slkinit.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,686 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,687 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:02,718 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./base/lib_slklab.c -o ../obj_s/lib_slklab.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,787 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./base/lib_slklab.c -o ../obj_s/lib_slklab.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,788 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynaminline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_slkrefr.c -o ../obj_s/lib_slkrefr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,788 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,892 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./bb_slkset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,892 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,892 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,997 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/./base/lib_slktouch.c -o ../obj_s/lib_slktouch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:02,997 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:03,020 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynaminline-insns-single=1200 -ase/lib_slkset.c -o ../obj_s/ligcc -DHAVE_CONFIG_H -I. -I../include gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_touch.c -o ../obj_s/lib_touch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,100 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynaminline-insns-single=1200 -ase/lib_slkset.c -o ../obj_s/ligcc -DHAVE_CONFIG_H -I. -I../include gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/lib_touch.c -o ../obj_s/lib_touch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,100 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tty/lib_tstp.c -o ../obj_s/lib_tstp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,100 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,204 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./base/lib_ungetch.c -o ../obj_s/lib_ungetch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,204 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,204 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:03,248 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -dynami_vidattr.c -o ../obj_s/lib_vidattr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,307 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -dynami_vidattr.c -o ../obj_s/lib_vidattr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,307 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,410 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic -c ../ncurses/./tty/libgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/lib_vline.c -o ../obj_s/lib_vline.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,410 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,519 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./blib_wattroff.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,521 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,624 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../tron.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,624 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/./base/lib_winch.c -o ../obj_s/lib_winch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,624 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,624 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:03 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,726 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ij_s/lib_window.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,728 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:03,806 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynaminline-insns-single=1200 -ase/lib_wattroff.c -o ../obj_s/gcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_wattron.c -o ../obj_s/lib_watgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dnline-insns-single=1200 -dynamic -c ../ncurses/./base/lib_window.c -o ../obnline-insns-single=1200 -dynamic -c ../ncurses/./base/nc_panel.c -o ../obj_s/nc_panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,833 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynaminline-insns-single=1200 -ase/lib_wattroff.c -o ../obj_s/gcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_wattron.c -o ../obj_s/lib_watgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dnline-insns-single=1200 -dynamic -c ../ncurses/./base/lib_window.c -o ../obnline-insns-single=1200 -dynamic -c ../ncurses/./base/nc_panel.c -o ../obj_s/nc_panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,833 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,934 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-igcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/safe_sprintf.c -o ../obj_s/safe_sprintf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:03,935 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,039 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./t_update.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,040 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:04,470 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -ty/tty_update.c -o ../obj_s/ttygcc -DHAVE_CONFIG_H -I. -I../include ncurses/./trace/varargs.c -o ../obj_s/varargs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,560 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -ty/tty_update.c -o ../obj_s/ttygcc -DHAVE_CONFIG_H -I. -I../include ncurses/./trace/varargs.c -o ../obj_s/varargs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,560 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/vsscanf.c -o ../obj_s/vsscanf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,561 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,561 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:04,592 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_freeall.c -o ../obj_s/lib_freeall.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,661 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/lib_freeall.c -o ../obj_s/lib_freeall.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,662 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,767 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/expanded.c -o ../obj_s/expanded.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,767 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./b/legacy_coding.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,767 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,767 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:04,789 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -ase/legacy_coding.c -o ../obj_sgcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_dft_fgbg.c -o ../obj_s/lib_dft_fgbg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,868 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -ase/legacy_coding.c -o ../obj_sgcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/lib_dft_fgbg.c -o ../obj_s/lib_dft_fgbg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,868 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/lib_print.c -o ../obj_s/lib_print.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,868 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:04,937 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/resizeterm.c -o ../obj_s/resizeterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,969 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/resizeterm.c -o ../obj_s/resizeterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,969 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:04,970 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,071 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/use_screen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,172 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami../obj_s/use_window.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,172 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,172 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:05,180 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -se_screen.c -o ../obj_s/ugcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/use_window.c -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/wresize.c -o ../obj_s/wresize.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,277 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -se_screen.c -o ../obj_s/ugcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/use_window.c -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/wresize.c -o ../obj_s/wresize.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,278 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,379 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/as.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,379 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:05,413 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ccess.c -o ../obj_s/accesgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/add_tries.c -o ../obj_s/add_tries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,482 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ccess.c -o ../obj_s/accesgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/add_tries.c -o ../obj_s/add_tries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,482 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,587 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamigcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/alloc_ttype.c -o ../obj_s/alloc_ttype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,587 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,796 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/codes.c -o ../obj_s/codes.o install_environment.STDOUT DEBUG 2017-11-18 16:58:05,860 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -dynamic -c ../ncurses/comp_captab.c -o ../obj_s/comp_captab.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,897 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -dynamic -c ../ncurses/comp_captab.c -o ../obj_s/comp_captab.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,898 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:05,899 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,000 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-igcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/comp_error.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,102 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami../obj_s/comp_hash.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,103 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,103 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:06,154 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -omp_error.c -o ../obj_s/cgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/comp_hash.c -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/tinfo/db_iterator.c -o ../obj_s/db_iterator.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,203 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -omp_error.c -o ../obj_s/cgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/comp_hash.c -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/tinfo/db_iterator.c -o ../obj_s/db_iterator.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,204 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,306 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/dloc.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,306 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:06,343 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -oalloc.c -o ../obj_s/doalnline-insns-single=1200 -dynamintries.c -o ../obj_s/entries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,412 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -oalloc.c -o ../obj_s/doalnline-insns-single=1200 -dynamintries.c -o ../obj_s/entries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,412 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,516 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic -c ../ncurses/./tinfo/egcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/fallback.c -o ../obj_s/fallback.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,516 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./tinfo/free_ttype.c -o ../obj_s/free_ttype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,516 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,516 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:06,615 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynaminline-insns-single=1200 -nline-insns-single=1200 -dynaminline-insns-single=1200 -dynamic -c ../info.c -o ../obj_s/home_terminfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,621 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic -c ../ncurses/./tinfo/getenv_num.c -o ../obj_s/getenv_num.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,621 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynaminline-insns-single=1200 -nline-insns-single=1200 -dynaminline-insns-single=1200 -dynamic -c ../info.c -o ../obj_s/home_terminfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,621 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:06,683 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamio ../obj_s/init_keytry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,723 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamio ../obj_s/init_keytry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,724 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,724 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,829 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-incurses/./tinfo/home_termgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/init_keytry.c -gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/tinfo/lib_acs.c -o ../obj_s/lib_acs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,829 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:06,888 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/l/lib_baudrate.o 127.0.0.1 - - [18/Nov/2017:16:58:06 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,933 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/l/lib_baudrate.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:06,933 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,034 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ib_baudrate.c -o ../obj_sgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/lib_cur_term.c o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,034 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,138 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami./obj_s/lib_data.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,138 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i/tinfo/lib_has_cap.c -o ../obj_s/lib_has_cap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,139 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,244 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-iernel.c -o ../obj_s/lib_kernel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,244 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,244 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,349 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ib_keyname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,349 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:07,447 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami-o ../obj_s/lib_cur_term.gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/lib_data.c -o .nline-insns-single=1200 -dynamic -c ../ncurses/.nline-insns-single=1200 -dynamic -c ../ncurses/./tinfo/lib_knline-insns-single=1200 -dynamic -c ../ncurses/lib_keyname.c -o ../obj_s/linline-insns-single=1200 -dynamic -c ../ncurses/./tinfo/lib_longname.c -o ../obj_s/lib_longnamenline-insns-single=1200 -dynamic -c ../ncurses/./tinfo/lib_napms.c -o ../obj_s/lib_napms.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,452 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,453 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami-o ../obj_s/lib_cur_term.gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/lib_data.c -o .nline-insns-single=1200 -dynamic -c ../ncurses/.nline-insns-single=1200 -dynamic -c ../ncurses/./tinfo/lib_knline-insns-single=1200 -dynamic -c ../ncurses/lib_keyname.c -o ../obj_s/linline-insns-single=1200 -dynamic -c ../ncurses/./tinfo/lib_longname.c -o ../obj_s/lib_longnamenline-insns-single=1200 -dynamic -c ../ncurses/./tinfo/lib_napms.c -o ../obj_s/lib_napms.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,453 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,557 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-igcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/llib_options.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,557 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,557 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:07,614 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ib_options.c -o ../obj_s/gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/lib_raw.c -o ../obj_s/lib_raw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,659 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ib_options.c -o ../obj_s/gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/lib_raw.c -o ../obj_s/lib_raw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,659 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,763 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamigcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/lib_setup.c -o ../obj_s/lib_setup.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,764 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,969 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./tlib_termcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:07,969 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:08,067 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -info/lib_termcap.c -o ../obj_s/gcc -DHAVE_CONFIG_H -I. -I../include ncurses/./tinfo/lib_termname.c -o ../obj_s/lib_tgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dgoto.c -o ../obj_s/lib_tgoto.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,070 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ermname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,070 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -info/lib_termcap.c -o ../obj_s/gcc -DHAVE_CONFIG_H -I. -I../include ncurses/./tinfo/lib_termname.c -o ../obj_s/lib_tgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dgoto.c -o ../obj_s/lib_tgoto.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,070 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,175 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/./tinfo/lib_tgcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/li.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,175 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,175 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,281 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami../obj_s/lib_tparm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,281 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:08,460 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ib_ti.c -o ../obj_s/lib_tgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/lib_tparm.c -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/tinfo/lib_tputs.c -o ../obj_s/lib_tputs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,486 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ib_ti.c -o ../obj_s/lib_tgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/lib_tparm.c -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/tinfo/lib_tputs.c -o ../obj_s/lib_tputs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,486 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:08,649 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ib_trace.c -o ../obj_s/ligcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/lib_ttyflags.c o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,692 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./trace/lb_trace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,692 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ib_trace.c -o ../obj_s/ligcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/lib_ttyflags.c o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,692 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,692 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:08,754 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami/obj_s/lib_twait.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,793 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami/obj_s/lib_twait.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,793 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,897 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami-o ../obj_s/lib_ttyflags.gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tty/lib_twait.c -o ..gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/tinfo/name_match.c -o ../obj_s/name_match.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:08,897 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:08,984 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.nline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/obsolete.c -o ../obj_s/obsolete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,002 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/names.c -o ../obj_s/names.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,002 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.nline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/obsolete.c -o ../obj_s/obsolete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,002 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,002 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,107 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamigcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/read_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,107 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:09,257 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ead_entry.c -o ../obj_s/rgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/read_termcap.c -o ../obj_s/read_termcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,310 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ead_entry.c -o ../obj_s/rgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/read_termcap.c -o ../obj_s/read_termcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,310 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:09,397 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -trings.c -o ../obj_s/strigcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/tries.c -o ../obj_s/tries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,414 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamigcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/sngs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,414 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -trings.c -o ../obj_s/strigcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./base/tries.c -o ../obj_s/tries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,414 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,414 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,515 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamigcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/trim_sgr0.c -o ../obj_s/trim_sgr0.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,516 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,621 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/unctrl.c -o ../obj_s/unctrl.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,621 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:09,674 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -dynamiisbuf.c -o ../obj_s/visbuf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,722 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -dynamiisbuf.c -o ../obj_s/visbuf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,723 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:09,770 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamio ../obj_s/alloc_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,825 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamio ../obj_s/alloc_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:09,825 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:09,940 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/./tinfo/captoinfo.c -o ../obj_s/captoinfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:10,029 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/./tinfo/captoinfo.c -o ../obj_s/captoinfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:10,029 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:09 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:10,236 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic -c ../ncurses/./trace/vgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/alloc_entry.c -gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWINgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dexpand.c -o ../obj_s/comp_expand.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:10,236 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:10,255 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/./tinfo/comp_gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/comp_parse.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:10,338 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/./tinfo/comp_gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./tinfo/comp_parse.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:10,338 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:10,440 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -omp_parse.c -o ../obj_s/cgcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/comp_scan.c -o ../obj_s/comp_scan.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:10,545 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:10,650 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./tparse_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:10,650 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:10,921 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynaminline-insns-single=1200 -info/parse_entry.c -o ../obj_s/gcc -DHAVE_CONFIG_H -I. -I../include ncurses/./tinfo/write_entry.c -o ../obj_s/write_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:10,964 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynaminline-insns-single=1200 -info/parse_entry.c -o ../obj_s/gcc -DHAVE_CONFIG_H -I. -I../include ncurses/./tinfo/write_entry.c -o ../obj_s/write_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:10,964 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,278 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/define_key.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,278 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:11,368 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -fine_key.c -o ../obj_s/degcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/hashed_db.c -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/key_defined.c -o ../obj_s/key_defined.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,379 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynami../obj_s/hashed_db.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,379 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -fine_key.c -o ../obj_s/degcc -DHAVE_CONFIG_H -I. -I../inc -c ../ncurses/./tinfo/hashed_db.c -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/base/key_defined.c -o ../obj_s/key_defined.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,379 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,480 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -dynamic -c ../ncurses/./base/keybound.c -o ../obj_s/keybound.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,480 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,480 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:11,576 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -ase/keyok.c -o ../obj_s/keyok.ogcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/version.c -o ../obj_s/version.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,581 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../ncurses/./b tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,581 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -ase/keyok.c -o ../obj_s/keyok.ogcc -DHAVE_CONFIG_H -I. -I../include ncurses/./base/version.c -o ../obj_s/version.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,581 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:11,647 .6.dylib install_environment.STDOUT DEBUG 2017-11-18 16:58:11,648 max-inline-insns-single=1200 -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/ncur89efd/lib/`basename ../licurrent_version 6 -o ../lib/libobj_s/lib_addch.o ../obj_s/lib_addstr.ogat.o ../obj_s/lib_clear.o ../obj_s/lib_clearok.obj_s/lib_delch.o ../obj_s/lib_delwin.o ../obj_s/lib_echo.o etstr.o ../obj_s/lib_hline.o ../obj_s/lib_immedok.o ../obj_s/lib_inchstr.o leaveok.o ../obj_s/lib_mouse.o ../obj_s/lib_move.o ../obj_s/lib_mvcur.o ../obj_s/lib_mvwin.o .b_restart.o ../obj_s/lib_scanw.o ../obj_s/lib_screen.o ../obj_s/lib_scroll.o ../obj_s/lib_scrollok.o ../obj_s/lib_scrr_slkinit.o ../obj_s/lib_slklab.o ../obj_s/lib_slkrefr.o ../obj_s/lib_slkset.o ../obj_s/lib_slktouch.o ../obj_s/lib_touch.o ../obj_s/lib_tstp.o ../os/expanded.o ../obj_s/legacy_coding.o ../obj_s/lib_dft_fgbg.o ../obj_s/lib_print.o ../obj_s/resizeterm.o ../obj_s/use_screen.o ../obj_s/use_window.o ../obj_s/wresize.o ../obj_s/access.ur_term.o ../obj_s/lib_data.o ../obj_s/lib_has_cap.o ../obj_s/lib_kernel.o ../obj_s/lib_keyname.o ../obj_s/lib_longname.o ../obj_s/lib_napms.o ../obj_s/lib_options.o ../obj_s/lib_raw.o ../obj_s/lib_setup.o ../obj_s/lib_termcap.o .parse.o ../obj_s/comp_scan.o ../obj_s/parse_entry.o ../obj_s/write_entry.o ../obj_s/define_key.o ../obj_s/hashed_db.o ../obj_s/key_defined.o ../obj_s/keybound.o ../obj_s/keyok.o ../obj_s/version.o -L../lib -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,682 .6.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,682 max-inline-insns-single=1200 -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/ncur89efd/lib/`basename ../licurrent_version 6 -o ../lib/libobj_s/lib_addch.o ../obj_s/lib_addstr.ogat.o ../obj_s/lib_clear.o ../obj_s/lib_clearok.obj_s/lib_delch.o ../obj_s/lib_delwin.o ../obj_s/lib_echo.o etstr.o ../obj_s/lib_hline.o ../obj_s/lib_immedok.o ../obj_s/lib_inchstr.o leaveok.o ../obj_s/lib_mouse.o ../obj_s/lib_move.o ../obj_s/lib_mvcur.o ../obj_s/lib_mvwin.o .b_restart.o ../obj_s/lib_scanw.o ../obj_s/lib_screen.o ../obj_s/lib_scroll.o ../obj_s/lib_scrollok.o ../obj_s/lib_scrr_slkinit.o ../obj_s/lib_slklab.o ../obj_s/lib_slkrefr.o ../obj_s/lib_slkset.o ../obj_s/lib_slktouch.o ../obj_s/lib_touch.o ../obj_s/lib_tstp.o ../os/expanded.o ../obj_s/legacy_coding.o ../obj_s/lib_dft_fgbg.o ../obj_s/lib_print.o ../obj_s/resizeterm.o ../obj_s/use_screen.o ../obj_s/use_window.o ../obj_s/wresize.o ../obj_s/access.ur_term.o ../obj_s/lib_data.o ../obj_s/lib_has_cap.o ../obj_s/lib_kernel.o ../obj_s/lib_keyname.o ../obj_s/lib_longname.o ../obj_s/lib_napms.o ../obj_s/lib_options.o ../obj_s/lib_raw.o ../obj_s/lib_setup.o ../obj_s/lib_termcap.o .parse.o ../obj_s/comp_scan.o ../obj_s/parse_entry.o ../obj_s/write_entry.o ../obj_s/define_key.o ../obj_s/hashed_db.o ../obj_s/key_defined.o ../obj_s/keybound.o ../obj_s/keyok.o ../obj_s/version.o -L../lib -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,683 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,785 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../linking ../lib/libncursesgcc -O2 -no-cpp-precomp --paramses/6.0/iuc/package_ncurses_6_0/0efde98b/libncurses.6.dylib` -compatibility_version 6 -ncurses.6.dylib ../obj_s/hardscroll.o ../obj_s/hashmap.o ../ ../obj_s/lib_beep.o ../obj_s/lib_bkgd.o ../obj_s/lib_box.o ../obj_s/lib_cho ../obj_s/lib_clrbot.o ../obj_s/lib_clreol.o ../obj_s/lib_color.o ../obj_s/lib_colorset.o ../../obj_s/lib_endwin.o ../obj_s/lib_erase.o ../obj_s/lib_flash.o ../obj_s/lib_gen.o ../obj_s/lib_getch.o ../obj_s/lib_g../obj_s/lib_initscr.o ../obj_s/lib_insch.o ../obj_s/lib_insdel.o ../obj_s/lib_insnstr.o ../obj_s/lib_instr.o ../obj_s/lib_isendwin.o ../obj_s/lib_./obj_s/lib_newterm.o ../obj_s/lib_newwin.o ../obj_s/lib_nl.o ../obj_s/lib_overlay.o ../obj_s/lib_pad.o ../obj_s/lib_printw.o ../obj_s/lib_redrawln.o ../obj_s/lib_refresh.o ../obj_s/lieg.o ../obj_s/lib_set_term.o ../obj_s/lib_slk.o ../obj_s/lib_slkatr_set.o ../obj_s/lib_slkatrof.o ../obj_s/lib_slkatron.o ../obj_s/lib_slkatrset.o ../obj_s/lib_slkattr.o ../obj_s/lib_slkclear.o ../obj_s/lib_slkcolor.o ../obj_s/libbj_s/lib_ungetch.o ../obj_s/lib_vidattr.o ../obj_s/lib_vline.o ../obj_s/lib_wattroff.o ../obj_s/lib_wattron.o ../obj_s/lib_winch.o ../obj_s/lib_window.o ../obj_s/nc_panel.o ../obj_s/safe_sprintf.o ../obj_s/tty_update.o ../obj_s/varargs.o ../obj_s/vsscanf.o ../obj_s/lib_freeall.o ../obj_o ../obj_s/add_tries.o ../obj_s/alloc_ttype.o ../obj_s/codes.o ../obj_s/comp_captab.o ../obj_s/comp_error.o ../obj_s/comp_hash.o ../obj_s/db_iterator.o ../obj_s/doalloc.o ../obj_s/entries.o ../obj_s/fallback.o ../obj_s/free_ttype.o ../obj_s/getenv_num.o ../obj_s/home_terminfo.o ../obj_s/init_keytry.o ../obj_s/lib_acs.o ../obj_s/lib_baudrate.o ../obj_s/lib_c./obj_s/lib_termname.o ../obj_s/lib_tgoto.o ../obj_s/lib_ti.o ../obj_s/lib_tparm.o ../obj_s/lib_tputs.o ../obj_s/lib_trace.o ../obj_s/lib_ttyflags.o ../obj_s/lib_twait.o ../obj_s/name_match.o ../obj_s/names.o ../obj_s/obsolete.o ../obj_s/read_entry.o ../obj_s/read_termcap.o ../obj_s/strings.o ../obj_s/tries.o ../obj_s/trim_sgr0.o ../obj_s/unctrl.o ../obj_s/visbuf.o ../obj_s/alloc_entry.o ../obj_s/captoinfo.o ../obj_s/comp_expand.o ../obj_s/comp_cd ../lib && (ln -s -f libncurses.6.dylib libncurses.dylib; ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,785 nline-insns-single=1200 -c ../ncurses/./tty/hardscroll.c -o ../objects/hardscroll.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,785 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,890 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 - ../objects/hashmap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:11,890 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:12,067 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-igcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tty/hashmap.c -ogcc -DHAVE_CONFIG_H -I. -I../include /base/lib_addch.c -o ../objects/lib_addch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,101 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-igcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tty/hashmap.c -ogcc -DHAVE_CONFIG_H -I. -I../include /base/lib_addch.c -o ../objects/lib_addch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,102 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,208 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_addstr.r.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,208 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:12,310 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c -o ../objects/lib_addstgcc -DHAVE_CONFIG_H -I. -I../innline-insns-single=1200 -c ../ncurses/.jects/lib_bkgd.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,311 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/lib_beep.c -o ../objects/lib_beep.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,311 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c -o ../objects/lib_addstgcc -DHAVE_CONFIG_H -I. -I../innline-insns-single=1200 -c ../ncurses/.jects/lib_bkgd.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,311 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,415 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i/base/lib_bkgd.c -o ../obgcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_box.c -o ../objects/lib_box.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,415 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,415 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,519 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/lib_co tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,519 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:12,531 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nnline-insns-single=1200 -hgat.c -o ../objects/lib_chgat.gcc -DHAVE_CONFIG_H -I. -I../include /base/lib_clear.c -o ../objects/lib_clear.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,620 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nnline-insns-single=1200 -hgat.c -o ../objects/lib_chgat.gcc -DHAVE_CONFIG_H -I. -I../include /base/lib_clear.c -o ../objects/lib_clear.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,620 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_clearok.c -o ../objects/lib_clearok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,620 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,620 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,721 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/lib_ct.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,722 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:12,723 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -lrbot.c -o ../objects/lib_clrbogcc -DHAVE_CONFIG_H -I. -I../include /base/lib_clreol.c -o ../objects/lib_clreol.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,824 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -lrbot.c -o ../objects/lib_clrbogcc -DHAVE_CONFIG_H -I. -I../include /base/lib_clreol.c -o ../objects/lib_clreol.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,824 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_color.c -o ../objects/lib_color.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,824 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:12,824 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:13,009 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -c ../n -o ../objects/lib_delch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,032 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/lib_colorset.c -o ../objects/lib_colorset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,032 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -c ../n -o ../objects/lib_delch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,032 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,032 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:13,090 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ns/lib_delwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,137 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ns/lib_delwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,137 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:13,170 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/lib_echo.c -o ../objects/lib_echo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,240 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/lib_echo.c -o ../objects/lib_echo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,240 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:13,247 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/lib_endwin.c -o ../objects/lib_endwin.o 127.0.0.1 - - [18/Nov/2017:16:58:13 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,345 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/lib_endwin.c -o ../objects/lib_endwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,345 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-icurses/./base/lib_delch.cgcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_delwin.c -o ../objectgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWINgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-erase.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,345 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,345 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:13,411 cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/lib_erase.c -o ../objects/lib_gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_flash.c -o ../objects/lib_flash.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,446 cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/lib_erase.c -o ../objects/lib_gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_flash.c -o ../objects/lib_flash.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,446 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:13,481 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -jects/lib_gen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,551 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -jects/lib_gen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,551 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,754 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -c ../ncurses/lib_gen.c -o ../obgcc -DHAVE_CONFIG_H -I. -I../include /base/lib_getch.c -o ../objects/lib_getch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,754 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,860 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/lib_gr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,860 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:13,866 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.nline-insns-single=1200 -etstr.c -o ../objects/lib_getstgcc -DHAVE_CONFIG_H -I. -I../include /base/lib_hline.c -o ../objects/lib_hline.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,961 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.nline-insns-single=1200 -etstr.c -o ../objects/lib_getstgcc -DHAVE_CONFIG_H -I. -I../include /base/lib_hline.c -o ../objects/lib_hline.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,962 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_immedokdok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:13,962 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,067 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nts/lib_inchstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,067 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,067 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:14,085 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -.c -o ../objects/lib_immegcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_inchstr.c -o ../objecgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_initscr.c -o ../objects/lib_initscr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,168 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -.c -o ../objects/lib_immegcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_inchstr.c -o ../objecgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_initscr.c -o ../objects/lib_initscr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,169 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/libgcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_insch.co tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,169 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,169 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,272 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ns/lib_insdel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,278 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:14,304 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 - -o ../objects/lib_insch.gcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_insdel.c -o ../objectgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_insnstr.c -o ../objects/lib_insnstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,379 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 - -o ../objects/lib_insch.gcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_insdel.c -o ../objectgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_insnstr.c -o ../objects/lib_insnstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,380 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/libgcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_instr.c -o ../objects/lib_instr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,380 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,483 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/lib_indwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,483 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,483 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:14,514 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -sendwin.c -o ../objects/lib_isegcc -DHAVE_CONFIG_H -I. -I../include /base/lib_leaveok.c -o ../objects/lib_leaveok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,584 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -sendwin.c -o ../objects/lib_isegcc -DHAVE_CONFIG_H -I. -I../include /base/lib_leaveok.c -o ../objects/lib_leaveok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,584 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_mouse.c -o ../objects/lib_mouse.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,584 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,689 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:14,784 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -ove.c -o ../objects/lib_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,792 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -ove.c -o ../objects/lib_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,895 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/lib_mgcc -DHAVE_CONFIG_H -I. -I../incurses/./tty/lib_mvcur.c -o ../objects/lib_mvcur.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,895 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:14,895 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:15,098 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nnline-insns-single=1200 -vwin.c -o ../objects/lib_mvwin.gcc -DHAVE_CONFIG_H -I. -I../include /base/lib_newterm.c -o ../objects/lib_newterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,102 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/lib_mo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,103 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nnline-insns-single=1200 -vwin.c -o ../objects/lib_mvwin.gcc -DHAVE_CONFIG_H -I. -I../include /base/lib_newterm.c -o ../objects/lib_newterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,103 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,205 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_newwin.n.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,205 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,206 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:15,380 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c -o ../objects/lib_newwigcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_nl.c -o ../objects/ligcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_overlay.c -o ../objects/lib_overlay.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,411 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nb_nl.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,411 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c -o ../objects/lib_newwigcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_nl.c -o ../objects/ligcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_overlay.c -o ../objects/lib_overlay.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,412 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,412 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:15,471 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o ../objects/lib_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,518 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o ../objects/lib_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,518 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,622 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/libgcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_pad.c -gcc -DHAVE_CONFIG_H -I. -I../include /base/lib_printw.c -o ../objects/lib_printw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,622 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,723 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/lib_rrawln.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,723 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:15,734 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.nline-insns-single=1200 -edrawln.c -o ../objects/lib_redgcc -DHAVE_CONFIG_H -I. -I../include /base/lib_refresh.c -o ../objects/lib_refresh.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,825 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.nline-insns-single=1200 -edrawln.c -o ../objects/lib_redgcc -DHAVE_CONFIG_H -I. -I../include /base/lib_refresh.c -o ../objects/lib_refresh.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,825 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,931 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_restartart.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,931 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../n/lib_scanw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,931 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:15,931 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:15,978 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -.c -o ../objects/lib_restgcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_scanw.c -o ../objectsgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_screen.c -o ../objects/lib_screen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,036 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -.c -o ../objects/lib_restgcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_scanw.c -o ../objectsgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_screen.c -o ../objects/lib_screen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,036 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,243 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/libgcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_scroll.l.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,244 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,350 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncts/lib_scrollok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,351 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:16,372 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c -o ../objects/lib_scrolgcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_scrollok.c -o ../objegcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_scrreg.c -o ../objects/lib_scrreg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,456 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c -o ../objects/lib_scrolgcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_scrollok.c -o ../objegcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_scrreg.c -o ../objects/lib_scrreg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,457 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/libgcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_set_ter_term.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,457 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:16 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,559 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:16,588 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -m.c -o ../objects/lib_setgcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_slk.c -o ../objects/lib_slk.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,661 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -m.c -o ../objects/lib_setgcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_slk.c -o ../objects/lib_slk.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,661 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,766 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ngcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_slkatr_lkatr_set.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,766 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:16,849 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -set.c -o ../objects/lib_sgcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_slkatrof.c -o ../objegcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_slkatron.c -o ../objects/lib_slkatron.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,870 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncts/lib_slkatrof.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,871 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -set.c -o ../objects/lib_sgcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_slkatrof.c -o ../objegcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_slkatron.c -o ../objects/lib_slkatron.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,871 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,871 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,975 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/libgcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_slkatrset.c -o ../objects/lib_slkatrset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:16,975 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:17,047 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -c ../nr.c -o ../objects/lib_slkclear.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,079 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/lib_slkattr.c -o ../objects/lib_slkattr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,080 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -c ../nr.c -o ../objects/lib_slkclear.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,080 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,080 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:17,119 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncts/lib_slkcolor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,182 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncts/lib_slkcolor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,182 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,286 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-icurses/./base/lib_slkcleagcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_slkcolor.c -o ../objegcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_slkinit.c -o ../objects/lib_slkinit.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,286 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/lib_sb.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,286 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,286 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:17,337 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/libnline-insns-single=1200 -lklab.c -o ../objects/lib_slklagcc -DHAVE_CONFIG_H -I. -I../include /base/lib_slkrefr.c -o ../objects/lib_slkrefr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,391 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/libnline-insns-single=1200 -lklab.c -o ../objects/lib_slklagcc -DHAVE_CONFIG_H -I. -I../include /base/lib_slkrefr.c -o ../objects/lib_slkrefr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,391 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,495 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_slkset.t.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,495 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:17,584 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c -o ../objects/lib_slksegcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_slktouch.c -o ../objenline-insns-single=1200 -c ../ncurses/./base/libb_touch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,600 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncts/lib_slktouch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,600 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c -o ../objects/lib_slksegcc -DHAVE_CONFIG_H -I. -I../incurses/./base/lib_slktouch.c -o ../objenline-insns-single=1200 -c ../ncurses/./base/libb_touch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,600 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,600 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,701 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i_touch.c -o ../objects/ligcc -DHAVE_CONFIG_H -I. -I../incurses/./tty/lib_tstp.c -o ../objects/lib_tstp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,701 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,803 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/lib_utch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,803 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:17,808 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nnline-insns-single=1200 -ngetch.c -o ../objects/lib_ungegcc -DHAVE_CONFIG_H -I. -I../include /tty/lib_vidattr.c -o ../objects/lib_vidattr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,906 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nnline-insns-single=1200 -ngetch.c -o ../objects/lib_ungegcc -DHAVE_CONFIG_H -I. -I../include /tty/lib_vidattr.c -o ../objects/lib_vidattr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:17,906 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,007 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_vline.c -o ../objects/lib_vline.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,008 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:18,082 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -attroff.c -o ../objects/lib_watgcc -DHAVE_CONFIG_H -I. -I../include /base/lib_wattron.c -o ../objects/lib_wattron.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,109 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/lib_wtroff.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,109 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -attroff.c -o ../objects/lib_watgcc -DHAVE_CONFIG_H -I. -I../include /base/lib_wattron.c -o ../objects/lib_wattron.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,110 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,110 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,214 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/lib_winch.c -o ../objects/lib_winch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,214 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,316 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/lib_window.c -o ../objects/lib_window.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,316 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:18,353 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -c ../n-o ../objects/nc_panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,417 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -c ../n-o ../objects/nc_panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,417 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,519 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-icurses/./base/nc_panel.c gcc -DHAVE_CONFIG_H -I. -I../incurses/./base/safe_sprintf.c -o ../objects/safe_sprintf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,519 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./tty/tty_up.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,519 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:18,623 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:19,014 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nnline-insns-single=1200 -date.c -o ../objects/tty_updategcc -DHAVE_CONFIG_H -I. -I../include /trace/varargs.c -o ../objects/varargs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,035 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nnline-insns-single=1200 -date.c -o ../objects/tty_updategcc -DHAVE_CONFIG_H -I. -I../include /trace/varargs.c -o ../objects/varargs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,035 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:19,085 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o ../objects/vsscanf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,138 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o ../objects/vsscanf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,138 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:19,228 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.nline-insns-single=1200 -o ../objects/expanded.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,239 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/vsscanf.c -gcc -DHAVE_CONFIG_H -I. -I../include /base/lib_freeall.c -o ../objects/lib_freeall.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,239 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.nline-insns-single=1200 -o ../objects/expanded.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,239 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:19 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/datasets/error?dataset_id=a799d38679e985db&__identifer=9nms4ovms1v" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:58:19,307 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nects/legacy_coding.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,341 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nects/legacy_coding.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,341 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,341 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,451 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/expanded.c -gcc -DHAVE_CONFIG_H -I. -I../incurses/./base/legacy_coding.c -o ../objgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_dft_fgbg.c -o ../objects/lib_dft_fgbg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,451 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:19 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:58:19,530 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/libgcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/lib_print.c -o ../objects/lib_print.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,557 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/libgcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/lib_print.c -o ../objects/lib_print.o 127.0.0.1 - - [18/Nov/2017:16:58:19 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,660 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/resizeterm.c -o ../objects/resizeterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,661 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:19 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,763 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:19,847 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -c ../ncurses/./tinfo/use_screen.c -o ../objects/use_screen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,864 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -c ../ncurses/./tinfo/use_screen.c -o ../objects/use_screen.o 127.0.0.1 - - [18/Nov/2017:16:58:19 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:58:19,940 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/use_ww.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,965 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/use_ww.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,965 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:19,965 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,068 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -indow.c -o ../objects/use_windogcc -DHAVE_CONFIG_H -I. -I../include /base/wresize.c -o ../objects/wresize.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,069 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,172 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o ../objects/access.o install_environment.STDOUT DEBUG 2017-11-18 16:58:20,257 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/access.c -gcc -DHAVE_CONFIG_H -I. -I../include /tinfo/add_tries.c -o ../objects/add_tries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,272 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/access.c -gcc -DHAVE_CONFIG_H -I. -I../include /tinfo/add_tries.c -o ../objects/add_tries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,272 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,373 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/alloc_ttyptype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,373 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,373 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:20,662 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -e.c -o ../objects/alloc_tgcc -DHAVE_CONFIG_H -I. -I../incurses/codes.c -o ../objects/codes.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,684 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -e.c -o ../objects/alloc_tgcc -DHAVE_CONFIG_H -I. -I../incurses/codes.c -o ../objects/codes.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,684 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:20,730 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -./objects/comp_captab.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,788 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -./objects/comp_captab.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,788 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,889 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ngcc -DHAVE_CONFIG_H -I. -c ../ncurses/comp_captab.c -o .gcc -DHAVE_CONFIG_H -I. -I../include /tinfo/comp_error.c -o ../objects/comp_error.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,994 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./tinfo/comp_hash.c -o ../objects/comp_hash.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,994 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:20,995 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:21,039 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.nline-insns-single=1200 -nline-insns-single=1200 -c ../nr.c -o ../objects/db_iterator.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,101 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.nline-insns-single=1200 -nline-insns-single=1200 -c ../nr.c -o ../objects/db_iterator.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,103 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:21 -0400] "GET /admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:58:21,195 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ndoalloc.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,208 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ndoalloc.o 127.0.0.1 - - [18/Nov/2017:16:58:21 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,314 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-icurses/./tinfo/db_iteratogcc -DHAVE_CONFIG_H -I. -I../incurses/./tinfo/doalloc.c -o ../objects/gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWINtries.c -o ../objects/entries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,314 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,315 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,420 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -bjects/fallback.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,420 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:21,450 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tinfo/engcc -DHAVE_CONFIG_H -I. -c ../ncurses/fallback.c -o ../ogcc -DHAVE_CONFIG_H -I. -I../include /tinfo/free_ttype.c -o ../objects/free_ttype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,522 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tinfo/engcc -DHAVE_CONFIG_H -I. -c ../ncurses/fallback.c -o ../ogcc -DHAVE_CONFIG_H -I. -I../include /tinfo/free_ttype.c -o ../objects/free_ttype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,522 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,627 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/getenv_num.c -o ../objects/getenv_num.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,627 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./tinfo/home_terminfo.c -o ../objects/home_terminfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,627 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,627 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,730 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-icurses/./tinfo/init_keytry.c -o ../objects/init_keytry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,730 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:21,738 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -c ../nnline-insns-single=1200 -c ../ncurses/.jects/lib_acs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,833 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -c ../nnline-insns-single=1200 -c ../ncurses/.jects/lib_acs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,834 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:21,846 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nects/lib_baudrate.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,934 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nects/lib_baudrate.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,934 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i/tinfo/lib_acs.c -o ../obgcc -DHAVE_CONFIG_H -I. -I../incurses/./tinfo/lib_baudrate.c -o ../objgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWINb_cur_term.c -o ../objects/lib_cur_term.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:21,935 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:22,008 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tinfo/ligcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/lib_data.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,039 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tinfo/ligcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/lib_data.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,040 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,040 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:22,075 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncts/lib_has_cap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,142 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncts/lib_has_cap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,142 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,246 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 - -o ../objects/lib_data.ogcc -DHAVE_CONFIG_H -I. -I../incurses/./tinfo/lib_has_cap.c -o ../objegcc -DHAVE_CONFIG_H -I. -I../include -D_DARWINb_kernel.c -o ../objects/lib_kernel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,246 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -./objects/lib_keyname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,246 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,348 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/..o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,348 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:22,418 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tinfo/ligcc -DHAVE_CONFIG_H -I. -c ../ncurses/lib_keyname.c -o .gcc -DHAVE_CONFIG_H -I. -I../include /tinfo/lib_longname.c -o ../objects/lib_longnamegcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -D ../objects/lib_napms.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,453 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tinfo/ligcc -DHAVE_CONFIG_H -I. -c ../ncurses/lib_keyname.c -o .gcc -DHAVE_CONFIG_H -I. -I../include /tinfo/lib_longname.c -o ../objects/lib_longnamegcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -D ../objects/lib_napms.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,453 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,453 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,556 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tinfo/lib_napms.c -ogcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/lib_options.c -o ../objects/lib_options.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,556 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:22,595 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -raw.c -o ../objects/lib_raw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,661 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -raw.c -o ../objects/lib_raw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,661 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:22,703 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ns/lib_setup.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,762 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ns/lib_setup.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,762 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,866 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./tinfo/lib_gcc -DHAVE_CONFIG_H -I. -I../incurses/./tinfo/lib_setup.c -o ../objectgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWINb_termcap.c -o ../objects/lib_termcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:22,866 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:23,030 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tinfo/linline-insns-single=1200 -nline-insns-single=1200 -c ../nc -o ../objects/lib_tgoto.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,068 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./tinfo/lib_termname.c -o ../objects/lib_termname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,068 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tinfo/linline-insns-single=1200 -nline-insns-single=1200 -c ../nc -o ../objects/lib_tgoto.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,069 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,069 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,170 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-icurses/./tinfo/lib_tgoto.gcc -DHAVE_CONFIG_H -I. -I../incurses/./tinfo/lib_ti.c -o ../objects/lib_ti.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,170 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,270 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./tinfo/lib_tparm.c -o ../objects/lib_tparm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,271 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,474 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-icurses/./tinfo/lib_tputs.c -o ../objects/lib_tputs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,474 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:23,575 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nnline-insns-single=1200 -nline-insns-single=1200 -c ../nnline-insns-single=1200 -c ../ncurses/.objects/lib_trace.o install_environment.STDOUT DEBUG 2017-11-18 16:58:23,643 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nects/lib_ttyflags.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,677 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nnline-insns-single=1200 -nline-insns-single=1200 -c ../nnline-insns-single=1200 -c ../ncurses/.objects/lib_trace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,679 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nects/lib_ttyflags.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,680 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,680 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,781 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i/trace/lib_trace.c -o ../gcc -DHAVE_CONFIG_H -I. -I../incurses/./tinfo/lib_ttyflags.c -o ../objgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWINtwait.c -o ../objects/lib_twait.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,781 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,884 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./tinfo/name_match.c -o ../objects/name_match.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,885 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:23,916 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tty/lib_nline-insns-single=1200 -nline-insns-single=1200 -c ../ncts/names.o install_environment.STDOUT DEBUG 2017-11-18 16:58:23,986 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../n/obsolete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,989 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tty/lib_nline-insns-single=1200 -nline-insns-single=1200 -c ../ncts/names.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,989 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../n/obsolete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:23,989 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,094 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-icurses/names.c -o ../objegcc -DHAVE_CONFIG_H -I. -I../incurses/./tinfo/obsolete.c -o ../objectsgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWINad_entry.c -o ../objects/read_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,094 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,094 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:24,257 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tinfo/regcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/read_termcermcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,305 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tinfo/regcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/read_termcermcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,305 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:24,330 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nstrings.o 127.0.0.1 - - [18/Nov/2017:16:58:24 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,409 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nstrings.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,409 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:24,488 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/trigcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/trim_sgr0.c -o ../objects/trim_sgr0.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,511 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ap.c -o ../objects/read_tgcc -DHAVE_CONFIG_H -I. -I../incurses/./tinfo/strings.c -o ../objects/gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWINes.c -o ../objects/tries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,511 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./base/trigcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/trim_sgr0.c -o ../objects/trim_sgr0.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,511 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,511 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,614 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -c ../ncurses/unctrl.c -o ../objects/unctrl.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,614 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,715 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./trace/visbuf.c -o ../objects/visbuf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,715 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:24,760 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -c ../ny.c -o ../objects/alloc_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,816 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -c ../ny.c -o ../objects/alloc_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:24,816 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:24,931 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ns/captoinfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:25,018 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ns/captoinfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:25,018 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:25,217 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tinfo/cogcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/comp_parsese.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:25,221 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-icurses/./tinfo/alloc_entrgcc -DHAVE_CONFIG_H -I. -I../incurses/./tinfo/captoinfo.c -o ../objectgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWINmp_expand.c -o ../objects/comp_expand.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:25,221 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/./tinfo/cogcc -DHAVE_CONFIG_H -I. -c ../ncurses/./tinfo/comp_parsese.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:25,221 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:25,326 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:25,426 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -.c -o ../objects/comp_pargcc -DHAVE_CONFIG_H -I. -I../incurses/./tinfo/comp_scan.c -o ../objects/comp_scan.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:25,427 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:25,634 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./tinfo/parsntry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:25,634 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:25,897 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nnline-insns-single=1200 -e_entry.c -o ../objects/parse_egcc -DHAVE_CONFIG_H -I. -I../include /tinfo/write_entry.c -o ../objects/write_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:25,942 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nnline-insns-single=1200 -e_entry.c -o ../objects/parse_egcc -DHAVE_CONFIG_H -I. -I../include /tinfo/write_entry.c -o ../objects/write_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:25,942 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:26,214 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/definy.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,252 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/definy.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,252 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,353 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.nline-insns-single=1200 -e_key.c -o ../objects/define_kegcc -DHAVE_CONFIG_H -I. -I../include /tinfo/hashed_db.c -o ../objects/hashed_db.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,353 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:26,356 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/key_definedned.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,458 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../ncurses/.gcc -DHAVE_CONFIG_H -I. -c ../ncurses/./base/key_definedned.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,459 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -.c -o ../objects/key_defigcc -DHAVE_CONFIG_H -I. -I../incurses/./base/keybound.c -o ../objects/keybound.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,463 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,463 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:26,499 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nnline-insns-single=1200 -.c -o ../objects/keyok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,564 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nnline-insns-single=1200 -.c -o ../objects/keyok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,565 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:26,640 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nobjects/lib_addstr.o ../objects/lib_beep.o ../objects/lib_bkgd.o ../objects/lib_box.o ../objects/lib_chgat.o ../objects/lib_clear.o ../objects/lib_clearok.o ../objects/lib_clrbot.o ../objects/lib_clreol.o ../objects/lib_color.o ../objects/lib_colorset.o ../objects/lib_delch.o ../objects/lib_delwin.o ../objects/lib_echo.o ../objects/lib_endwin.o ../objects/lib_erase.o ../objects/lib_flash.o ../objects/lib_gen.o ../objects/lib_getch.o ../objects/lib_getstr.o ../objects/lib_hline.o ../objects/lib_immedok.o ../objects/lib_inchstr.o ../objects/lib_initscr.o ../objects/lib_insch.o ../objects/lib_insdel.o ../objects/lib_insnstr.o ../objects/lib_instr.o ../objects/lib_isendwin.o ../objects/lib_leaveok.o ../objects/lib_mouse.o ../objects/lib_move.o ../objects/lib_mvcur.o ../objects/lib_mvwin.o ../objects/lib_newterm.o ../objects/lib_newwin.o ../objects/lib_nl.o ../objects/lib_overlay.o ../objects/lib_pad.o ../objects/lib_printw.o ../objects/lib_redrawln.o ../objects/lib_refresh.o ../objects/lib_restart.o ../objects/lib_scanw.o ../objects/lib_scoll.o ../objects/lib_scrollok.o ../objects/lib_scrreg.o ../objects/lib_set_term.o ../objects/lib_slk.o ../objects/lib_slkatr_set.o ../objects/lib_slkatrof.o ../objects/lib_slkatron.o ../objects/lib_slkatrset.o ../objects/lib_slkattr.o ../objects/lib_slkclear.o ../objects/lib_slkcolor.o uch.o ../objects/lib_touch.o ../objects/lib_tstp.o ../objects/lib_ungetch.o ../objects/lib_vidattr.o ../objects/lib_vline.o ../objects/lib_wattroff.o ../objects/lib_wattron.o ../objects/lib_winch.o ../objects/lib_window.o ../objects/nc_panel.o ../objects/safe_sprintf.o ../objects/tty_update.o ../objects/varargs.o ../objects/vsscanf.o ../objects/lib_freeall.o ../objects/expanded.o ../objects/legacy_coding.o ../objects/lib_dft_fgbg.o ../objects/lib_print.o ../objects/resizeterm.o ../objects/use_screen.o ../objects/use_window.o ../objects/wresize.o ../objects/access.o ../objects/add_tries.o ../objects/alloc_ttype.o ../objects/codes.o ../objects/comp_captab.o ../objects/comp_error.o ../objects/comp_hash.o ../objects/db_iterator.o ../objects/doalloc.o ../objects/entries.o ../objects/fallback.o ../objecinfo.o ../objects/init_keytry.o ../objects/lib_acs.o ../objects/lib_baudrate.o ../objects/lib_cur_term.o ../objects/lib_data.o ../objects/lib_has_cap.o ../objects/lib_kernel.o ../objects/lib_keyname.o ../objects/lib_longname.o ../objects/lib_napms.o ../objects/lib_options.o ../objects/lib_raw.o ../objects/lib_setup.o ../objects/lib_termcap.o ../objects/lib_termname.o ../objects/lib_tgoto.o ../objects/lib_ti.o ../objects/lib_tparm.o ../objects/lib_tputs.o ../objects/lib_trace.o ../objects/lib_ttyflags.o ../objects/lib_twait.o ../objects/name_match.o ../objtermcap.o ../objects/strings.o ../objects/tries.o ../objects/trim_sgr0.o ../objects/unctrl.o ../objects/visbuf.o ../objects/alloc_entry.o ../objects/captoinfo.o ../objects/comp_expand.o ../objects/comp_parse.o ../objects/comp_scan.o ../objects/parse_entry.o ../objects/write_entry.o ../objects/define_key.o ../objects/hashed_db.o ../objects/key_defined.o ../objects/keybound.o ../objects/keyok.o ../objects/version.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,666 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ic ../ncurses/./base/keyokgcc -DHAVE_CONFIG_H -I. -I../incurses/./base/version.c -o ../objects/version.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,666 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../nobjects/lib_addstr.o ../objects/lib_beep.o ../objects/lib_bkgd.o ../objects/lib_box.o ../objects/lib_chgat.o ../objects/lib_clear.o ../objects/lib_clearok.o ../objects/lib_clrbot.o ../objects/lib_clreol.o ../objects/lib_color.o ../objects/lib_colorset.o ../objects/lib_delch.o ../objects/lib_delwin.o ../objects/lib_echo.o ../objects/lib_endwin.o ../objects/lib_erase.o ../objects/lib_flash.o ../objects/lib_gen.o ../objects/lib_getch.o ../objects/lib_getstr.o ../objects/lib_hline.o ../objects/lib_immedok.o ../objects/lib_inchstr.o ../objects/lib_initscr.o ../objects/lib_insch.o ../objects/lib_insdel.o ../objects/lib_insnstr.o ../objects/lib_instr.o ../objects/lib_isendwin.o ../objects/lib_leaveok.o ../objects/lib_mouse.o ../objects/lib_move.o ../objects/lib_mvcur.o ../objects/lib_mvwin.o ../objects/lib_newterm.o ../objects/lib_newwin.o ../objects/lib_nl.o ../objects/lib_overlay.o ../objects/lib_pad.o ../objects/lib_printw.o ../objects/lib_redrawln.o ../objects/lib_refresh.o ../objects/lib_restart.o ../objects/lib_scanw.o ../objects/lib_scoll.o ../objects/lib_scrollok.o ../objects/lib_scrreg.o ../objects/lib_set_term.o ../objects/lib_slk.o ../objects/lib_slkatr_set.o ../objects/lib_slkatrof.o ../objects/lib_slkatron.o ../objects/lib_slkatrset.o ../objects/lib_slkattr.o ../objects/lib_slkclear.o ../objects/lib_slkcolor.o uch.o ../objects/lib_touch.o ../objects/lib_tstp.o ../objects/lib_ungetch.o ../objects/lib_vidattr.o ../objects/lib_vline.o ../objects/lib_wattroff.o ../objects/lib_wattron.o ../objects/lib_winch.o ../objects/lib_window.o ../objects/nc_panel.o ../objects/safe_sprintf.o ../objects/tty_update.o ../objects/varargs.o ../objects/vsscanf.o ../objects/lib_freeall.o ../objects/expanded.o ../objects/legacy_coding.o ../objects/lib_dft_fgbg.o ../objects/lib_print.o ../objects/resizeterm.o ../objects/use_screen.o ../objects/use_window.o ../objects/wresize.o ../objects/access.o ../objects/add_tries.o ../objects/alloc_ttype.o ../objects/codes.o ../objects/comp_captab.o ../objects/comp_error.o ../objects/comp_hash.o ../objects/db_iterator.o ../objects/doalloc.o ../objects/entries.o ../objects/fallback.o ../objecinfo.o ../objects/init_keytry.o ../objects/lib_acs.o ../objects/lib_baudrate.o ../objects/lib_cur_term.o ../objects/lib_data.o ../objects/lib_has_cap.o ../objects/lib_kernel.o ../objects/lib_keyname.o ../objects/lib_longname.o ../objects/lib_napms.o ../objects/lib_options.o ../objects/lib_raw.o ../objects/lib_setup.o ../objects/lib_termcap.o ../objects/lib_termname.o ../objects/lib_tgoto.o ../objects/lib_ti.o ../objects/lib_tparm.o ../objects/lib_tputs.o ../objects/lib_trace.o ../objects/lib_ttyflags.o ../objects/lib_twait.o ../objects/name_match.o ../objtermcap.o ../objects/strings.o ../objects/tries.o ../objects/trim_sgr0.o ../objects/unctrl.o ../objects/visbuf.o ../objects/alloc_entry.o ../objects/captoinfo.o ../objects/comp_expand.o ../objects/comp_parse.o ../objects/comp_scan.o ../objects/parse_entry.o ../objects/write_entry.o ../objects/define_key.o ../objects/hashed_db.o ../objects/key_defined.o ../objects/keybound.o ../objects/keyok.o ../objects/version.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,667 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:26,668 a - ../objects/hashmap.o install_environment.STDOUT DEBUG 2017-11-18 16:58:26,669 a - ../objects/lib_scrollok.o install_environment.STDOUT DEBUG 2017-11-18 16:58:26,670 a - ../objects/nc_panel.o install_environment.STDOUT DEBUG 2017-11-18 16:58:26,670 a - ../objects/home_terminfo.o install_environment.STDOUT DEBUG 2017-11-18 16:58:26,670 a - ../objects/write_entry.o install_environment.STDOUT DEBUG 2017-11-18 16:58:26,691 nline-insns-single=1200 -g -DTRACE -c ../ncurses/./tty/hardscroll.c -o ../obj_g/hardscroll.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,767 ar -curv ../lib/libncurses.a ../objects/hardscroll.o ../objects/hashmap.o ../objects/lib_addch.o ../reen.o ../objects/lib_scr../objects/lib_slkinit.o ../objects/lib_slklab.o ../objects/lib_slkrefr.o ../objects/lib_slkset.o ../objects/lib_slktots/free_ttype.o ../objects/getenv_num.o ../objects/home_termects/names.o ../objects/obsolete.o ../objects/read_entry.o ../objects/read_a - ../objects/hardscroll.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,768 a - ../objects/lib_addch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,768 a - ../objects/lib_addstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,768 a - ../objects/lib_beep.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,768 a - ../objects/lib_bkgd.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,768 a - ../objects/lib_box.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,768 a - ../objects/lib_chgat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,768 a - ../objects/lib_clear.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,768 a - ../objects/lib_clearok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,768 a - ../objects/lib_clrbot.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,769 a - ../objects/lib_clreol.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,769 a - ../objects/lib_color.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,769 a - ../objects/lib_colorset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,769 a - ../objects/lib_delch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,769 a - ../objects/lib_delwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,769 a - ../objects/lib_echo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,769 a - ../objects/lib_endwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,769 a - ../objects/lib_erase.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,770 a - ../objects/lib_flash.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,770 a - ../objects/lib_gen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,770 a - ../objects/lib_getch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,770 a - ../objects/lib_getstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,770 a - ../objects/lib_hline.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,770 a - ../objects/lib_immedok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,770 a - ../objects/lib_inchstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,770 a - ../objects/lib_initscr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,771 a - ../objects/lib_insch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,771 a - ../objects/lib_insdel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,771 a - ../objects/lib_insnstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,771 a - ../objects/lib_instr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,771 a - ../objects/lib_isendwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,771 a - ../objects/lib_leaveok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,771 a - ../objects/lib_mouse.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,771 a - ../objects/lib_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,771 a - ../objects/lib_mvcur.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,772 a - ../objects/lib_mvwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,772 a - ../objects/lib_newterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,772 a - ../objects/lib_newwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,772 a - ../objects/lib_nl.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,772 a - ../objects/lib_overlay.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,772 a - ../objects/lib_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,772 a - ../objects/lib_printw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,772 a - ../objects/lib_redrawln.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,773 a - ../objects/lib_refresh.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,773 a - ../objects/lib_restart.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,773 a - ../objects/lib_scanw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,773 a - ../objects/lib_screen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,773 a - ../objects/hashmap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,773 a - ../objects/lib_scroll.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,773 a - ../objects/lib_scrreg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,773 a - ../objects/lib_set_term.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,773 a - ../objects/lib_slk.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,773 a - ../objects/lib_slkatr_set.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,773 a - ../objects/lib_slkatrof.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,774 a - ../objects/lib_slkatron.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,774 a - ../objects/lib_slkatrset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,774 a - ../objects/lib_slkattr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,774 a - ../objects/lib_slkclear.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,774 a - ../objects/lib_slkcolor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,774 a - ../objects/lib_slkinit.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,774 a - ../objects/lib_slklab.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,774 a - ../objects/lib_slkrefr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,775 a - ../objects/lib_slkset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,775 a - ../objects/lib_slktouch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,775 a - ../objects/lib_touch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,775 a - ../objects/lib_tstp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,775 a - ../objects/lib_ungetch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,775 a - ../objects/lib_vidattr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,775 a - ../objects/lib_vline.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,775 a - ../objects/lib_wattroff.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,775 a - ../objects/lib_wattron.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,776 a - ../objects/lib_winch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,776 a - ../objects/lib_scrollok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,776 a - ../objects/lib_window.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,776 a - ../objects/safe_sprintf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,776 a - ../objects/tty_update.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,776 a - ../objects/varargs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,776 a - ../objects/vsscanf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,776 a - ../objects/lib_freeall.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,777 a - ../objects/expanded.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,777 a - ../objects/legacy_coding.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,777 a - ../objects/lib_dft_fgbg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,777 a - ../objects/lib_print.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,777 a - ../objects/resizeterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,777 a - ../objects/use_screen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,777 a - ../objects/use_window.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,777 a - ../objects/wresize.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,777 a - ../objects/access.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,778 a - ../objects/add_tries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,778 a - ../objects/alloc_ttype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,778 a - ../objects/codes.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,778 a - ../objects/comp_captab.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,778 a - ../objects/comp_error.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,778 a - ../objects/comp_hash.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,778 a - ../objects/db_iterator.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,778 a - ../objects/doalloc.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,779 a - ../objects/entries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,779 a - ../objects/fallback.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,779 a - ../objects/free_ttype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,779 a - ../objects/nc_panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,779 a - ../objects/getenv_num.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,779 a - ../objects/init_keytry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,779 a - ../objects/lib_acs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,779 a - ../objects/lib_baudrate.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,779 a - ../objects/lib_cur_term.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,780 a - ../objects/lib_data.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,780 a - ../objects/lib_has_cap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,780 a - ../objects/lib_kernel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,781 a - ../objects/lib_keyname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,781 a - ../objects/lib_longname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,781 a - ../objects/lib_napms.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,781 a - ../objects/lib_options.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,781 a - ../objects/lib_raw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,781 a - ../objects/lib_setup.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,781 a - ../objects/lib_termcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,781 a - ../objects/lib_termname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,781 a - ../objects/lib_tgoto.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,781 a - ../objects/lib_ti.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,781 a - ../objects/lib_tparm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,781 a - ../objects/lib_tputs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,782 a - ../objects/lib_trace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,782 a - ../objects/lib_ttyflags.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,782 a - ../objects/lib_twait.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,782 a - ../objects/name_match.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,782 a - ../objects/names.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,782 a - ../objects/obsolete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,782 a - ../objects/read_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,782 a - ../objects/read_termcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,782 a - ../objects/strings.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,782 a - ../objects/tries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,782 a - ../objects/trim_sgr0.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,782 a - ../objects/unctrl.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,782 a - ../objects/visbuf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,783 a - ../objects/alloc_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,783 a - ../objects/captoinfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,783 a - ../objects/comp_expand.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,783 a - ../objects/comp_parse.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,783 a - ../objects/comp_scan.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,783 a - ../objects/home_terminfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,783 a - ../objects/parse_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,783 a - ../objects/define_key.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,783 a - ../objects/hashed_db.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,783 a - ../objects/key_defined.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,783 a - ../objects/keybound.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,783 a - ../objects/keyok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,784 a - ../objects/version.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,784 ranlib ../lib/libncurses.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,784 a - ../objects/write_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,784 nline-insns-single=1200 -g -DTRACE -c ../ncurses/./tty/hardscroll.c -o ../obj_g/hardscroll.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,784 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,887 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-igcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./tty/hmap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:26,887 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,197 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR ../obj_g/lib_addch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,197 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:27,248 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ashmap.c -o ../obj_g/hashgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_addch.c -ogcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./base/lib_addstr.c -o ../obj_g/lib_addstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,301 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ashmap.c -o ../obj_g/hashgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_addch.c -ogcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./base/lib_addstr.c -o ../obj_g/lib_addstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,301 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,402 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/b_beep.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,402 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:27 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:58:27,431 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -lib_beep.c -o ../obj_g/ligcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_bkgd.c -o ../obj_g/lib_bkgd.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,505 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -lib_beep.c -o ../obj_g/ligcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_bkgd.c -o ../obj_g/lib_bkgd.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,505 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,609 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/_box.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,609 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:27,710 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -lib_box.c -o ../obj_g/libgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_chgat.c -online-insns-single=1200 -g -DTRACE -c ../ncurses/obj_g/lib_clear.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,711 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR ../obj_g/lib_chgat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,711 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -lib_box.c -o ../obj_g/libgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_chgat.c -online-insns-single=1200 -g -DTRACE -c ../ncurses/obj_g/lib_clear.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,712 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,812 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i/./base/lib_clear.c -o ..gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_clearok.c -o ../obj_g/lib_clearok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,812 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,812 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:27,848 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/lib_clrbot.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,914 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/lib_clrbot.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:27,915 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,017 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -lib_clrbot.c -o ../obj_g/gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_clreol.c -o ../obj_g/lib_clreol.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,017 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/.ib_color.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,017 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,122 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:28,183 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -/base/lib_color.c -o ../obj_g/lgcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./base/lib_colorset.c -o ../obj_g/lib_colorset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,226 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -/base/lib_color.c -o ../obj_g/lgcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./base/lib_colorset.c -o ../obj_g/lib_colorset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,227 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,331 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .gcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/ib_delch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,331 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:28,410 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -lib_delch.c -o ../obj_g/lgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_delwin.c -o ../obj_g/lib_delwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,435 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -lib_delch.c -o ../obj_g/lgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_delwin.c -o ../obj_g/lib_delwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,435 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,539 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/lib_echo.c -o ../obj_g/lib_echo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,539 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,642 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/.lib_endwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,642 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,744 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .se.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,745 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:28,747 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -/base/lib_endwin.c -o ../obj_g/gcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./base/lib_erase.c -o ../obj_g/lib_eragcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dflash.c -o ../obj_g/lib_flash.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,848 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -/base/lib_endwin.c -o ../obj_g/gcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./base/lib_erase.c -o ../obj_g/lib_eragcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dflash.c -o ../obj_g/lib_flash.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,848 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./base/lib_gcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/lib_gen.c -o ../obj_g/lib_gen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,848 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:28,848 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,163 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/.ib_getch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,163 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:29,254 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -/base/lib_getch.c -o ../obj_g/lgcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./base/lib_getstr.c -o ../obj_g/lib_getstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,263 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -/base/lib_getch.c -o ../obj_g/lgcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./base/lib_getstr.c -o ../obj_g/lib_getstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,366 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .gcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/lib_hline.c -o ../obj_g/lib_hline.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,366 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,366 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,472 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/./lib_immedok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,472 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:29,515 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -/base/lib_immedok.c -o ../obj_gnline-insns-single=1200 -g -DTRACE -c .str.c -o ../obj_g/lib_inchstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,572 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -/base/lib_immedok.c -o ../obj_gnline-insns-single=1200 -g -DTRACE -c .str.c -o ../obj_g/lib_inchstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,573 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,676 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i./ncurses/./base/lib_inchgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_initscr.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,676 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR ../obj_g/lib_insch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,676 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,780 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:29,796 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR-o ../obj_g/lib_initscr.ogcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_insch.c -ogcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./base/lib_insdel.c -o ../obj_g/lib_insdel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,881 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR-o ../obj_g/lib_initscr.ogcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_insch.c -ogcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./base/lib_insdel.c -o ../obj_g/lib_insdel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,881 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/lib_insnstr.c -o ../obj_g/lib_insnstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,881 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,984 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/./base/lib_instr.c -o ../obj_g/lib_instr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:29,984 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,086 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-iACE -c ../ncurses/./base/.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,086 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,086 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:30,127 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -g -DTRlib_isendwin.c -o ../obj_g/lib_isendwingcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./base/lib_leaveok.c -o ../obj_g/lib_leaveok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,189 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -g -DTRlib_isendwin.c -o ../obj_g/lib_isendwingcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./base/lib_leaveok.c -o ../obj_g/lib_leaveok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,189 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:30,199 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./base/lib_mouse.c -o ../obj_g/lib_mouse.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,292 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./base/lib_mouse.c -o ../obj_g/lib_mouse.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,292 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,497 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesgcc -DHAVE_CONFIG_H -I. -gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_move.c -o ../obj_g/lib_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,497 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:30 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:58:30,520 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -g -DTRACE -c ../ncurses/./tty/lib_mvcur.c -o ../obj_g/lib_mvcur.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,598 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -g -DTRACE -c ../ncurses/./tty/lib_mvcur.c -o ../obj_g/lib_mvcur.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,598 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:30,793 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/./base/lib_mvwin.c -o ../obj_g/lib_mvwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,803 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/./base/lib_mvwin.c -o ../obj_g/lib_mvwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,908 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_newterm.c -o ../obj_g/lib_newterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,908 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:30,908 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,013 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/.lib_newwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,013 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:31,111 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -/base/lib_newwin.c -o ../obj_g/gcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./base/lib_nl.c -o ../obj_g/lib_nl.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,118 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -/base/lib_newwin.c -o ../obj_g/gcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./base/lib_nl.c -o ../obj_g/lib_nl.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,221 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .gcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base//lib_overlay.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,221 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,222 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:31,294 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -lib_overlay.c -o ../obj_ggcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_pad.c -o ../obj_g/lib_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,326 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -lib_overlay.c -o ../obj_ggcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_pad.c -o ../obj_g/lib_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,327 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,427 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/lib_printw.c -o ../obj_g/lib_printw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,529 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/./base/lib_redrawln.c -o ../obj_g/lib_redrawln.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,530 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,530 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,631 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-iACE -c ../ncurses/./base/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,632 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:31,682 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -g -DTRlib_refresh.c -o ../obj_g/lib_refresh.ogcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./base/lib_restart.c -o ../obj_g/lib_restart.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,734 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -g -DTRlib_refresh.c -o ../obj_g/lib_refresh.ogcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./base/lib_restart.c -o ../obj_g/lib_restart.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,734 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:31,762 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./base/lib_scanw.c -o ../obj_g/lib_scanw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,839 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./base/lib_scanw.c -o ../obj_g/lib_scanw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,839 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:31,843 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-iACE -c ../ncurses/./base/lib_screen.c -o ../obj_g/lib_screen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,943 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-iACE -c ../ncurses/./base/lib_screen.c -o ../obj_g/lib_screen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:31,943 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:32,089 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .roll.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,151 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .roll.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,151 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,254 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesgcc -DHAVE_CONFIG_H -I. -nline-insns-single=1200 -g -DTRgcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./base/lib_scroll.c -o ../obj_g/lib_scgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dscrollok.c -o ../obj_g/lib_scrollok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,255 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:32,295 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./base/lib_gcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/lib_scrreg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,355 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./base/lib_gcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/lib_scrreg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,355 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,458 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -lib_scrreg.c -o ../obj_g/gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_set_term.c.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,459 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,563 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR./obj_g/lib_slk.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,563 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:32,671 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR -o ../obj_g/lib_set_termgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_slk.c -o .gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./base/lib_slkatr_set.c -o ../obj_g/lib_slkatr_set.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,772 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR -o ../obj_g/lib_set_termgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_slk.c -o .gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./base/lib_slkatr_set.c -o ../obj_g/lib_slkatr_set.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,772 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/lib_slkatrof.c -o ../obj_g/lib_slkatrof.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,772 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,772 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,877 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/.g/lib_slkatron.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,877 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:32,899 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -/base/lib_slkatron.c -o ../obj_gcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./base/lib_slkatrset.c -o ../obj_g/lib_slkatrset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,980 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -/base/lib_slkatron.c -o ../obj_gcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./base/lib_slkatrset.c -o ../obj_g/lib_slkatrset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,980 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .gcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base//lib_slkattr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:32,980 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:33,048 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -lib_slkattr.c -o ../obj_ggcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_slkclear.c.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,082 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -lib_slkattr.c -o ../obj_ggcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_slkclear.c.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,083 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,083 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,187 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR -o ../obj_g/lib_slkcleargcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_slkcolor.c.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,187 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:33,195 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR -o ../obj_g/lib_slkcolorgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_slkinit.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,292 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR -o ../obj_g/lib_slkcolorgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_slkinit.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,292 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR-o ../obj_g/lib_slkinit.ogcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_slklab.c -o ../obj_g/lib_slklab.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,292 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,292 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,393 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/./lib_slkrefr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,393 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,497 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .kset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,497 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:33,579 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -/base/lib_slkrefr.c -o ../obj_ggcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./base/lib_slkset.c -o ../obj_g/lib_slgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dslktouch.c -o ../obj_g/lib_slktouch.o 127.0.0.1 - - [18/Nov/2017:16:58:33 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,602 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -/base/lib_slkrefr.c -o ../obj_ggcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./base/lib_slkset.c -o ../obj_g/lib_slgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dslktouch.c -o ../obj_g/lib_slktouch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,602 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,705 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./base/lib_gcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/lib_touch.c -o ../obj_g/lib_touch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,705 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,807 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/._g/lib_tracedmp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,807 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:33,908 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ._tracemse.o install_environment.STDOUT DEBUG 2017-11-18 16:58:34,007 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -/trace/lib_tracedmp.c -o ../objgcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./trace/lib_tracemse.c -o ../obj_g/libgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dstp.c -o ../obj_g/lib_tstp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,009 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -/trace/lib_tracedmp.c -o ../objgcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./trace/lib_tracemse.c -o ../obj_g/libgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dstp.c -o ../obj_g/lib_tstp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,010 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,112 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./tty/lib_tgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/lib_ungetch.c -o ../obj_g/lib_ungetch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,113 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,113 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,217 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/./tty/lib_vidattr.c -o ../obj_g/lib_vidattr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,217 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:34,400 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -g -DTRnline-insns-single=1200 -g -DTRACE -c .roff.c -o ../obj_g/lib_wattroff.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,426 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-iACE -c ../ncurses/./base/lib_vline.c -o ../obj_g/lib_vline.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,426 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -g -DTRnline-insns-single=1200 -g -DTRACE -c .roff.c -o ../obj_g/lib_wattroff.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,426 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,426 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,528 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i./ncurses/./base/lib_wattgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_wattron.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,529 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:34,624 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR-o ../obj_g/lib_wattron.ogcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_winch.c -o ../obj_g/lib_winch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,630 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR-o ../obj_g/lib_wattron.ogcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_winch.c -o ../obj_g/lib_winch.o install_environment.STDOUT DEBUG 2017-11-18 16:58:34,703 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -lib_window.c -o ../obj_g/lib_window.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,733 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -lib_window.c -o ../obj_g/lib_window.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,734 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,734 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,839 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/gcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./base/nc_panel.c -o ../obj_g/nc_panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,942 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/.g/safe_sprintf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,942 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:34,942 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:35,047 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .ate.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:35,047 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:35,618 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .nline-insns-single=1200 -/base/safe_sprintf.c -o ../obj_gcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./tty/tty_update.c -o ../obj_g/tty_updgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dargs.c -o ../obj_g/varargs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:35,670 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .nline-insns-single=1200 -/base/safe_sprintf.c -o ../obj_gcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./tty/tty_update.c -o ../obj_g/tty_updgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dargs.c -o ../obj_g/varargs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:35,670 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:35,774 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./trace/vargcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/canf.o install_environment.STDOUT DEBUG 2017-11-18 16:58:35,838 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -vsscanf.c -o ../obj_g/vssgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_freeall.c -o ../obj_g/lib_freeall.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:35,875 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -vsscanf.c -o ../obj_g/vssgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/lib_freeall.c -o ../obj_g/lib_freeall.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:35,875 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:35,876 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:35,979 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRgcc -DHAVE_CONFIG_H -I. -o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:35,979 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:36,058 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/expanded.c -o ../obj_g/expanded.nline-insns-single=1200 -g -DTRACE -c .nline-insns-single=1200 -g -DTRACE -c ../ncurses ../obj_g/lib_dft_fgbg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,081 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i./ncurses/./base/legacy_coding.c -o ../obj_g/legacy_coding.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,081 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/expanded.c -o ../obj_g/expanded.nline-insns-single=1200 -g -DTRACE -c .nline-insns-single=1200 -g -DTRACE -c ../ncurses ../obj_g/lib_dft_fgbg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,081 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,081 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,184 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i/./base/lib_dft_fgbg.c -ogcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/lib_print.c -o ../obj_g/lib_print.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,184 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,288 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/.resizeterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,288 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,388 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .ce_xnames.o install_environment.STDOUT DEBUG 2017-11-18 16:58:36,470 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -/base/resizeterm.c -o ../obj_g/gcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./trace/trace_xnames.c -o ../obj_g/tragcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -D_screen.c -o ../obj_g/use_screen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,493 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -/base/resizeterm.c -o ../obj_g/gcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./trace/trace_xnames.c -o ../obj_g/tragcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -D_screen.c -o ../obj_g/use_screen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,494 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,494 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,599 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./tinfo/usegcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./base/use_window.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,599 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:36 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,700 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR./obj_g/wresize.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,701 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,802 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./tinfo/access.c -o ../obj_g/access.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:36,906 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:36,919 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -use_window.c -o ../obj_g/gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/wresize.c -o .gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWINnline-insns-single=1200 -g -DTRACE -c ../ncurses/./tinfo/addtries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,011 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -use_window.c -o ../obj_g/gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/wresize.c -o .gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWINnline-insns-single=1200 -g -DTRACE -c ../ncurses/./tinfo/addtries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,011 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i_tries.c -o ../obj_g/add_gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/alloc_ttype.co tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,011 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,112 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:37,400 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR -o ../obj_g/alloc_ttype.gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/codes.c -o ../obj_g/cgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/comp_captab.c -o ../obj_g/comp_captab.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,417 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRodes.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,417 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR -o ../obj_g/alloc_ttype.gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/codes.c -o ../obj_g/cgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/comp_captab.c -o ../obj_g/comp_captab.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,417 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,417 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,624 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./tinfo/comp_error.c -o ../obj_g/comp_error.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,624 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/./tinfo/comp_hash.c -o ../obj_g/comp_hash.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,624 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,728 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-iACE -c ../ncurses/./tinfo/db_iterator.c -o ../obj_g/db_iterator.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,728 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,728 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:37,903 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -g -DTRnline-insns-single=1200 -g -DTRACE -c .nline-insns-single=1200 -g -DTRACE -c ../ncursesobj_g/entries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,933 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i./ncurses/./tinfo/doalloc.c -o ../obj_g/doalloc.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,933 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -nline-insns-single=1200 -g -DTRnline-insns-single=1200 -g -DTRACE -c .nline-insns-single=1200 -g -DTRACE -c ../ncursesobj_g/entries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,933 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:37,934 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:38,017 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRg/fallback.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,038 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRg/fallback.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,038 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,138 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i/./tinfo/entries.c -o ../gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/fallback.c -o ../obj_gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./tinfo/free_ttype.c -o ../obj_g/free_ttype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,139 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,241 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/./tinfo/getenv_num.c -o ../obj_g/getenv_num.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,241 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-iACE -c ../ncurses/./tinfo/home_terminfo.c -o ../obj_g/home_terminfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,241 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:38,302 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesnline-insns-single=1200 -nline-insns-single=1200 -g -DTRnline-insns-single=1200 -g -DTRACE -c .ytry.c -o ../obj_g/init_keytry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,343 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesnline-insns-single=1200 -nline-insns-single=1200 -g -DTRnline-insns-single=1200 -g -DTRACE -c .ytry.c -o ../obj_g/init_keytry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,343 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,343 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:38,392 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR../obj_g/lib_acs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,448 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR../obj_g/lib_acs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,448 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,552 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-i./ncurses/./tinfo/init_kegcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/lib_acs.c -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./tinfo/lib_baudrate.c -o ../obj_g/lib_baudrate.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,552 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,653 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/._g/lib_cur_term.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,653 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:38,684 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesnline-insns-single=1200 -/tinfo/lib_cur_term.c -o ../objgcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./tinfo/lib_data.c -o ../obj_g/lib_data.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,759 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesnline-insns-single=1200 -/tinfo/lib_cur_term.c -o ../objgcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./tinfo/lib_data.c -o ../obj_g/lib_data.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,759 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .gcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./tinfog/lib_has_cap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,759 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:38,836 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -/lib_has_cap.c -o ../obj_gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/lib_kernel.c -o ../obj_g/lib_kernel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,862 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -/lib_has_cap.c -o ../obj_gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/lib_kernel.c -o ../obj_g/lib_kernel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,862 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,862 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:38,920 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/lyname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,967 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/lyname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:38,968 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:39,030 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ._longname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,070 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ._longname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,070 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,172 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -ib_keyname.c -o ../obj_g/lib_kegcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./tinfo/lib_longname.c -o ../obj_g/libgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -D_napms.c -o ../obj_g/lib_napms.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,172 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:39,191 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./tinfo/libgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./tinfog/lib_options.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,278 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./tinfo/libgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./tinfog/lib_options.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,278 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:39,300 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR../obj_g/lib_raw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,381 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR../obj_g/lib_raw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,381 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,486 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -/lib_options.c -o ../obj_gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/lib_raw.c -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./tinfo/lib_setup.c -o ../obj_g/lib_setup.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,487 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:39,578 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./tinfog/lib_termcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,590 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./tinfog/lib_termcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,696 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:39 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,804 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -/lib_termcap.c -o ../obj_gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/lib_termname.e.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,804 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:39,861 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRc -o ../obj_g/lib_termnamgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/lib_tgoto.c -o ../obj_g/lib_tgoto.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,909 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRc -o ../obj_g/lib_termnamgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/lib_tgoto.c -o ../obj_g/lib_tgoto.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:39,909 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:40,015 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./tinfo_ti.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:40,015 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:40,120 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRo ../obj_g/lib_tparm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:40,120 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:40,368 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -/lib_ti.c -o ../obj_g/libgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/lib_tparm.c -gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./tinfo/lib_tputs.c -o ../obj_g/lib_tputs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:40,426 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -/lib_ti.c -o ../obj_g/libgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/lib_tparm.c -gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./tinfo/lib_tputs.c -o ../obj_g/lib_tputs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:40,427 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:40,532 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./tracelib_trace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:40,636 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:40,665 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -/lib_trace.c -o ../obj_g/gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./trace/lib_traceatr.r.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:40,741 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -/lib_trace.c -o ../obj_g/gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./trace/lib_traceatr.r.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:40,742 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:40,846 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRc -o ../obj_g/lib_traceatgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./trace/lib_tracebitsits.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:40,846 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:40,866 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR.c -o ../obj_g/lib_tracebgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./trace/lib_tracechr.c -o ../obj_g/lib_tracechr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:40,950 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR.c -o ../obj_g/lib_tracebgcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./trace/lib_tracechr.c -o ../obj_g/lib_tracechr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:40,950 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:40,971 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/./tinfo/lib_ttyflags.c -o ../obj_g/lib_ttyflags.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,056 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/./tinfo/lib_ttyflags.c -o ../obj_g/lib_ttyflags.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,056 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:41,086 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR../obj_g/lib_twait.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,160 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR../obj_g/lib_twait.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,160 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:41,257 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesnline-insns-single=1200 -ames.c -o ../obj_g/names.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,263 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tty/lib_twait.c -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./tinfo/name_match.c -o ../obj_g/name_match.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,263 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesnline-insns-single=1200 -ames.c -o ../obj_g/names.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,263 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:41,334 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR ../obj_g/obsolete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,368 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR ../obj_g/obsolete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,369 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,369 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,473 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/ngcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/obsolete.c -ogcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./tinfo/read_entry.c -o ../obj_g/read_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,473 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,677 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/./tinfo/read_termcap.c -o ../obj_g/read_termcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,677 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:41,731 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesnline-insns-single=1200 -nline-insns-single=1200 -g -DTR/strings.c -o ../obj_g/strings.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,778 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesnline-insns-single=1200 -nline-insns-single=1200 -g -DTR/strings.c -o ../obj_g/strings.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,779 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,882 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-iACE -c ../ncurses/./tinfogcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./trace/trace_buf.c -o ../obj_g/trace_buf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,883 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,984 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/./trace/trace_tries.c -o ../obj_g/trace_tries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,984 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-iACE -c ../ncurses/./base/tries.c -o ../obj_g/tries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,984 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:41,984 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:42,089 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .gr0.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:42,090 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:42,242 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -nline-insns-single=1200 -g -DTRgcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./tinfo/trim_sgr0.c -o ../obj_g/trim_sgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -D ../obj_g/unctrl.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:42,295 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -nline-insns-single=1200 -g -DTRgcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./tinfo/trim_sgr0.c -o ../obj_g/trim_sgcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -D ../obj_g/unctrl.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:42,295 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:42,396 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/unctrl.c -ogcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./trace/visbuf.c -o ../obj_g/visbuf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:42,396 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:42,503 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./tinfog/alloc_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:42,604 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./tinfog/alloc_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:42,604 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:42,708 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -/alloc_entry.c -o ../obj_gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/captoinfo.c -o ../obj_g/captoinfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:42,708 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:42 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:43,019 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/.g/comp_expand.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:43,019 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:43,120 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c .parse.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:43,120 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:43,274 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -/tinfo/comp_expand.c -o ../obj_gcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./tinfo/comp_parse.c -o ../obj_g/comp_gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dp_scan.c -o ../obj_g/comp_scan.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:43,327 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRnline-insns-single=1200 -/tinfo/comp_expand.c -o ../obj_gcc -DHAVE_CONFIG_H -I. -I../include ./ncurses/./tinfo/comp_parse.c -o ../obj_g/comp_gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dp_scan.c -o ../obj_g/comp_scan.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:43,328 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:43,533 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncurses/./tinfo/comgcc -DHAVE_CONFIG_H -I. -g -DTRACE -c ../ncurses/./tinfog/parse_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:43,534 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:43,893 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -/parse_entry.c -o ../obj_gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/write_entry.co tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:43,940 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -/parse_entry.c -o ../obj_gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./tinfo/write_entry.co tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:43,940 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:44,263 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRo ../obj_g/define_key.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,355 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRo ../obj_g/define_key.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,355 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTR -o ../obj_g/write_entry.gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/define_key.c -gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./tinfo/hashed_db.c -o ../obj_g/hashed_db.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,355 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,456 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-ig -DTRACE -c ../ncurses/./base/key_defined.c -o ../obj_g/key_defined.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,456 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,456 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:44,488 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesnline-insns-single=1200 -nline-insns-single=1200 -g -DTRkeybound.c -o ../obj_g/keybound.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,559 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesnline-insns-single=1200 -nline-insns-single=1200 -g -DTRkeybound.c -o ../obj_g/keybound.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,559 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:44,562 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRobj_g/keyok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,660 clude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRobj_g/keyok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,660 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-iACE -c ../ncurses/./base/gcc -DHAVE_CONFIG_H -I. -I../inACE -c ../ncurses/./base/keyok.c -o ../gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN/./base/version.c -o ../obj_g/version.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,660 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:44,717 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesar -curv ../lib/libncurseib_beep.o ../obj_g/lib_bkgd.o ../obj_g/lib_box.o ../obj_g/lib_chgat.o ../obj_g/lib_clear.o ../obj_g/lib_clearok.o ../obj_g/lib_clrbot.o ../obj_g/lib_clreol.o ../obj_g/lib_color.o ../obj_g/lib_colorset.o ../obj_g/lib_delch.o ../obj_g/lib_delwin.o ../obj_g/lib_echo.o ../obj_g/lib_endwin.o ../obj_g/lib_erase.o ../obj_g/lib_flash.o ../obj_g/lib_gen.o ../obj_g/lib_getch.o ../obj_g/lib_getstr.o ../obj_g/lib_hline.o ../obj_g/lib_immedok.o ../obj_g/lib_inchstr.o ../obj_g/lib_initscr.o ../obj_g/lib_insch.o ../obj_g/lib_insdel.o ../obj_g/lib_insnstr.o ../obj_g/lib_instr.o ../obj_g/lib_isendwin.o ../obj_g/lib_leaveo../obj_g/lib_move.o ../obj_g/lib_mvcur.o ../obj_g/lib_mvwin.o ../obj_g/lib_newterm.o ../obj_g/lib_newwin.o ../obj_g/lib_nl.o ../obj_g/lib_overlay.o ../obj_g/lib_pad.o ../obj_g/lib_prin/obj_g/lib_refresh.o ../obj_g/lib_restart.o ../obj_g/lib_scanw.o ../obj_g/lib_screen.o ../obj_g/lib_scroll.o ../obj_g/lib_scrollok.o ../obj_g/lib_scrreg.o ../obj_g/lib_set_term.o ../obj_g/lib_slk.o ../obj_g/lib_slkatr_set.o ../obj.o ../obj_g/lib_slkatrset.o ../obj_g/lib_slkattr.o ../obj_g/lib_slkclear.o ../obj_g/lib_slkcolor.o ../obj_g/lib_slkinit.o ../obj_g/lib_slklab.o ../obj_g/lib_slkrefr.o ../obj_g/lib_slkset.o ../obj_g/lib_slktouch.o ../obj_g/lib_touch.o ../obj_g/lib_tracedmp.o ../obj_g/lib_tracemse.o ../obib_vidattr.o ../obj_g/lib_vline.o ../obj_g/lib_wattroff.o ../obj_g/lib_wattron.o ../obj_g/lib_winch.o ../obj_g/lib_window.o ../obj_g/nc_panel.o ../obj_g/safe_sprintf.o ../obj_g/tty_update.o ../obj_g/varargs.o ../obj_g/vsscanf.o ../obj_g/lib_freeall.o ../obj_g/expanded.o ../obj_g/legacy_coding.o ../obj_g/lib_dft_fgbg.o ../obj_g/lib_print.o ../obj_g/resizeterse_window.o ../obj_g/wresize.o ../obj_g/access.o ../obj_g/add_tries.o ../obj_g/alloc_ttype.o ../obj_g/codes.o ../obj_g/comp_captab.o ../obj_g/comp_error.o ../obj_g/comp_hash.o ../obj_g/db_iterator.o ../obj_g/doalloc.o ../obj_g/entries.o ../obj_g/fallback.o ../obj_g/free_ttype.o ../obj_g/getenv_num.o ../obj_g/home_terminfo.o ../obj_g/init_keytry.o ../obj_g/lib_acs.o ../obj_g/lib_baudrate.o ../obj_g/lib_cur_term.o ../obj_g/lib_data.o ../obj_g/lib_e.o ../obj_g/lib_napms.o ../obj_g/lib_options.o ../obj_g/lib_raw.o ../obj_g/lib_setup.o ../obj_g/lib_termcap.o ../obj_g/lib_termname.o ../obj_g/lib_tgoto.o ../obj_g/lib_ti.o ../obj_g/lib_tparm.o ../obj_g/lib_tputs.o ../obj_g/lib_trace.o ../obj_g/lib_traceatr.o ../obj_g/lib_tracebits.o ../obj_g/lib_tracechr.o ../obj_g/lib_ttyflags.o ../obj_g/lib_twait.o ../obj_g/name_match.o ../obj_g/names.o ../obj_g/obsolete.o ../obj_g/read_entry.o ../obj_g/read_termcap.o ../obj_g/strings.o ../obj_g/trace_buf.o ../obj_g/trace_tries.o ../obj_g/tries.o ../obj_g/trim_sgr0.o expand.o ../obj_g/comp_parse.o ../obj_g/comp_scan.o ../obj_g/parse_entry.o ../obj_g/write_entry.o ../obj_g/define_key.o ../obj_g/hashed_db.o ../obj_g/key_defined.o ../obj_g/keybound.o ../obj_g/keyok.o ../obj_g/version.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,761 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../ncursesar -curv ../lib/libncurseib_beep.o ../obj_g/lib_bkgd.o ../obj_g/lib_box.o ../obj_g/lib_chgat.o ../obj_g/lib_clear.o ../obj_g/lib_clearok.o ../obj_g/lib_clrbot.o ../obj_g/lib_clreol.o ../obj_g/lib_color.o ../obj_g/lib_colorset.o ../obj_g/lib_delch.o ../obj_g/lib_delwin.o ../obj_g/lib_echo.o ../obj_g/lib_endwin.o ../obj_g/lib_erase.o ../obj_g/lib_flash.o ../obj_g/lib_gen.o ../obj_g/lib_getch.o ../obj_g/lib_getstr.o ../obj_g/lib_hline.o ../obj_g/lib_immedok.o ../obj_g/lib_inchstr.o ../obj_g/lib_initscr.o ../obj_g/lib_insch.o ../obj_g/lib_insdel.o ../obj_g/lib_insnstr.o ../obj_g/lib_instr.o ../obj_g/lib_isendwin.o ../obj_g/lib_leaveo../obj_g/lib_move.o ../obj_g/lib_mvcur.o ../obj_g/lib_mvwin.o ../obj_g/lib_newterm.o ../obj_g/lib_newwin.o ../obj_g/lib_nl.o ../obj_g/lib_overlay.o ../obj_g/lib_pad.o ../obj_g/lib_prin/obj_g/lib_refresh.o ../obj_g/lib_restart.o ../obj_g/lib_scanw.o ../obj_g/lib_screen.o ../obj_g/lib_scroll.o ../obj_g/lib_scrollok.o ../obj_g/lib_scrreg.o ../obj_g/lib_set_term.o ../obj_g/lib_slk.o ../obj_g/lib_slkatr_set.o ../obj.o ../obj_g/lib_slkatrset.o ../obj_g/lib_slkattr.o ../obj_g/lib_slkclear.o ../obj_g/lib_slkcolor.o ../obj_g/lib_slkinit.o ../obj_g/lib_slklab.o ../obj_g/lib_slkrefr.o ../obj_g/lib_slkset.o ../obj_g/lib_slktouch.o ../obj_g/lib_touch.o ../obj_g/lib_tracedmp.o ../obj_g/lib_tracemse.o ../obib_vidattr.o ../obj_g/lib_vline.o ../obj_g/lib_wattroff.o ../obj_g/lib_wattron.o ../obj_g/lib_winch.o ../obj_g/lib_window.o ../obj_g/nc_panel.o ../obj_g/safe_sprintf.o ../obj_g/tty_update.o ../obj_g/varargs.o ../obj_g/vsscanf.o ../obj_g/lib_freeall.o ../obj_g/expanded.o ../obj_g/legacy_coding.o ../obj_g/lib_dft_fgbg.o ../obj_g/lib_print.o ../obj_g/resizeterse_window.o ../obj_g/wresize.o ../obj_g/access.o ../obj_g/add_tries.o ../obj_g/alloc_ttype.o ../obj_g/codes.o ../obj_g/comp_captab.o ../obj_g/comp_error.o ../obj_g/comp_hash.o ../obj_g/db_iterator.o ../obj_g/doalloc.o ../obj_g/entries.o ../obj_g/fallback.o ../obj_g/free_ttype.o ../obj_g/getenv_num.o ../obj_g/home_terminfo.o ../obj_g/init_keytry.o ../obj_g/lib_acs.o ../obj_g/lib_baudrate.o ../obj_g/lib_cur_term.o ../obj_g/lib_data.o ../obj_g/lib_e.o ../obj_g/lib_napms.o ../obj_g/lib_options.o ../obj_g/lib_raw.o ../obj_g/lib_setup.o ../obj_g/lib_termcap.o ../obj_g/lib_termname.o ../obj_g/lib_tgoto.o ../obj_g/lib_ti.o ../obj_g/lib_tparm.o ../obj_g/lib_tputs.o ../obj_g/lib_trace.o ../obj_g/lib_traceatr.o ../obj_g/lib_tracebits.o ../obj_g/lib_tracechr.o ../obj_g/lib_ttyflags.o ../obj_g/lib_twait.o ../obj_g/name_match.o ../obj_g/names.o ../obj_g/obsolete.o ../obj_g/read_entry.o ../obj_g/read_termcap.o ../obj_g/strings.o ../obj_g/trace_buf.o ../obj_g/trace_tries.o ../obj_g/tries.o ../obj_g/trim_sgr0.o expand.o ../obj_g/comp_parse.o ../obj_g/comp_scan.o ../obj_g/parse_entry.o ../obj_g/write_entry.o ../obj_g/define_key.o ../obj_g/hashed_db.o ../obj_g/key_defined.o ../obj_g/keybound.o ../obj_g/keyok.o ../obj_g/version.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,761 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:44,778 a - ../obj_g/hashmap.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,779 a - ../obj_g/lib_addstr.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,779 a - ../obj_g/lib_beep.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,779 a - ../obj_g/lib_bkgd.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,780 a - ../obj_g/lib_getch.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,780 a - ../obj_g/lib_immedok.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,780 a - ../obj_g/lib_nl.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,781 a - ../obj_g/lib_overlay.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,781 a - ../obj_g/varargs.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,782 a - ../obj_g/lib_tputs.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,782 a - ../obj_g/lib_trace.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,782 a - ../obj_g/lib_tracechr.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,782 a - ../obj_g/lib_ttyflags.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,783 a - ../obj_g/names.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,783 a - ../obj_g/obsolete.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,783 a - ../obj_g/write_entry.o install_environment.STDOUT DEBUG 2017-11-18 16:58:44,842 y/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib" all install_environment.STDOUT DEBUG 2017-11-18 16:58:44,849 ../include/Caps >termsort.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,863 s_g.a ../obj_g/hardscroll.o ../obj_g/hashmap.o ../obj_g/lib_addch.o ../obj_g/lib_addstr.o ../obj_g/lk.o ../obj_g/lib_mouse.o tw.o ../obj_g/lib_redrawln.o .._g/lib_slkatrof.o ../obj_g/lib_slkatronj_g/lib_tstp.o ../obj_g/lib_ungetch.o ../obj_g/lm.o ../obj_g/trace_xnames.o ../obj_g/use_screen.o ../obj_g/uhas_cap.o ../obj_g/lib_kernel.o ../obj_g/lib_keyname.o ../obj_g/lib_longnam../obj_g/unctrl.o ../obj_g/visbuf.o ../obj_g/alloc_entry.o ../obj_g/captoinfo.o ../obj_g/comp_a - ../obj_g/hardscroll.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,863 a - ../obj_g/hashmap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,863 a - ../obj_g/lib_addstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,863 a - ../obj_g/lib_beep.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,863 a - ../obj_g/lib_addch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,863 a - ../obj_g/lib_box.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,864 a - ../obj_g/lib_chgat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,864 a - ../obj_g/lib_clear.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,864 a - ../obj_g/lib_clearok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,864 a - ../obj_g/lib_clrbot.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,864 a - ../obj_g/lib_clreol.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,864 a - ../obj_g/lib_color.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,864 a - ../obj_g/lib_colorset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,864 a - ../obj_g/lib_delch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,864 a - ../obj_g/lib_delwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,864 a - ../obj_g/lib_echo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,864 a - ../obj_g/lib_endwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,864 a - ../obj_g/lib_erase.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,864 a - ../obj_g/lib_flash.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,864 a - ../obj_g/lib_bkgd.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_gen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_getstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_getch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_hline.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_inchstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_initscr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_insch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_insdel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_insnstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_instr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_isendwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_leaveok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_mouse.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,865 a - ../obj_g/lib_mvcur.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,866 a - ../obj_g/lib_mvwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,866 a - ../obj_g/lib_newterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,866 a - ../obj_g/lib_immedok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,866 a - ../obj_g/lib_nl.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,866 a - ../obj_g/lib_newwin.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,866 a - ../obj_g/lib_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,866 a - ../obj_g/lib_printw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,866 a - ../obj_g/lib_redrawln.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,866 a - ../obj_g/lib_refresh.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,866 a - ../obj_g/lib_restart.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,866 a - ../obj_g/lib_scanw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,866 a - ../obj_g/lib_screen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,867 a - ../obj_g/lib_scroll.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,867 a - ../obj_g/lib_scrollok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,867 a - ../obj_g/lib_scrreg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,867 a - ../obj_g/lib_set_term.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,867 a - ../obj_g/lib_slk.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,867 a - ../obj_g/lib_slkatr_set.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,867 a - ../obj_g/lib_slkatrof.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,867 a - ../obj_g/lib_slkatron.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,868 a - ../obj_g/lib_slkatrset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,868 a - ../obj_g/lib_slkattr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,868 a - ../obj_g/lib_slkclear.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,868 a - ../obj_g/lib_slkcolor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,868 a - ../obj_g/lib_slkinit.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,868 a - ../obj_g/lib_slklab.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,868 a - ../obj_g/lib_slkrefr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,868 a - ../obj_g/lib_slkset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,868 a - ../obj_g/lib_slktouch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,868 a - ../obj_g/lib_touch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,868 a - ../obj_g/lib_tracedmp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,869 a - ../obj_g/lib_tracemse.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,869 a - ../obj_g/lib_tstp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,869 a - ../obj_g/lib_ungetch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,869 a - ../obj_g/lib_vidattr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,870 a - ../obj_g/lib_vline.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,870 a - ../obj_g/lib_wattroff.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,870 a - ../obj_g/lib_wattron.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,870 a - ../obj_g/lib_winch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,870 a - ../obj_g/lib_window.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,871 a - ../obj_g/nc_panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,871 a - ../obj_g/safe_sprintf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,871 a - ../obj_g/lib_overlay.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,871 a - ../obj_g/tty_update.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,871 a - ../obj_g/vsscanf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,871 a - ../obj_g/lib_freeall.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,872 a - ../obj_g/expanded.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,872 a - ../obj_g/legacy_coding.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,872 a - ../obj_g/lib_dft_fgbg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,872 a - ../obj_g/lib_print.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,872 a - ../obj_g/resizeterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,872 a - ../obj_g/trace_xnames.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,872 a - ../obj_g/use_screen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,872 a - ../obj_g/use_window.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,872 a - ../obj_g/wresize.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,872 a - ../obj_g/access.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,872 a - ../obj_g/add_tries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,872 a - ../obj_g/alloc_ttype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,873 a - ../obj_g/codes.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,873 a - ../obj_g/comp_captab.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,873 a - ../obj_g/comp_error.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,873 a - ../obj_g/comp_hash.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,873 a - ../obj_g/db_iterator.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,873 a - ../obj_g/doalloc.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,873 a - ../obj_g/entries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,873 a - ../obj_g/fallback.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,873 a - ../obj_g/free_ttype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,873 a - ../obj_g/getenv_num.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,873 a - ../obj_g/home_terminfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,873 a - ../obj_g/init_keytry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,873 a - ../obj_g/lib_acs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,874 a - ../obj_g/lib_baudrate.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,874 a - ../obj_g/lib_cur_term.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,874 a - ../obj_g/lib_data.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,874 a - ../obj_g/lib_has_cap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,874 a - ../obj_g/lib_kernel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,874 a - ../obj_g/lib_keyname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,874 a - ../obj_g/lib_longname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,874 a - ../obj_g/lib_napms.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,874 a - ../obj_g/lib_options.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,874 a - ../obj_g/lib_raw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,874 a - ../obj_g/lib_setup.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,874 a - ../obj_g/lib_termcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,875 a - ../obj_g/lib_termname.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,875 a - ../obj_g/lib_tgoto.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,875 a - ../obj_g/lib_ti.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,875 a - ../obj_g/varargs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,875 a - ../obj_g/lib_tputs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,875 a - ../obj_g/lib_tparm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,875 a - ../obj_g/lib_traceatr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,875 a - ../obj_g/lib_trace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,875 a - ../obj_g/lib_tracechr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,875 a - ../obj_g/lib_tracebits.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,875 a - ../obj_g/lib_twait.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,875 a - ../obj_g/lib_ttyflags.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,876 a - ../obj_g/names.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,876 a - ../obj_g/name_match.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,876 a - ../obj_g/read_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,876 a - ../obj_g/read_termcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,876 a - ../obj_g/strings.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,876 a - ../obj_g/trace_buf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,876 a - ../obj_g/trace_tries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,876 a - ../obj_g/tries.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,876 a - ../obj_g/trim_sgr0.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,876 a - ../obj_g/unctrl.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,876 a - ../obj_g/visbuf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,876 a - ../obj_g/alloc_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,876 a - ../obj_g/captoinfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,877 a - ../obj_g/comp_expand.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,877 a - ../obj_g/comp_parse.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,877 a - ../obj_g/comp_scan.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,877 a - ../obj_g/obsolete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,877 a - ../obj_g/parse_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,877 a - ../obj_g/define_key.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,877 a - ../obj_g/hashed_db.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,877 a - ../obj_g/key_defined.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,877 a - ../obj_g/keybound.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,877 a - ../obj_g/keyok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,878 a - ../obj_g/version.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,878 ranlib ../lib/libncurses_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,878 a - ../obj_g/write_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,878 y/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib" all tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:44,878 ../include/Caps >termsort.c install_environment.STDOUT DEBUG 2017-11-18 16:58:44,983 >transform.h install_environment.STDOUT DEBUG 2017-11-18 16:58:44,986 ansform.h install_environment.STDOUT DEBUG 2017-11-18 16:58:44,991 install_environment.STDOUT DEBUG 2017-11-18 16:58:44,994 >>transform.h install_environment.STDOUT DEBUG 2017-11-18 16:58:44,996 ; fi' install_environment.STDOUT DEBUG 2017-11-18 16:58:44,999 transform.h install_environment.STDOUT DEBUG 2017-11-18 16:58:45,040 echo "#define PROG_RESET \"`echo reset| sed 's/$//'|sed 's,x,x,'|sed 's/$//'`\"" >>transfecho "#define PROG_INIT echo "#endif /* __TRANSFORM_H *gcc -DHAVE_CONFIG_H -I. -I../include progs/tic.c -o ../obj_s/tic.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:45,083 >transform.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:45,083 ansform.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:45,083 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:45,188 >>transform.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:45,188 ; fi' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:45,188 transform.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:45,188 cd progs && /Library/Developer/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxsh ./MKtermsort.sh awk ./echo "#ifndef __TRANSFORM_H" echo "#define __TRANSFORM_H 1" >>trecho "#include <progs.priv.h>" >>transform.hecho "extern bool same_program(const char *, const char *);"sh -c 'if test -n "" ; then echo "#define SUFFIX_IGNORED \"\"">>transform.hecho "#define PROG_CAPTOINFO \"`echo captoinfo| sed 's/$//'|sed 's,x,x,'|sed 's/$//'`\"" >>echo "#define PROG_INFOTOCAP \"`echo infotocap| sed 's/$//'|sed 's,x,x,'|sed 's/$//'`\"" >>transform.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:45,188 orm.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:45,189 \"`echo init| sed 's/$//'|sed 's,x,x,'|sed 's/$//'`\"" >>transform.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:45,189 /" >>transform.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:45,189 echo "#define PROG_RESET \"`echo reset| sed 's/$//'|sed 's,x,x,'|sed 's/$//'`\"" >>transfecho "#define PROG_INIT echo "#endif /* __TRANSFORM_H *gcc -DHAVE_CONFIG_H -I. -I../include progs/tic.c -o ../obj_s/tic.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:45,707 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../gcc -DHAVE_CONFIG_H -I. -dynamic -c ../progs/dump_entry.c -o ../obj_s/dump_entry.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:45,707 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:45 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,016 gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-idynamic -c ../progs/tparmo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,017 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:46,037 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -_type.c -o ../obj_s/tparm_type.gcc -DHAVE_CONFIG_H -I. -I../include progs/transform.c -o ../obj_s/transform.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,119 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -nline-insns-single=1200 -_type.c -o ../obj_s/tparm_type.gcc -DHAVE_CONFIG_H -I. -I../include progs/transform.c -o ../obj_s/transform.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,119 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../gcc ../obj_s/tic.o ../objONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -L../lib -lncurses -lncurses -o tic tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,120 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,221 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o ../obj_s/infocmp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,221 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:46,497 _s/dump_entry.o ../obj_s/tparm_type.o ../obj_s/transform.o -L../lib -Wl,-search_paths_first -DHAVE_Cgcc -DHAVE_CONFIG_H -I. -dynamic -c ../progs/infocmp.c -gcc ../obj_s/infocmp.o ../obj_s/dump_enG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -L../lib -lncurses -lncurses -o infocmp tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,525 _s/dump_entry.o ../obj_s/tparm_type.o ../obj_s/transform.o -L../lib -Wl,-search_paths_first -DHAVE_Cgcc -DHAVE_CONFIG_H -I. -dynamic -c ../progs/infocmp.c -gcc ../obj_s/infocmp.o ../obj_s/dump_enG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -L../lib -lncurses -lncurses -o infocmp install_environment.STDOUT DEBUG 2017-11-18 16:58:46,527 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -../obj_s/clear.o install_environment.STDOUT DEBUG 2017-11-18 16:58:46,591 ch_paths_first -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --curses -o clear tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,629 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -../obj_s/clear.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,629 ch_paths_first -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --curses -o clear tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,629 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,734 try.o -L../lib -Wl,-search_paths_first -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUgcc -DHAVE_CONFIG_H -I. -dynamic -c ../progs/clear.c -o gcc ../obj_s/clear.o -L../lib -Wl,-searparam max-inline-insns-single=1200 -dynamic -lngcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -Dj_s/tabs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,735 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:46,795 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../progs/tabs.c -o ../obgcc ../obj_s/tabs.o -L../pp-precomp --param max-inline-insns-single=1200 -dynamic -lncurses -o tabs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,842 NDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../progs/tabs.c -o ../obgcc ../obj_s/tabs.o -L../pp-precomp --param max-inline-insns-single=1200 -dynamic -lncurses -o tabs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,842 lib -Wl,-search_paths_first -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cgcc -DHAVE_CONFIG_H -I. -dynamic -c ../progs/tput.c -o ../obj_s/tput.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:46,842 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:46,951 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -VE_CONFIG_H -I. -I../incl-DNDEBUG -O2 -no-cpp-precomp --200 -dynamic -lncurses -o tput tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,052 I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -VE_CONFIG_H -I. -I../incl-DNDEBUG -O2 -no-cpp-precomp --200 -dynamic -lncurses -o tput tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,052 gcc ../obj_s/tput.o ../obj_s/tparm_type.o ../obj_s/transform.o -L../lib -Wl,-search_paths_first -DHAude -D_DARWIN_C_SOURCE param max-inline-insns-single=1gcc -DHAVE_CONFIG_H -I. -I../include progs/tset.c -o ../obj_s/tset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,052 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:47,207 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../gcc ../obj_s/tset.o ../obCE -DNDEBUG -O2 -no-cpp-precomp-single=1200 -dynamic -lncurses -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN.c -o ../obj_s/toe.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,258 j_s/transform.o -L../lib -Wl,-search_paths_first -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOUR --param max-inline-insnstset tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,258 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../gcc ../obj_s/tset.o ../obCE -DNDEBUG -O2 -no-cpp-precomp-single=1200 -dynamic -lncurses -o gcc -DHAVE_CONFIG_H -I. -I../include -D_DARWIN.c -o ../obj_s/toe.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,258 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:47,392 gcc ../obj_s/toe.o -L../lib -Wl,-search_paths_first -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_Sp-precomp --param max-inline-insns-single=1200 -dynamic -L../lib -lncurses -lncurses -o toe install_environment.STDOUT DEBUG 2017-11-18 16:58:47,423 CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib" all install_environment.STDOUT DEBUG 2017-11-18 16:58:47,433 cp ./panel.h ../include/panel.h install_environment.STDOUT DEBUG 2017-11-18 16:58:47,436 --param max-inline-insns-single=1200 -dynamic -c ../panel/panel.c -o ../obj_s/panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,460 gcc ../obj_s/toe.o -L../lib -Wl,-search_paths_first -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_Sp-precomp --param max-inline-insns-single=1200 -dynamic -L../lib -lncurses -lncurses -o toe tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,460 CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib" all tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,461 _C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../progs/toeOURCE -DNDEBUG -O2 -no-cpcd panel && /Library/Developer/rm -f ../include/panel.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,461 cp ./panel.h ../include/panel.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,461 --param max-inline-insns-single=1200 -dynamic -c ../panel/panel.c -o ../obj_s/panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,461 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,565 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../panel/p_above.c -o ../obj_s/p_above.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,565 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:47,636 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-./panel/p_below.c -o ../obj_s/pgcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../panel/p_bottom.c -o ../obj_s/p_bottom.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,667 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c ._below.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,667 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-./panel/p_below.c -o ../obj_s/pgcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../panel/p_bottom.c -o ../obj_s/p_bottom.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,667 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,667 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,772 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dgcc -I../ncurses -DHAVE_C./panel/p_delete.c -o ../obj_s/p_delete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,773 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:47,813 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c .--param max-inline-insns-singlel/p_hide.c -o ../obj_s/p_hide.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,874 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c .--param max-inline-insns-singlel/p_hide.c -o ../obj_s/p_hide.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,874 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,977 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -dynamic -c ../panegcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../panel/p_hidden.c -o ../obj_s/p_hidden.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,977 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c ../panel/p_move.c -o ../obj_s/p_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:47,978 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:48,053 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns---param max-inline-insns-singlel/p_new.c -o ../obj_s/p_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,080 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns---param max-inline-insns-singlel/p_new.c -o ../obj_s/p_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,080 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,080 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,185 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -dynamic -c ../panegcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../panel/p_replace.c -o ../obj_s/p_replace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,185 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,290 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c ../panel/p_show.c -o ../obj_s/p_show.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,290 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:48,300 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns---param max-inline-insns-singlel/p_top.c -o ../obj_s/p_top.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,392 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns---param max-inline-insns-singlel/p_top.c -o ../obj_s/p_top.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,392 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -dynamic -c ../panegcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../panel/p_update.c -o ../obj_s/p_update.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,392 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,392 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,492 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c .user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,492 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:48,513 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns-./panel/p_user.c -o ../obj_s/p_gcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../panel/p_win.c -o ../obj_s/p_win.o install_environment.STDOUT DEBUG 2017-11-18 16:58:48,585 .dylib install_environment.STDOUT DEBUG 2017-11-18 16:58:48,585 max-inline-insns-single=1200 -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/ncur89efd/lib/`basename ../lirrent_version 6 -o ../lib/libpaelow.o ../obj_s/p_bottom.o ../obj_s/p_dnew.o ../obj_s/p_replace.o ../obj_s/p_show.o ../search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,595 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns-./panel/p_user.c -o ../obj_s/p_gcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../panel/p_win.c -o ../obj_s/p_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,595 .dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,595 max-inline-insns-single=1200 -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/ncur89efd/lib/`basename ../lirrent_version 6 -o ../lib/libpaelow.o ../obj_s/p_bottom.o ../obj_s/p_dnew.o ../obj_s/p_replace.o ../obj_s/p_show.o ../search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,595 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,696 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dlinking ../lib/libpanel.6gcc -O2 -no-cpp-precomp --paramses/6.0/iuc/package_ncurses_6_0/0efde98b/libpanel.6.dylib` -compatibility_version 6 -cunel.6.dylib ../obj_s/panel.o ../obj_s/p_above.o ../obj_s/p_belete.o ../obj_s/p_hide.o ../obj_s/p_hidden.o ../obj_s/p_move.o ../obj_s/p_obj_s/p_top.o ../obj_s/p_update.o ../obj_s/p_user.o ../obj_s/p_win.o -L../lib -lncurses -Wl,-cd ../lib && (ln -s -f libpanel.6.dylib libpanel.dylib; ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,696 --param max-inline-insns-single=1200 -c ../panel/panel.c -o ../objects/panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,696 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:48,706 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -c ../panel/p_aboveo install_environment.STDOUT DEBUG 2017-11-18 16:58:48,774 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../panel/p_below.c -o ../objects/p_below.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,797 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -c ../panel/p_aboveo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,797 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../panel/p_below.c -o ../objects/p_below.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,797 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,797 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,902 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-.c -o ../objects/p_above.gcc -I../ncurses -DHAVE_CONFIG_gcc -I../ncurses -DHAVE_CONFIG_H -I. -I ../panel/p_bottom.c -o ../objects/p_bottom.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:48,902 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:48,929 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -cgcc -I../ncurses -DHAVE_Csingle=1200 -c ../panel/p_delete.o 127.0.0.1 - - [18/Nov/2017:16:58:48 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,007 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -cgcc -I../ncurses -DHAVE_Csingle=1200 -c ../panel/p_delete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,007 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:49,025 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singles/p_hide.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,111 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singles/p_hide.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,112 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,214 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-e.c -o ../objects/p_deletgcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../panel/p_hide.c -o ../objectgcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ/p_hidden.c -o ../objects/p_hidden.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,214 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../panel/p_move.c -o ../objects/p_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,214 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,214 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:49,272 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../panel--param max-inline-insns---param max-inline-insns-single -o ../objects/p_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,319 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../panel--param max-inline-insns---param max-inline-insns-single -o ../objects/p_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,319 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,422 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -c ../panel/p_new.cgcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../panel/p_replace.c -o ../objects/p_replace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,422 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:49,424 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns-_show.c -o ../objects/p_show.o install_environment.STDOUT DEBUG 2017-11-18 16:58:49,509 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single/p_top.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,527 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns-_show.c -o ../objects/p_show.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,527 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single/p_top.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,527 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,527 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,632 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../panel/pgcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../panel/p_top.c -o ../objectsgcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ/p_update.c -o ../objects/p_update.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,632 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:49,668 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../panel--param max-inline-insns-_user.c -o ../objects/p_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,733 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../panel--param max-inline-insns-_user.c -o ../objects/p_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,733 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:49,737 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single/p_win.o install_environment.STDOUT DEBUG 2017-11-18 16:58:49,815 ar -curv ../lib/libpanel.a ../objects/panel.o ../objects/p_above.o ../objects/p_below.o ../objects/pe.o ../objects/p_hidden.o.o ../objects/p_show.o ../objeca - ../objects/panel.o install_environment.STDOUT DEBUG 2017-11-18 16:58:49,815 a - ../objects/p_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,834 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single/p_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,834 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../panel/pgcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../panel/p_win.c -o ../objects_bottom.o ../objects/p_delete.o ../objects/p_hid ../objects/p_move.o ../objects/p_new.o ../objects/p_replacets/p_top.o ../objects/p_update.o ../objects/p_user.o ../objects/p_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,834 a - ../objects/p_above.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,834 a - ../objects/p_below.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,834 a - ../objects/p_bottom.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,835 a - ../objects/p_delete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,835 a - ../objects/p_hide.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,835 ar -curv ../lib/libpanel.a ../objects/panel.o ../objects/p_above.o ../objects/p_below.o ../objects/pe.o ../objects/p_hidden.o.o ../objects/p_show.o ../objeca - ../objects/panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,835 a - ../objects/p_hidden.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,835 a - ../objects/p_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,835 a - ../objects/p_replace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,835 a - ../objects/p_show.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,835 a - ../objects/p_top.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,835 a - ../objects/p_update.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,835 a - ../objects/p_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,835 a - ../objects/p_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,836 a - ../objects/p_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,836 ranlib ../lib/libpanel.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,836 --param max-inline-insns-single=1200 -g -DTRACE -c ../panel/panel.c -o ../obj_g/panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,836 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,836 /Library/Developer/CommandLineTools/usr/bin/ranlib: file: ../lib/libpanel.a(panel.o) has no symbols tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,836 /Library/Developer/CommandLineTools/usr/bin/ranlib: file: ../lib/libpanel.a(panel.o) has no symbols install_environment.STDOUT DEBUG 2017-11-18 16:58:49,915 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../panel/p_above.c -o ../obj_g/p_above.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,939 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../panel/p_above.c -o ../obj_g/p_above.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,939 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:49,939 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,042 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../panel/p_below.c -o ../obj_g/p_below.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,042 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,146 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -cg/p_bottom.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,146 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:50,158 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../panel/p_bottom.c -o ../obj_gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../panel/p_delete.c -o ../obj_g/p_delete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,249 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../panel/p_bottom.c -o ../obj_gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../panel/p_delete.c -o ../obj_g/p_delete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,249 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,351 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ggcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../panel/p_hide.c -o ../obj_g/p_hide.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,351 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,451 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -cg/p_hidden.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,451 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,452 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,452 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:50,524 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../panel/p_hidden.c -o ../obj_gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../panel/p_move.c -o ../obj_g/p_movegcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIp_new.c -o ../obj_g/p_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,555 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../panel/p_hidden.c -o ../obj_gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../panel/p_move.c -o ../obj_g/p_movegcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIp_new.c -o ../obj_g/p_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,555 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,657 N_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../panel/gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../pa_g/p_replace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,657 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,762 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singleo ../obj_g/p_show.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,762 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:50,777 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-nel/p_replace.c -o ../objgcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../panel/p_show.c -gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../panel/p_top.c -o ../obj_g/p_top.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,864 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-nel/p_replace.c -o ../objgcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../panel/p_show.c -gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../panel/p_top.c -o ../obj_g/p_top.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,864 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../panel/p_update.c -o ../obj_g/p_update.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,864 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,965 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -cp_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,965 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:50,965 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,070 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,070 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:51,091 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../panel/p_user.c -o ../obj_g/gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../panel/p_win.c -o ../obj_g/p_win.oar -curv ../lib/libpanel_g.a ../obj_g/panel.o ../obj_g/p_aboo ../obj_g/p_move.o ../obj_g/p_new.o ../obj_g/p_replace.o ../obj_g/p_show.og/p_update.o ../obj_g/p_user.o ../obj_g/p_win.o install_environment.STDOUT DEBUG 2017-11-18 16:58:51,103 a - ../obj_g/p_above.o install_environment.STDOUT DEBUG 2017-11-18 16:58:51,103 a - ../obj_g/p_bottom.o install_environment.STDOUT DEBUG 2017-11-18 16:58:51,103 a - ../obj_g/p_win.o install_environment.STDOUT DEBUG 2017-11-18 16:58:51,125 cd menu && /Library/Developer/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxyrm -f ../include/menu.h install_environment.STDOUT DEBUG 2017-11-18 16:58:51,129 rm -f ../include/eti.h install_environment.STDOUT DEBUG 2017-11-18 16:58:51,133 rm -f ../include/mf_common.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,170 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../panel/p_user.c -o ../obj_g/gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../panel/p_win.c -o ../obj_g/p_win.oar -curv ../lib/libpanel_g.a ../obj_g/panel.o ../obj_g/p_aboo ../obj_g/p_move.o ../obj_g/p_new.o ../obj_g/p_replace.o ../obj_g/p_show.og/p_update.o ../obj_g/p_user.o ../obj_g/p_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,171 ve.o ../obj_g/p_below.o ../obj_g/p_bottom.o ../obj_g/p_delete.o ../obj_g/p_hide.o ../obj_g/p_hidden. ../obj_g/p_top.o ../obj_a - ../obj_g/panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,171 a - ../obj_g/p_above.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,171 a - ../obj_g/p_below.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,171 a - ../obj_g/p_delete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,171 a - ../obj_g/p_hide.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,171 a - ../obj_g/p_hidden.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,171 a - ../obj_g/p_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,171 a - ../obj_g/p_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,171 a - ../obj_g/p_replace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,171 a - ../obj_g/p_show.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,171 a - ../obj_g/p_top.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,171 a - ../obj_g/p_update.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,172 a - ../obj_g/p_bottom.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,172 a - ../obj_g/p_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,172 a - ../obj_g/p_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,172 ranlib ../lib/libpanel_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,172 /database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib" all tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,172 cd menu && /Library/Developer/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxyrm -f ../include/menu.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,172 cp ./menu.h ../include/menu.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,172 rm -f ../include/eti.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,172 cp ./eti.h ../include/eti.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,172 rm -f ../include/mf_common.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,172 cp ./mf_common.h ../include/mf_common.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,172 --param max-inline-insns-single=1200 -dynamic -c ../menu/m_attribs.c -o ../obj_s/m_attribs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,172 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:51,223 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../menu_cursor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,277 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../menu_cursor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,278 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:51,298 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single ../obj_s/m_driver.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,380 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single ../obj_s/m_driver.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,381 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,482 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/m_cursor.c -o ../obj_s/mgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../menu/m_driver.c -ogcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ ../menu/m_format.c -o ../obj_s/m_format.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,482 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:51,499 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -cgcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../menu_global.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,583 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -cgcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../menu_global.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,584 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:51,633 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single./obj_s/m_hook.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,684 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single./obj_s/m_hook.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,685 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,785 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/m_global.c -o ../obj_s/mgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../menu/m_hook.c -o .gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ ../menu/m_item_cur.c -o ../obj_s/m_item_cur.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,785 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c ../menu/m_item_nam.c -o ../obj_s/m_item_nam.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,785 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:51,856 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c--param max-inline-insns-gcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../menu/m_item_new.c -o ../obj_s/m_item_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,890 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c--param max-inline-insns-gcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../menu/m_item_new.c -o ../obj_s/m_item_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,891 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,891 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,999 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlegcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../menu/m_item_opt.c -o ../obj_s/m_item_opt.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:51,999 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:51 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,105 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c ./m_item_top.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,105 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:52,178 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-./menu/m_item_top.c -o ../obj_sgcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../menu/m_item_use.c -o ../obj_s/m_itegcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWItem_val.c -o ../obj_s/m_item_val.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,208 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dm_use.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,208 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-./menu/m_item_top.c -o ../obj_sgcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../menu/m_item_use.c -o ../obj_s/m_itegcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWItem_val.c -o ../obj_s/m_item_val.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,208 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,208 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,309 N_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../menu/m_igcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../menu/m_item_vis.c -o ../obj_s/m_item_vis.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,309 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:52,388 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-./menu/m_items.c -o ../obj_s/m_gcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../menu/m_new.c -o ../obj_s/m_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,413 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c .items.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,413 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-./menu/m_items.c -o ../obj_s/m_gcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../menu/m_new.c -o ../obj_s/m_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,414 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,414 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,518 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dgcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../menupts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,519 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:52,540 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/m_opts.c -o ../obj_s/m_ogcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../menu/m_pad.c -o ../obj_s/m_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,619 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/m_opts.c -o ../obj_s/m_ogcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../menu/m_pad.c -o ../obj_s/m_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,619 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlegcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../menu/m_pattern.c -o ../obj_s/m_pattern.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,619 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:52,689 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-gcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../menu/m_post.c -o ../obj_s/m_post.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,721 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-gcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../menu/m_post.c -o ../obj_s/m_post.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,721 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,721 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:52,817 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c ./m_req_name.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,826 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c ./m_req_name.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,929 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-./menu/m_req_name.c -o ../obj_sgcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../menu/m_scale.c -o ../obj_s/m_scale.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,929 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:52,929 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:53,028 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -d--param max-inline-insns-./menu/m_spacing.c -o ../obj_s/gcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../menu/m_sub.c -o ../obj_s/m_sub.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,030 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c .m_spacing.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,030 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -d--param max-inline-insns-./menu/m_spacing.c -o ../obj_s/gcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../menu/m_sub.c -o ../obj_s/m_sub.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,030 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,131 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dgcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../menu/m_userptr.c -o ../obj_s/m_userptr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,131 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,131 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,232 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c ../menu/m_win.c -o ../obj_s/m_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,232 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:53,235 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-gcc -O2 -no-cpp-precomp --paramses/6.0/iuc/package_ncurses_6_0/0efde98b/libmenu.6.dylib` -compatibility_version 6 -curu.6.dylib ../obj_s/m_attribs.o ../obj_s/m_cursor.o ../obj_s//m_global.o ../obj_s/m_hook.o ../obj_s/m_item_cur.o ../obj_s/m_item_nam.o .j_s/m_item_top.o ../obj_s/m_item_use.o ../obj_s/m_item_val.o ../obj_s/m_item_vis.o ../obj_s/m_../obj_s/m_pattern.o ../obj_s/m_post.o ../obj_s/m_req_name.o ../obj_s/m_scale.o ../obj_s/m_spacing.o ../obj_s/m_sub.o _first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,336 linking ../lib/libmenu.6.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,337 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-gcc -O2 -no-cpp-precomp --paramses/6.0/iuc/package_ncurses_6_0/0efde98b/libmenu.6.dylib` -compatibility_version 6 -curu.6.dylib ../obj_s/m_attribs.o ../obj_s/m_cursor.o ../obj_s//m_global.o ../obj_s/m_hook.o ../obj_s/m_item_cur.o ../obj_s/m_item_nam.o .j_s/m_item_top.o ../obj_s/m_item_use.o ../obj_s/m_item_val.o ../obj_s/m_item_vis.o ../obj_s/m_../obj_s/m_pattern.o ../obj_s/m_post.o ../obj_s/m_req_name.o ../obj_s/m_scale.o ../obj_s/m_spacing.o ../obj_s/m_sub.o _first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,337 max-inline-insns-single=1200 -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/ncur89efd/lib/`basename ../lirent_version 6 -o ../lib/libmenm_driver.o ../obj_s/m_format.o ../obj_s./obj_s/m_item_new.o ../obj_s/m_item_opt.o ../obitems.o ../obj_s/m_new.o ../obj_s/m_opts.o ../obj_s/m_pad.o ../obj_s/m_userptr.o ../obj_s/m_win.o -L../lib -lncurses -Wl,-search_pathscd ../lib && (ln -s -f libmenu.6.dylib libmenu.dylib; ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,337 --param max-inline-insns-single=1200 -c ../menu/m_attribs.c -o ../objects/m_attribs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,337 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:53,348 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -c ../menu/m_cursor.o install_environment.STDOUT DEBUG 2017-11-18 16:58:53,425 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlets/m_driver.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,439 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -c ../menu/m_cursor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,439 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlets/m_driver.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,440 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,440 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:53,612 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../menu/gcc -I../ncurses -DHAVE_Csingle=1200 -c ../menu/m_global.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,645 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-.c -o ../objects/m_cursorgcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../menu/m_driver.c -o ../objecgcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includm_format.c -o ../objects/m_format.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,645 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../menu/gcc -I../ncurses -DHAVE_Csingle=1200 -c ../menu/m_global.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,645 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,645 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:53,726 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single/m_hook.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,749 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single/m_hook.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,749 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:53,800 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../menu/m_item_cur.c -o ../objects/m_item_cur.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,854 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../menu/m_item_cur.c -o ../objects/m_item_cur.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,854 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:53,948 N_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../menu/m_item_nam.cgcc -I../ncurses -DHAVE_Csingle=1200 -c ../menu/m_item_n_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,958 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-.c -o ../objects/m_globalgcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../menu/m_hook.c -o ../objectsgcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includgcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWI -o ../objects/m_item_nam.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,959 N_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../menu/m_item_nam.cgcc -I../ncurses -DHAVE_Csingle=1200 -c ../menu/m_item_n_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:53,959 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:54,037 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../menu/m_item_opt.c -o ../objects/m_item_opt.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,060 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../menu/m_item_opt.c -o ../objects/m_item_opt.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,061 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,061 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,166 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-ew.c -o ../objects/m_itemgcc -I../ncurses -DHAVE_CONFIG_gcc -I../ncurses -DHAVE_CONFIG_H -I. -I ../menu/m_item_top.c -o ../objects/m_item_top.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,166 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:54,251 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c--param max-inline-insns-item_use.c -o ../objects/m_itemgcc -I../ncurses -DHAVE_CONFIG_H -I. -I ../menu/m_item_val.c -o ../objects/m_item_val.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,268 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../menu/m__use.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,268 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c--param max-inline-insns-item_use.c -o ../objects/m_itemgcc -I../ncurses -DHAVE_CONFIG_H -I. -I ../menu/m_item_val.c -o ../objects/m_item_val.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,268 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,268 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,371 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -cgcc -I../ncurses -DHAVE_Csingle=1200 -c ../menu/m_item_vis.c -o ../objects/m_item_vis.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,371 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,472 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../menu/m_items.c -o ../objects/m_items.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,472 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:54,472 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns---param max-inline-insns-single-o ../objects/m_new.o install_environment.STDOUT DEBUG 2017-11-18 16:58:54,545 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single/m_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,575 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns---param max-inline-insns-single-o ../objects/m_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,575 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single/m_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,575 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,575 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,678 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -c ../menu/m_new.c gcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../menu/m_opts.c -o ../objectsgcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includm_pad.c -o ../objects/m_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,678 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:54,765 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../menu/gcc -I../ncurses -DHAVE_Csingle=1200 -c ../menu/m_patter--param max-inline-insns-single=1200 -cbjects/m_post.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,779 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-n.c -o ../objects/m_pattern.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,779 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../menu/gcc -I../ncurses -DHAVE_Csingle=1200 -c ../menu/m_patter--param max-inline-insns-single=1200 -cbjects/m_post.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,780 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,780 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,986 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp ../menu/m_post.c -o ../ogcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../menu/m_req_name.c -o ../objects/m_req_name.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,986 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../menu/m_scale.c -o ../objects/m_scale.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,986 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:54,986 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:55,025 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns---param max-inline-insns-singleg.c -o ../objects/m_spacing.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,091 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns---param max-inline-insns-singleg.c -o ../objects/m_spacing.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,091 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:55 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,196 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -c ../menu/m_spacingcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../menu/m_sub.c -o ../objects/m_sub.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,196 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../menu/m_tr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,196 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,297 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../menu/m_win.c -o ../objects/m_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,297 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,298 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:55,324 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns-userptr.c -o ../objects/m_userpgcc -I../ncurses -DHAVE_CONFIG_H -I. -Icts/m_format.o ../objects/m_global.o ../objects/m_cur.o ../objects/m_item_nam.o ../objects/m_item_new.o ../om_item_top.o ../objects/m_item_use.o ../objects/m_item_val.o ../objects/m_its/m_new.o ../objects/m_opts.o ../objects/m_pad.o ../objects/m_pattern.o ../objects/m_post.o .bjects/m_spacing.o ../objects/m_sub.o ../objects/m_userptr.o ../objects/m_win.o install_environment.STDOUT DEBUG 2017-11-18 16:58:55,334 a - ../objects/m_cursor.o install_environment.STDOUT DEBUG 2017-11-18 16:58:55,335 a - ../objects/m_format.o install_environment.STDOUT DEBUG 2017-11-18 16:58:55,335 a - ../objects/m_hook.o install_environment.STDOUT DEBUG 2017-11-18 16:58:55,335 a - ../objects/m_item_nam.o install_environment.STDOUT DEBUG 2017-11-18 16:58:55,335 a - ../objects/m_item_opt.o install_environment.STDOUT DEBUG 2017-11-18 16:58:55,335 a - ../objects/m_item_use.o install_environment.STDOUT DEBUG 2017-11-18 16:58:55,335 a - ../objects/m_item_vis.o install_environment.STDOUT DEBUG 2017-11-18 16:58:55,336 a - ../objects/m_new.o install_environment.STDOUT DEBUG 2017-11-18 16:58:55,336 a - ../objects/m_pad.o install_environment.STDOUT DEBUG 2017-11-18 16:58:55,336 a - ../objects/m_post.o install_environment.STDOUT DEBUG 2017-11-18 16:58:55,336 a - ../objects/m_scale.o install_environment.STDOUT DEBUG 2017-11-18 16:58:55,336 a - ../objects/m_sub.o install_environment.STDOUT DEBUG 2017-11-18 16:58:55,336 a - ../objects/m_win.o install_environment.STDOUT DEBUG 2017-11-18 16:58:55,337 ranlib ../lib/libmenu.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,400 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns-userptr.c -o ../objects/m_userpgcc -I../ncurses -DHAVE_CONFIG_H -I. -Icts/m_format.o ../objects/m_global.o ../objects/m_cur.o ../objects/m_item_nam.o ../objects/m_item_new.o ../om_item_top.o ../objects/m_item_use.o ../objects/m_item_val.o ../objects/m_its/m_new.o ../objects/m_opts.o ../objects/m_pad.o ../objects/m_pattern.o ../objects/m_post.o .bjects/m_spacing.o ../objects/m_sub.o ../objects/m_userptr.o ../objects/m_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,401 ar -curv ../lib/libmenu.a ../objects/m_attribs.o ../objects/m_cursor.o ../objects/m_driver.o ../objem_hook.o ../objects/m_itebjects/m_item_opt.o ../objects/tem_vis.o ../objects/m_items.o ../objec./objects/m_req_name.o ../objects/m_scale.o ../oa - ../objects/m_attribs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,402 a - ../objects/m_cursor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,402 a - ../objects/m_driver.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,402 a - ../objects/m_format.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,402 a - ../objects/m_global.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,402 a - ../objects/m_hook.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,402 a - ../objects/m_item_cur.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,402 a - ../objects/m_item_nam.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,402 a - ../objects/m_item_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,402 a - ../objects/m_item_opt.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,403 a - ../objects/m_item_top.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,403 a - ../objects/m_item_use.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,403 a - ../objects/m_item_val.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,403 a - ../objects/m_item_vis.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,403 a - ../objects/m_items.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,403 a - ../objects/m_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,403 a - ../objects/m_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,403 a - ../objects/m_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,403 a - ../objects/m_pattern.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,404 a - ../objects/m_post.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,404 a - ../objects/m_req_name.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,404 a - ../objects/m_scale.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,404 a - ../objects/m_spacing.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,404 a - ../objects/m_sub.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,404 a - ../objects/m_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,404 ranlib ../lib/libmenu.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,404 a - ../objects/m_userptr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,404 --param max-inline-insns-single=1200 -g -DTRACE -c ../menu/m_attribs.c -o ../obj_g/m_attribs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,404 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:55,475 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../menu/m_cursor.c -o ../obj_g/m_cursor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,507 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../menu/m_cursor.c -o ../obj_g/m_cursor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,507 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:55,586 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -c/m_driver.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,611 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -c/m_driver.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,611 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,816 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../menu/m_driver.c -o ../obj_ggcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../menu/m_format.c -o ../obj_g/m_format.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,816 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,919 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -c ../menu/m_global.c -o ../obj_g/m_global.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:55,919 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:56,038 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g--param max-inline-insns---param max-inline-insns-singlenu/m_hook.c -o ../obj_g/m_hook.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,126 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g--param max-inline-insns---param max-inline-insns-singlenu/m_hook.c -o ../obj_g/m_hook.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,126 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,231 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -g -DTRACE -c ../megcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_item_cur.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,231 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:56,284 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlec -o ../obj_g/m_item_cur.gcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_item_nam.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,335 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlec -o ../obj_g/m_item_cur.gcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_item_nam.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,335 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,438 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlec -o ../obj_g/m_item_nam.gcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_item_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,438 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:56,530 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlec -o ../obj_g/m_item_new.gcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_item_opt.c -o ../obj_g/m_item_opt.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,539 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlec -o ../obj_g/m_item_new.gcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_item_opt.c -o ../obj_g/m_item_opt.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,640 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,741 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlegcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../menu/m_item_top.c -o ../obj_g/m_item_top.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,741 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,846 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -c_g/m_item_use.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,846 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:56,864 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../menu/m_item_use.c -o ../objgcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../menu/m_item_val.c -o ../obj_g/m_item_val.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,948 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../menu/m_item_use.c -o ../objgcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../menu/m_item_val.c -o ../obj_g/m_item_val.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:56,948 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,052 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ggcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../me_g/m_item_vis.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,052 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,154 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singleo ../obj_g/m_items.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,154 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:57,184 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-nu/m_item_vis.c -o ../objgcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_items.c -gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../menu/m_new.c -o ../obj_g/m_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,259 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-nu/m_item_vis.c -o ../objgcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_items.c -gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../menu/m_new.c -o ../obj_g/m_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,259 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,360 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../me_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,361 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,466 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single../obj_g/m_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,466 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:57,534 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-nu/m_opts.c -o ../obj_g/mgcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_pad.c -o gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../menu/m_pattern.c -o ../obj_g/m_pattern.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,569 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-nu/m_opts.c -o ../obj_g/mgcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_pad.c -o gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../menu/m_pattern.c -o ../obj_g/m_pattern.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,570 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,670 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../me_post.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,775 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:57,814 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-nu/m_post.c -o ../obj_g/mgcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_req_name.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,877 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-nu/m_post.c -o ../obj_g/mgcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_req_name.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,877 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:57,942 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singleo ../obj_g/m_scale.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,978 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singleo ../obj_g/m_scale.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:57,979 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,080 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlec -o ../obj_g/m_req_name.gcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_scale.c -gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../menu/m_spacing.c -o ../obj_g/m_spacing.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,080 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,185 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../menu/m_sub.c -o ../obj_g/m_sub.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,186 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:58:58 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:58:58,278 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE gcc -I../ncurses -DHAVE_C--param max-inline-insns-singlenu/m_trace.c -o ../obj_g/m_trace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,289 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE gcc -I../ncurses -DHAVE_C--param max-inline-insns-singlenu/m_trace.c -o ../obj_g/m_trace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,393 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,493 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -g -DTRACE -c ../megcc -I../ncurses -DHAVE_CONFIG_nu/m_userptr.c -o ../obj_g/m_userptr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,494 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,598 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single../obj_g/m_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,599 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:58,616 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../megcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_win.c -o ar -curv ../lib/libmenu_g.a ../obj_g/m_attribs.o./obj_g/m_item_cur.o ../obj_g/m_item_nam.o ../obj_g/m_item_new.o ../obj_g/m_item_opt.o ../obj_g/m_item_top.o ../obj_g/m_item_use.o ../obj_g/m_item_val.o ../obj_g/m_item_vis.o ../obj_g/m_items.o ../obj_g/m_new.o ../obj_g/m_opts.o ../obj_g/m_pad.o ../obj_g/m_pattern.o ../obj_g/m_post.o ../obj_g/m_req_name.o ../obj_g/m_scale.o ../obj_g/m_spacing.o ../obj_g/m_sub.o ../obj_g/m_trace.o ../obj_g/m_userptr.o ../obj_g/m_win.o install_environment.STDOUT DEBUG 2017-11-18 16:58:58,637 a - ../obj_g/m_cursor.o install_environment.STDOUT DEBUG 2017-11-18 16:58:58,663 cd form && /Library/Developer/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxyrm -f ../include/form.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,700 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../megcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../menu/m_win.c -o ar -curv ../lib/libmenu_g.a ../obj_g/m_attribs.o./obj_g/m_item_cur.o ../obj_g/m_item_nam.o ../obj_g/m_item_new.o ../obj_g/m_item_opt.o ../obj_g/m_item_top.o ../obj_g/m_item_use.o ../obj_g/m_item_val.o ../obj_g/m_item_vis.o ../obj_g/m_items.o ../obj_g/m_new.o ../obj_g/m_opts.o ../obj_g/m_pad.o ../obj_g/m_pattern.o ../obj_g/m_post.o ../obj_g/m_req_name.o ../obj_g/m_scale.o ../obj_g/m_spacing.o ../obj_g/m_sub.o ../obj_g/m_trace.o ../obj_g/m_userptr.o ../obj_g/m_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,701 ../obj_g/m_cursor.o ../obj_g/m_driver.o ../obj_g/m_format.o ../obj_g/m_global.o ../obj_g/m_hook.o .a - ../obj_g/m_attribs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,701 a - ../obj_g/m_driver.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,701 a - ../obj_g/m_format.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,701 a - ../obj_g/m_global.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,701 a - ../obj_g/m_hook.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,701 a - ../obj_g/m_item_cur.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,701 a - ../obj_g/m_item_nam.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,701 a - ../obj_g/m_item_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,701 a - ../obj_g/m_item_opt.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,701 a - ../obj_g/m_item_top.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,701 a - ../obj_g/m_item_use.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,701 a - ../obj_g/m_item_val.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,701 a - ../obj_g/m_item_vis.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,701 a - ../obj_g/m_items.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 a - ../obj_g/m_new.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 a - ../obj_g/m_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 a - ../obj_g/m_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 a - ../obj_g/m_pattern.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 a - ../obj_g/m_post.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 a - ../obj_g/m_req_name.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 a - ../obj_g/m_scale.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 a - ../obj_g/m_spacing.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 a - ../obj_g/m_sub.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 a - ../obj_g/m_trace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 a - ../obj_g/m_userptr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 a - ../obj_g/m_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 a - ../obj_g/m_cursor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 ranlib ../lib/libmenu_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,702 /database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib" all tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,703 cd form && /Library/Developer/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxyrm -f ../include/form.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,703 cp ./form.h ../include/form.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,703 --param max-inline-insns-single=1200 -dynamic -c ../form/fld_arg.c -o ../obj_s/fld_arg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,703 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:58,740 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../formld_attr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,807 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../formld_attr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,807 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,910 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/fld_attr.c -o ../obj_s/fgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fld_current.co tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,910 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single../obj_s/fld_def.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,910 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:58,910 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:58,983 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single -o ../obj_s/fld_current.gcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fld_def.c -o gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ ../form/fld_dup.c -o ../obj_s/fld_dup.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,015 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single -o ../obj_s/fld_current.gcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fld_def.c -o gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ ../form/fld_dup.c -o ../obj_s/fld_dup.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,015 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,120 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -cgcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../form_s/fld_ftchoice.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,121 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:59,138 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/fld_ftchoice.c -o ../objgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fld_ftlink.c -o ../obj_s/fld_ftlink.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,221 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/fld_ftchoice.c -o ../objgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fld_ftlink.c -o ../obj_s/fld_ftlink.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,221 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlegcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../formld_info.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,221 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:59,284 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/fld_info.c -o ../obj_s/fgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fld_just.c -o ../obj_s/fld_just.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,326 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/fld_info.c -o ../obj_s/fgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fld_just.c -o ../obj_s/fld_just.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,327 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,327 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,428 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlegcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../form/fld_link.c -o ../obj_s/fld_link.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,428 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:59,504 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns---param max-inline-insns-single/fld_move.c -o ../obj_s/fld_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,534 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c ../form/fld_max.c -o ../obj_s/fld_max.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,534 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns---param max-inline-insns-single/fld_move.c -o ../obj_s/fld_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,534 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,534 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,639 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -dynamic -c ../formgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fld_newftyp.co tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,639 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:59,715 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single -o ../obj_s/fld_newftyp.gcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fld_opts.c -ogcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ ../form/fld_pad.c -o ../obj_s/fld_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,740 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single ../obj_s/fld_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,740 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single -o ../obj_s/fld_newftyp.gcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fld_opts.c -ogcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ ../form/fld_pad.c -o ../obj_s/fld_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,740 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,740 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,843 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -cgcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../formld_page.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,843 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:58:59,933 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/fld_page.c -o ../obj_s/fgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fld_stat.c -ogcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ ../form/fld_type.c -o ../obj_s/fld_type.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,946 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single ../obj_s/fld_stat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,946 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/fld_page.c -o ../obj_s/fgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fld_stat.c -ogcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ ../form/fld_type.c -o ../obj_s/fld_type.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:58:59,946 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,047 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -cgcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../formld_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,047 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,048 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,148 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single-o ../obj_s/frm_cursor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,148 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:00,156 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/fld_user.c -o ../obj_s/fgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/frm_cursor.c gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ ../form/frm_data.c -o ../obj_s/frm_data.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,249 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/fld_user.c -o ../obj_s/fgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/frm_cursor.c gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ ../form/frm_data.c -o ../obj_s/frm_data.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,249 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -cgcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../form/frm_def.c -o ../obj_s/frm_def.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,249 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,349 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c ./frm_driver.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,350 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,455 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:00,956 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-./form/frm_driver.c -o ../obj_sgcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../form/frm_hook.c -o ../obj_s/frm_hoogcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWI_opts.c -o ../obj_s/frm_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,978 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dk.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,978 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-./form/frm_driver.c -o ../obj_sgcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../form/frm_hook.c -o ../obj_s/frm_hoogcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWI_opts.c -o ../obj_s/frm_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,979 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:00,979 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,083 N_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../form/frmgcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../formrm_page.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,083 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:01,102 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/frm_page.c -o ../obj_s/fgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/frm_post.c -o ../obj_s/frm_post.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,187 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/frm_page.c -o ../obj_s/fgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/frm_post.c -o ../obj_s/frm_post.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,187 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,290 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlegcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../form_s/frm_req_name.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,290 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singleo ../obj_s/frm_scale.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,291 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,291 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:59:01 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:59:01,333 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/frm_req_name.c -o ../objgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/frm_scale.c -gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ ../form/frm_sub.c -o ../obj_s/frm_sub.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,394 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/frm_req_name.c -o ../objgcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/frm_scale.c -gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ ../form/frm_sub.c -o ../obj_s/frm_sub.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,395 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,499 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -cgcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../form/frm_user.c -o ../obj_s/frm_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,499 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c .m_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,499 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,499 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:01,556 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-./form/frm_win.c -o ../obj_s/frgcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../form/fty_alnum.c -o ../obj_s/fty_alnum.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,602 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-./form/frm_win.c -o ../obj_s/frgcc -I../ncurses -DHAVE_CONFIG_H -I. -Iynamic -c ../form/fty_alnum.c -o ../obj_s/fty_alnum.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,602 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,707 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dgcc -I../ncurses -DHAVE_Csingle=1200 -dynamic -c ../formfty_alpha.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,707 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:01,727 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/fty_alpha.c -o ../obj_s/gcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fty_enum.c -o ../obj_s/fty_enum.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,812 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-/fty_alpha.c -o ../obj_s/gcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fty_enum.c -o ../obj_s/fty_enum.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,812 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:01,873 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c ../form/fty_generic.c -o ../obj_s/fty_generic.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,917 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c ../form/fty_generic.c -o ../obj_s/fty_generic.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:01,917 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,022 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns-gcc -I../ncurses -DHAVE_CONFIG_=1200 -dynamic -c ../form/fty_int.c -o ../obj_s/fty_int.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,022 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,127 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -dynamic -c .ty_ipv4.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,127 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:02,221 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns-./form/fty_ipv4.c -o ../obj_s/fgcc -I../ncurses -DHAVE_CONFIG_H -I. -Igcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ ../form/fty_regex.c -o ../obj_s/fty_regex.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,232 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../form/fty_num.c -o ../obj_s/fty_num.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,232 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns-./form/fty_ipv4.c -o ../obj_s/fgcc -I../ncurses -DHAVE_CONFIG_H -I. -Igcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ ../form/fty_regex.c -o ../obj_s/fty_regex.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,232 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:02,304 dylib install_environment.STDOUT DEBUG 2017-11-18 16:59:02,304 bj_s/fty_int.o ../obj_s/fty_ipv4.o ../obj_s/fty_num.o ../obj_s/fty_regex.o -L../lib -lncurses -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,336 dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,336 bj_s/fty_int.o ../obj_s/fty_ipv4.o ../obj_s/fty_num.o ../obj_s/fty_regex.o -L../lib -lncurses -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,336 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:02,421 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -c ../form/fld_attr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,441 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -clinking ../lib/libform.6.gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/`basename ../lib/libform.6.dylib` -compatibility_version 6 -current_version 6 -o ../lib/libform.6.dylib ../obj_s/fld_arg.o ../obj_s/fld_attr.o ../obj_s/fld_current.o ../obj_s/fld_def.o ../obj_s/fld_dup.o ../obj_s/fld_ftchoice.o ../obj_s/fld_ftlink.o ../obj_s/fld_info.o ../obj_s/fld_just.o ../obj_s/fld_link.o ../obj_s/fld_max.o ../obj_s/fld_move.o ../obj_s/fld_newftyp.o ../obj_s/fld_opts.o ../obj_s/fld_pad.o ../obj_s/fld_page.o ../obj_s/fld_stat.o ../obj_s/fld_type.o ../obj_s/fld_user.o ../obj_s/frm_cursor.o ../obj_s/frm_data.o ../obj_s/frm_def.o ../obj_s/frm_driver.o ../obj_s/frm_hook.o ../obj_s/frm_opts.o ../obj_s/frm_page.o ../obj_s/frm_post.o ../obj_s/frm_req_name.o ../obj_s/frm_scale.o ../obj_s/frm_sub.o ../obj_s/frm_user.o ../obj_s/frm_win.o ../obj_s/fty_alnum.o ../obj_s/fty_alpha.o ../obj_s/fty_enum.o ../obj_s/fty_generic.o ../ocd ../lib && (ln -s -f libform.6.dylib libform.dylib; ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,441 --param max-inline-insns-single=1200 -c ../form/fld_arg.c -o ../objects/fld_arg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,442 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -c ../form/fld_attr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,442 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,442 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,546 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-.c -o ../objects/fld_attrgcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../form/fld_current.c -o ../objects/fld_current.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,546 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,651 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../form/fld_def.c -o ../objects/fld_def.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,652 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:02,666 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns---param max-inline-insns-singlec -o ../objects/fld_dup.o install_environment.STDOUT DEBUG 2017-11-18 16:59:02,751 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlebjects/fld_ftchoice.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,755 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns---param max-inline-insns-singlec -o ../objects/fld_dup.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,755 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlebjects/fld_ftchoice.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,755 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,856 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -c ../form/fld_dup.gcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../form/fld_ftchoice.c -o ../ogcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includfld_ftlink.c -o ../objects/fld_ftlink.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,856 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,856 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:02,895 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../form/gcc -I../ncurses -DHAVE_Csingle=1200 -c ../form/fld_info.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,960 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../form/gcc -I../ncurses -DHAVE_Csingle=1200 -c ../form/fld_info.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:02,961 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,066 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-.c -o ../objects/fld_infogcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../form/fld_just.c -o ../objects/fld_just.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,066 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../form/fl.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,066 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,066 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:03,108 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns-d_link.c -o ../objects/fld_linkgcc -I../ncurses -DHAVE_CONFIG_H -I. -I ../form/fld_max.c -o ../objects/fld_max.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,169 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns-d_link.c -o ../objects/fld_linkgcc -I../ncurses -DHAVE_CONFIG_H -I. -I ../form/fld_max.c -o ../objects/fld_max.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,169 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:03,262 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-.c -o ../objects/fld_movegcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../form/fld_newftyp.c -o ../objects/fld_newftyp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,271 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -cgcc -I../ncurses -DHAVE_Csingle=1200 -c ../form/fld_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,271 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-.c -o ../objects/fld_movegcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../form/fld_newftyp.c -o ../objects/fld_newftyp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,271 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,373 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlegcc -I../ncurses -DHAVE_Csingle=1200 -c ../form/fld_opts.c -o ../objects/fld_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,373 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,373 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:03,467 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-d_pad.c -o ../objects/fld_pad.ogcc -I../ncurses -DHAVE_CONFIG_H -I. -I ../form/fld_page.c -o ../objects/fld_page.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,476 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../form/fl tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,476 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns-d_pad.c -o ../objects/fld_pad.ogcc -I../ncurses -DHAVE_CONFIG_H -I. -I ../form/fld_page.c -o ../objects/fld_page.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,476 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:03,547 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../form/fld_stat.c -o ../objects/fld_stat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,580 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../form/fld_stat.c -o ../objects/fld_stat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,580 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,580 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:03,618 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlets/fld_type.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,685 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlets/fld_type.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,685 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,787 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -cgcc -I../ncurses -DHAVE_Cgcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../form/fld_type.c -o ../objecgcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includfld_user.c -o ../objects/fld_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,787 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../form/frrsor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,787 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,787 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:03,834 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../form/--param max-inline-insns-m_cursor.c -o ../objects/frm_cugcc -I../ncurses -DHAVE_CONFIG_H -I. -I ../form/frm_data.c -o ../objects/frm_data.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,891 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../form/--param max-inline-insns-m_cursor.c -o ../objects/frm_cugcc -I../ncurses -DHAVE_CONFIG_H -I. -I ../form/frm_data.c -o ../objects/frm_data.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,891 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,992 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -cgcc -I../ncurses -DHAVE_Csingle=1200 -c ../form/frm_def. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:03,993 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:04,094 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singleects/frm_driver.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:04,094 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:59:04 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:59:04,585 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-c -o ../objects/frm_def.ogcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../form/frm_driver.c -o ../objgcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includfrm_hook.c -o ../objects/frm_hook.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:04,610 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-c -o ../objects/frm_def.ogcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../form/frm_driver.c -o ../objgcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includfrm_hook.c -o ../objects/frm_hook.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:04,610 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:04,662 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../form/frm_opts.c -o ../objects/frm_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:04,714 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../form/frm_opts.c -o ../objects/frm_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:04,714 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:04,740 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlets/frm_page.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:04,815 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlets/frm_page.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:04,815 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../form/gcc -I../ncurses -DHAVE_Cgcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../form/frm_page.c -o ../objecgcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includfrm_post.c -o ../objects/frm_post.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:04,815 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:04,892 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../form/gcc -I../ncurses -DHAVE_Csingle=1200 -c ../form/frm_req_req_name.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:04,916 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -c ../form/gcc -I../ncurses -DHAVE_Csingle=1200 -c ../form/frm_req_req_name.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:04,916 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:04,916 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,021 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-name.c -o ../objects/frm_gcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../form/frm_scale.c -o ../objects/frm_scale.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,021 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:05,036 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlegcc -I../ncurses -DHAVE_Csingle=1200 -c ../form/frm_sub. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,126 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-singlegcc -I../ncurses -DHAVE_Csingle=1200 -c ../form/frm_sub. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,126 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-c -o ../objects/frm_sub.ogcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../form/frm_user.c -o ../objects/frm_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,126 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,126 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,230 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../form/frm_win.c -o ../objects/frm_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,230 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:05,321 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns---param max-inline-insns-single--param max-inline-insns-single=1200 -c./objects/fty_alpha.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,330 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -c ../form/fty_alnum.c -o ../objects/fty_alnum.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,330 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns---param max-inline-insns-single--param max-inline-insns-single=1200 -c./objects/fty_alpha.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,331 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,435 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp ../form/fty_alpha.c -o .gcc -I../ncurses -DHAVE_CONFIG_=1200 -c ../form/fty_enum.c -o ../objects/fty_enum.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,435 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,435 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,643 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../form/fty_generic.c -o ../objects/fty_generic.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,643 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -c ../form/fty_int.c -o ../objects/fty_int.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,643 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,644 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:05,705 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns---param max-inline-insns-single--param max-inline-insns-single=1200 -c ../form/fty_ipv4.c -o ../objects/fty_ipv4.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,748 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns---param max-inline-insns-single--param max-inline-insns-single=1200 -c ../form/fty_ipv4.c -o ../objects/fty_ipv4.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,748 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,851 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-y_num.c -o ../objects/fty_num.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,851 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:05,878 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../form/ft--param max-inline-insns-singlex.c -o ../objects/fty_regex.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,957 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -c ../form/ft--param max-inline-insns-singlex.c -o ../objects/fty_regex.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:05,957 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:05,977 jects/fld_arg.o ../objects/fld_attr.o ../objects/fld_current.o ../objects/fld_def.o ../objects/fld_dts/fld_ftlink.o ../objects/fld_info.o ../objects/fld_just.o ../objects/fld_link.o ../objects/fld_max.o ../objects/fld_move.o ../objects/fld_newftyp.o ../objects/fld_opts.o ../objects/fld_pad.o ../objectsa - ../objects/fld_attr.o install_environment.STDOUT DEBUG 2017-11-18 16:59:05,977 a - ../objects/frm_opts.o install_environment.STDOUT DEBUG 2017-11-18 16:59:05,977 a - ../objects/frm_post.o install_environment.STDOUT DEBUG 2017-11-18 16:59:05,977 a - ../objects/frm_user.o install_environment.STDOUT DEBUG 2017-11-18 16:59:05,977 a - ../objects/fty_alnum.o install_environment.STDOUT DEBUG 2017-11-18 16:59:05,986 --param max-inline-insns-single=1200 -g -DTRACE -c ../form/f_trace.c -o ../obj_g/f_trace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,062 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -c ../form/fty_regear -curv ../lib/libform.a ../obup.o ../objects/fld_ftchoice.o ../objec/fld_page.o ../objects/fld_stat.o ../objects/fld_type.o ../objects/fld_user.o ../objects/frm_cursor.o ../objects/frm_data.o ../objects/frm_def.o ../objects/frm_driver.o ../objects/frm_hook.o ../objects/frm_opts.o ../objects/frm_page.o ../objects/frm_post.o ../objects/frm_req_name.o ../objects/frm_scale.o ../objects/frm_sub.o ../objects/frm_user.o ../objects/frm_win.o ../objects/fty_alnum.o ../objects/fty_alpha.o ../objects/fty_enum.o ../objects/fty_generic.o ../objects/fty_int.o ../objects/fty_ipv4.o ../objects/fty_num.o ../objects/fty_regex.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,062 a - ../objects/fld_arg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,062 a - ../objects/fld_current.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,062 a - ../objects/fld_def.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,062 a - ../objects/fld_dup.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,062 a - ../objects/fld_ftchoice.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,062 a - ../objects/fld_ftlink.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,063 a - ../objects/fld_info.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,063 a - ../objects/fld_just.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,063 a - ../objects/fld_link.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,063 a - ../objects/fld_max.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,063 a - ../objects/fld_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,063 a - ../objects/fld_newftyp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,063 a - ../objects/fld_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,063 a - ../objects/fld_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,063 a - ../objects/fld_page.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,063 a - ../objects/fld_stat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,063 a - ../objects/fld_type.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,063 a - ../objects/fld_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,064 a - ../objects/frm_cursor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,064 a - ../objects/frm_data.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,064 a - ../objects/frm_def.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,064 a - ../objects/frm_driver.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,064 jects/fld_arg.o ../objects/fld_attr.o ../objects/fld_current.o ../objects/fld_def.o ../objects/fld_dts/fld_ftlink.o ../objects/fld_info.o ../objects/fld_just.o ../objects/fld_link.o ../objects/fld_max.o ../objects/fld_move.o ../objects/fld_newftyp.o ../objects/fld_opts.o ../objects/fld_pad.o ../objectsa - ../objects/fld_attr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,064 a - ../objects/frm_hook.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,064 a - ../objects/frm_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,064 a - ../objects/frm_page.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,064 a - ../objects/frm_req_name.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,064 a - ../objects/frm_scale.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,064 a - ../objects/frm_post.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,064 a - ../objects/frm_sub.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,065 a - ../objects/frm_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,065 a - ../objects/frm_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,065 a - ../objects/fty_alpha.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,065 a - ../objects/fty_enum.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,065 a - ../objects/fty_generic.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,065 a - ../objects/fty_int.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,065 a - ../objects/fty_ipv4.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,065 a - ../objects/fty_num.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,065 a - ../objects/fty_regex.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,065 ranlib ../lib/libform.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,065 a - ../objects/fty_alnum.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,065 --param max-inline-insns-single=1200 -g -DTRACE -c ../form/f_trace.c -o ../obj_g/f_trace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,066 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,170 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../fofld_arg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,170 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,273 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single-o ../obj_g/fld_attr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,273 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:06,334 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-rm/fld_arg.c -o ../obj_g/gcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../form/fld_attr.c gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../form/fld_current.c -o ../obj_g/fld_current.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,374 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-rm/fld_arg.c -o ../obj_g/gcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../form/fld_attr.c gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../form/fld_current.c -o ../obj_g/fld_current.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,374 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,478 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../form/fld_def.c -o ../obj_g/fld_def.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,478 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,684 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -cfld_dup.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,684 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:06,712 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../form/fld_dup.c -o ../obj_g/gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../form/fld_ftchoice.c -o ../obj_g/fld_ftchoice.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,790 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../form/fld_dup.c -o ../obj_g/gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../form/fld_ftchoice.c -o ../obj_g/fld_ftchoice.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,790 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,890 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ggcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../fo_g/fld_ftlink.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,890 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,995 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single-o ../obj_g/fld_info.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:06,996 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:07,049 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-rm/fld_ftlink.c -o ../objgcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../form/fld_info.c gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../form/fld_just.c -o ../obj_g/fld_just.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,099 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-rm/fld_ftlink.c -o ../objgcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../form/fld_info.c gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../form/fld_just.c -o ../obj_g/fld_just.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,099 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,201 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../form/fld_link.c -o ../obj_g/fld_link.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,202 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,303 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -cfld_max.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,303 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:07,383 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../form/fld_max.c -o ../obj_g/gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../form/fld_move.c -o ../obj_g/fld_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,409 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../form/fld_max.c -o ../obj_g/gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../form/fld_move.c -o ../obj_g/fld_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,410 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:59:07 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,513 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ggcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../form/fld_newftyp.c -o ../obj_g/fld_newftyp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,513 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,615 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -c ../form/fld_opts.c -o ../obj_g/fld_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,716 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -g -DTRACE -c ../form/fld_pad.c -o ../obj_g/fld_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,716 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,818 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,921 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp -DTRACE -c ../form/fld_page.c -o ../obj_g/fld_page.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:07,921 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:07,928 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns---param max-inline-insns-single--param max-inline-insns-single=1200 -g--param max-inline-insns-single=1200 -g -DTRACE ../obj_g/fld_stat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:08,027 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns---param max-inline-insns-single--param max-inline-insns-single=1200 -g--param max-inline-insns-single=1200 -g -DTRACE ../obj_g/fld_stat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:08,027 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:08,040 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single-o ../obj_g/fld_type.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:08,132 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single-o ../obj_g/fld_type.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:08,132 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:08,234 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp -c ../form/fld_stat.c -o gcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../form/fld_type.c gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../form/fld_user.c -o ../obj_g/fld_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:08,234 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:08,257 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../form/frm_cursor.c -o ../obj_g/frm_cursor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:08,336 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../form/frm_cursor.c -o ../obj_g/frm_cursor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:08,336 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:08,441 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../form/frm_data.c -o ../obj_g/frm_data.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:08,441 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:08,546 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -cfrm_def.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:08,547 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:08,636 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../form/frm_def.c -o ../obj_g/gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../form/frm_driver.c -o ../obj_g/frm_driver.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:08,651 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns---param max-inline-insns- ../form/frm_def.c -o ../obj_g/gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../form/frm_driver.c -o ../obj_g/frm_driver.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:08,754 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:09,374 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -ggcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../fo/frm_hook.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:09,477 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:09,579 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single-o ../obj_g/frm_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:09,580 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:09,589 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-rm/frm_hook.c -o ../obj_ggcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../form/frm_opts.c gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../form/frm_page.c -o ../obj_g/frm_page.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:09,684 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-rm/frm_hook.c -o ../obj_ggcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../form/frm_opts.c gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../form/frm_page.c -o ../obj_g/frm_page.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:09,684 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:09,786 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE gcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../fo/frm_post.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:09,786 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:09,816 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-rm/frm_post.c -o ../obj_ggcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../form/frm_req_name.c -o ../obj_g/frm_req_name.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:09,890 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-rm/frm_post.c -o ../obj_ggcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../form/frm_req_name.c -o ../obj_g/frm_req_name.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:09,890 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:09,936 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -cg/frm_scale.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:09,995 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -cg/frm_scale.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:09,995 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:10,049 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gb.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:10,100 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gb.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:10,100 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:10,203 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single--param max-inline-insns- ../form/frm_scale.c -o ../obj_gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../form/frm_sub.c -o ../obj_g/frm_sugcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIrm_user.c -o ../obj_g/frm_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:10,308 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -c ../form/frm_win.c -o ../obj_g/frm_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:10,308 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:10,408 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -g -DTRACE -c ../form/fty_alnum.c -o ../obj_g/fty_alnum.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:10,408 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:10,513 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' 127.0.0.1 - - [18/Nov/2017:16:59:10 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:59:10,530 N_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../form/f--param max-inline-insns---param max-inline-insns-single--param max-inline-insns-single=1200 -glpha.c -o ../obj_g/fty_alpha.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:10,619 N_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../form/f--param max-inline-insns---param max-inline-insns-single--param max-inline-insns-single=1200 -glpha.c -o ../obj_g/fty_alpha.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:10,619 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:10,642 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single-o ../obj_g/fty_enum.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:10,720 H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single-o ../obj_g/fty_enum.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:10,720 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:10,921 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp -DTRACE -c ../form/fty_agcc -I../ncurses -DHAVE_CONFIG_=1200 -g -DTRACE -c ../form/fty_enum.c gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../includ-c ../form/fty_generic.c -o ../obj_g/fty_generic.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:10,922 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,024 gcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp single=1200 -g -DTRACE -cfty_int.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,026 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,128 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -gpv4.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,128 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:11,188 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE --param max-inline-insns- ../form/fty_int.c -o ../obj_g/gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../form/fty_ipv4.c -o ../obj_g/fty_igcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIty_num.c -o ../obj_g/fty_num.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,233 e -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE --param max-inline-insns- ../form/fty_int.c -o ../obj_g/gcc -I../ncurses -DHAVE_CONFIG_H -I. -I -DTRACE -c ../form/fty_ipv4.c -o ../obj_g/fty_igcc -I../ncurses -DHAVE_CONFIG_H -I. -I../include -D_DARWIty_num.c -o ../obj_g/fty_num.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,234 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,339 N_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -g -DTRACE -c ../form/fgcc -I../ncurses -DHAVE_Csingle=1200 -g -DTRACE -c ../form/fty_regex.c -o ../obj_g/fty_regex.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,339 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,443 ar -curv ../lib/libform_g.a ../obj_g/f_trace.o ../obj_g/fld_arg.o ../obj_g/fld_attr.o ../obj_g/fld_c.o ../obj_g/fld_dup.o ../obj_g/fld_ftchoice.o ../obj_g/fld_ftlink.o ../obj_g/fld_info.o ../obj_g/fld_just.o ../obj_g/fld_link.o ../obj_g/fld_max.o ../obj_g/fld_move.o ../obj_g/fld_newftyp.o ../obj_g/fld_opts.o ../obj_g/fld_pad.o ../obj_g/fld_page.o ../obj_g/fld_stat.o ../obj_g/fld_type.o ../obj_g/fld_user.o ../obj_g/frm_cursor.o ../obj_g/frm_data.o ../obj_g/frm_def.o ../obj_g/frm_driver.o ../obj_g/frm_hook.o ../obj_g/frm_opts.o ../obj_g/frm_page.o ../obj_g/frm_post.o ../obj_g/frm_req_name.o ../obj_g/frm_scale.o ../obj_g/frm_sub.o ../obj_g/frm_user.o ../obj_g/frm_win.o ../obj_g/fty_alnum.o ../obj_g/fty_alpha.o ../obj_g/fty_enum.o ../obj_g/fty_generic.o ../obj_g/fty_int.o ../obj_g/fty_ipv4.o ../obj_g/fty_num.o ../obj_g/fty_regex.o install_environment.STDOUT DEBUG 2017-11-18 16:59:11,461 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-urrent.o ../obj_g/fld_defa - ../obj_g/fld_arg.o install_environment.STDOUT DEBUG 2017-11-18 16:59:11,461 a - ../obj_g/fld_opts.o install_environment.STDOUT DEBUG 2017-11-18 16:59:11,462 a - ../obj_g/fty_enum.o install_environment.STDOUT DEBUG 2017-11-18 16:59:11,462 a - ../obj_g/fty_int.o install_environment.STDOUT DEBUG 2017-11-18 16:59:11,489 cd test && /Library/Developer/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxygcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c ./obj_s/background.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,543 a - ../obj_g/f_trace.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,544 a - ../obj_g/fld_attr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,544 a - ../obj_g/fld_current.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,544 a - ../obj_g/fld_def.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,544 a - ../obj_g/fld_dup.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,544 a - ../obj_g/fld_ftchoice.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,545 a - ../obj_g/fld_ftlink.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,545 a - ../obj_g/fld_info.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,545 a - ../obj_g/fld_just.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,545 a - ../obj_g/fld_link.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,545 a - ../obj_g/fld_max.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,545 a - ../obj_g/fld_move.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,545 ONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-urrent.o ../obj_g/fld_defa - ../obj_g/fld_arg.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,545 a - ../obj_g/fld_newftyp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,546 a - ../obj_g/fld_pad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,546 a - ../obj_g/fld_page.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,546 a - ../obj_g/fld_stat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,546 a - ../obj_g/fld_type.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,546 a - ../obj_g/fld_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,546 a - ../obj_g/frm_cursor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,546 a - ../obj_g/frm_data.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,546 a - ../obj_g/frm_def.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,546 a - ../obj_g/frm_driver.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,546 a - ../obj_g/frm_hook.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,546 a - ../obj_g/frm_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,547 a - ../obj_g/frm_page.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,547 a - ../obj_g/frm_post.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,547 a - ../obj_g/frm_req_name.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,547 a - ../obj_g/frm_scale.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,547 a - ../obj_g/frm_sub.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,547 a - ../obj_g/frm_user.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,547 a - ../obj_g/frm_win.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,547 a - ../obj_g/fty_alnum.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,547 a - ../obj_g/fld_opts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,547 a - ../obj_g/fty_alpha.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,547 a - ../obj_g/fty_enum.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,547 a - ../obj_g/fty_generic.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,548 a - ../obj_g/fty_ipv4.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,548 a - ../obj_g/fty_num.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,548 a - ../obj_g/fty_regex.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,548 a - ../obj_g/fty_int.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,548 ranlib ../lib/libform_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,548 /database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib" all tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,548 cd test && /Library/Developer/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxygcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c ./obj_s/background.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,548 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:11,600 max-inline-insns-single=1200 -o background ../obj_s/background.o -Wl,-search_paths_first -I. -I. -]*//'` -lutil install_environment.STDOUT DEBUG 2017-11-18 16:59:11,631 pp-precomp --param max-inline-insns-single=1200 -dynamic -c ../test/blue.c -o ../obj_s/blue.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,649 max-inline-insns-single=1200 -o background ../obj_s/background.o -Wl,-search_paths_first -I. -I. -]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,650 pp-precomp --param max-inline-insns-single=1200 -dynamic -c ../test/blue.c -o ../obj_s/blue.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,754 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:11,854 -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --paramgcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c ../test/bs.c -o ../obj_s/bs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,860 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-i./test/background.c -o ..gcc -O2 -no-cpp-precomp --paramI../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cgcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o blue ../obj_s/blue.o -Wl,-search_paths_first -I. -I. max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,860 -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --paramgcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c ../test/bs.c -o ../obj_s/bs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:11,964 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:12,231 -param max-inline-insns-single=1200 -o bs ../obj_s/bs.o -Wl,-search_paths_first -I. -I. -I../test - -D_DARWIN_C_SOURCE -DNnline-insns-single=1200 -dynamses " | sed -e 's/-lform.*-lpanel[^ ]gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/cardfile.c -o ../obj_s/cardfile.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,278 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-igcc -O2 -no-cpp-precomp -DHAVE_CONFIG_H -I. -I../includeDEBUG -O2 -no-cpp-precomp --param max-iic `echo "-L../lib -lform -lmenu -lpanel -lncur*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,278 -param max-inline-insns-single=1200 -o bs ../obj_s/bs.o -Wl,-search_paths_first -I. -I. -I../test - -D_DARWIN_C_SOURCE -DNnline-insns-single=1200 -dynamses " | sed -e 's/-lform.*-lpanel[^ ]gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/cardfile.c -o ../obj_s/cardfile.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,278 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:12,425 -param max-inline-insns-single=1200 -o cardfile ../obj_s/cardfile.o -Wl,-search_paths_first -I. -I.gcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c .s/chgat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,485 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp - -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -L../lib -lform -lmenu -lpanel -lncurses -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,485 -param max-inline-insns-single=1200 -o cardfile ../obj_s/cardfile.o -Wl,-search_paths_first -I. -I.gcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c .s/chgat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,485 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:12,536 max-inline-insns-single=1200 -o chgat ../obj_s/chgat.o -Wl,-search_paths_first -I. -I. -I../test -RWIN_C_SOURCE -DNDEBUG -Oe=1200 -dynamic `echo "-L../llpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,587 max-inline-insns-single=1200 -o chgat ../obj_s/chgat.o -Wl,-search_paths_first -I. -I. -I../test -RWIN_C_SOURCE -DNDEBUG -Oe=1200 -dynamic `echo "-L../llpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,588 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-i./test/chgat.c -o ../obj_gcc -O2 -no-cpp-precomp --paramDHAVE_CONFIG_H -I. -I../include -D_DA2 -no-cpp-precomp --param max-inline-insns-singlib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCEc -o ../obj_s/clip_printw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,693 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:12,713 -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../test/clip_printw.gcc -O2 -no-cpp-precomp -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,794 -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../test/clip_printw.gcc -O2 -no-cpp-precomp -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,795 -param max-inline-insns-single=1200 -o clip_printw ../obj_s/clip_printw.o -Wl,-search_paths_first -gcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c .obj_s/color_set.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,795 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:12,853 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-i./test/color_set.c -o ../gcc -O2 -no-cpp-precomp --param./test -DHAVE_CONFIG_H -I. -I../includecomp --param max-inline-insns-single=1200 -dynays.c -o ../obj_s/demo_altkeys.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,900 max-inline-insns-single=1200 -o color_set ../obj_s/color_set.o -Wl,-search_paths_first -I. -I. -I. -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,900 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-i./test/color_set.c -o ../gcc -O2 -no-cpp-precomp --param./test -DHAVE_CONFIG_H -I. -I../includecomp --param max-inline-insns-single=1200 -dynays.c -o ../obj_s/demo_altkeys.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:12,900 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:12,951 max-inline-insns-single=1200 -o demo_altkeys ../obj_s/demo_altkeys.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil install_environment.STDOUT DEBUG 2017-11-18 16:59:12,990 I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=12s/demo_defkey.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,002 max-inline-insns-single=1200 -o demo_altkeys ../obj_s/demo_altkeys.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,002 I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=12s/demo_defkey.o install_environment.STDOUT DEBUG 2017-11-18 16:59:13,101 -o demo_defkey ../obj_s/demo_defkey.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H -Ix-inline-insns-single=120 ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,107 -o demo_defkey ../obj_s/demo_defkey.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H -Ix-inline-insns-single=120 ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,107 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:13,143 nline-insns-single=1200 -dynamic -c ../test/demo_forms.c -o ../obj_s/demo_forms.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,209 nline-insns-single=1200 -dynamic -c ../test/demo_forms.c -o ../obj_s/demo_forms.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,209 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:13,327 amic -c ../test/edit_field.c -o ../obj_s/edit_field.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,414 amic -c ../test/edit_field.c -o ../obj_s/edit_field.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,415 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,515 gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-premic -c ../test/demo_altkegcc -O2 -no-cpp-precomp --paramgcc -I. -I. -I../test -DHAVE_CONFIG_H -00 -dynamic -c ../test/demo_defkey.c -o ../obj_gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param ma0 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-igcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dyngcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o demo_forms ../obj_s/demo_forms.o ../obj_s/edit_field.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H -I. -Idynamic -L../lib -lform -lmenu -lpanel -lncurses -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,515 gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-prensns-single=1200 -dynami/obj_s/demo_keyok.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,515 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:13,526 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -comp --param max-inline-ic -c ../test/demo_keyok.c -o ..gcc -O2 -no-cpp-precomp --param max-inl -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil 127.0.0.1 - - [18/Nov/2017:16:59:13 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,618 ../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -comp --param max-inline-ic -c ../test/demo_keyok.c -o ..gcc -O2 -no-cpp-precomp --param max-inl -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,618 ine-insns-single=1200 -o demo_keyok ../obj_s/demo_keyok.o -Wl,-search_paths_first -I. -I. -I../testgcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c ../test/demo_menus.c -o ../obj_s/demo_menus.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,618 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:13,751 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-il,-search_paths_first -I.gcc -I. -I. -I../test -DHAVE_COingle=1200 -dynamic -c ../test/demo_paanels.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,825 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o demo_menus ../obj_s/demo_menus.o -W -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -L../lib -lform -lmenu -lpanel -lncurses -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,826 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-il,-search_paths_first -I.gcc -I. -I. -I../test -DHAVE_COingle=1200 -dynamic -c ../test/demo_paanels.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:13,826 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,034 NFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-snels.c -o ../obj_s/demo_pgcc -O2 -no-cpp-precomp --param -I../test -DHAVE_CONFIG_H -I. -I../inc -DNDEBUG -O2 -no-cpp-precomp --param max-inlineL../lib -lform -lmenu -lpanel -lncurses -lutil install_environment.STDOUT DEBUG 2017-11-18 16:59:14,038 max-inline-insns-single=1200 -o demo_panels ../obj_s/demo_panels.o -Wl,-search_paths_first -I. -I.lude -D_DARWIN_C_SOURCE-insns-single=1200 -dynamic -gcc -I. -I. -I../test -DHAVE_CONFIG_H -00 -dynamic -c ../test/demo_termcap.c -o ../obj_s/demo_termcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,135 max-inline-insns-single=1200 -o demo_panels ../obj_s/demo_panels.o -Wl,-search_paths_first -I. -I.lude -D_DARWIN_C_SOURCE-insns-single=1200 -dynamic -gcc -I. -I. -I../test -DHAVE_CONFIG_H -00 -dynamic -c ../test/demo_termcap.c -o ../obj_s/demo_termcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,135 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,236 I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=12gcc -O2 -no-cpp-precomp -ths_first -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -lncurses -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,339 gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-prensns-single=1200 -dynamic -c ../test/demo_terminfo.c -o ../obj_s/demo_terminfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,340 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:14,495 -param max-inline-insns-single=1200 -o demo_termcap ../obj_s/demo_termcap.o -L../lib -Wl,-search_pacomp --param max-inline-io.o -L../lib -Wl,-search_paths_DHAVE_CONFIG_H -I. -I../include -D_DAcpp-precomp --param max-inline-insns-single=1200gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_st/ditto.c -o ../obj_s/ditto.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,544 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o demo_terminfo ../obj_s/demo_terminffirst -I. -I. -I../test -RWIN_C_SOURCE -DNDEBUG -O2 -no- -dynamic -lncurses -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,545 -param max-inline-insns-single=1200 -o demo_termcap ../obj_s/demo_termcap.o -L../lib -Wl,-search_pacomp --param max-inline-io.o -L../lib -Wl,-search_paths_DHAVE_CONFIG_H -I. -I../include -D_DAcpp-precomp --param max-inline-insns-single=1200gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_st/ditto.c -o ../obj_s/ditto.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,545 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,648 DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../tegcc -O2 -no-cpp-precomp -test -DHAVE_CONFIG_H -I. -I../iCE -DNDEBUG -O2 -no-cpp-precomp --param-dynamic `echo "-L../lib -lform -lmenu -lpanel el[^ ]*//'` -lutil install_environment.STDOUT DEBUG 2017-11-18 16:59:14,649 -param max-inline-insns-single=1200 -o ditto ../obj_s/ditto.o -Wl,-search_paths_first -I. -I. -I../nclude -D_DARWIN_C_SOUR max-inline-insns-single=1200 -lncurses " | sed -e 's/-lform.*-lpangcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/dots.c -o ../obj_s/dots.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,748 -param max-inline-insns-single=1200 -o ditto ../obj_s/ditto.o -Wl,-search_paths_first -I. -I. -I../nclude -D_DARWIN_C_SOUR max-inline-insns-single=1200 -lncurses " | sed -e 's/-lform.*-lpangcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/dots.c -o ../obj_s/dots.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,748 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp -. -I../test -DHAVE_CONFIG_H -I._C_SOURCE -DNDEBUG -O2 -no-cpp-precomp =1200 -dynamic -lncurses -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,748 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,851 I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=12s/dots_curses.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,851 -o dots_curses ../obj_s/dots_curses.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H -Ix-inline-insns-single=120 ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,851 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,956 nline-insns-single=1200 -dynamic -c ../test/dots_mvcur.c -o ../obj_s/dots_mvcur.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:14,956 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:14,961 -param max-inline-insns-single=1200 -o dots ../obj_s/dots.o -L../lib -Wl,-search_paths_first -I. -I -I../include -D_DARWIN--param max-inline-insns-singlegcc -I. -I. -I../test -DHAVE_CONFIG_H -00 -dynamic -c ../test/dots_curses.c -o ../obj_gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param ma0 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-igcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o dots_mvcur ../obj_s/dots_mvcur.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,057 -param max-inline-insns-single=1200 -o dots ../obj_s/dots.o -L../lib -Wl,-search_paths_first -I. -I -I../include -D_DARWIN--param max-inline-insns-singlegcc -I. -I. -I../test -DHAVE_CONFIG_H -00 -dynamic -c ../test/dots_curses.c -o ../obj_gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param ma0 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-igcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o dots_mvcur ../obj_s/dots_mvcur.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,057 CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insnsgcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c ../test/dots_termcap.c -o ../obj_s/dots_termcap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,057 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:15,107 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-io -L../lib -Wl,-search_past -DHAVE_CONFIG_H -I. -I../incBUG -O2 -no-cpp-precomp --param max-inlses -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,160 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-io -L../lib -Wl,-search_past -DHAVE_CONFIG_H -I. -I../incBUG -O2 -no-cpp-precomp --param max-inlses -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,160 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o dots_termcap ../obj_s/dots_termcap.ths_first -I. -I. -I../telude -D_DARWIN_C_SOURCE -DNDEine-insns-single=1200 -dynamic -lncurgcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/echochar.c -o ../obj_s/echochar.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,161 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:15,216 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp - -I../test -DHAVE_CONFIG_H -I. C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil install_environment.STDOUT DEBUG 2017-11-18 16:59:15,253 NFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-sc -o ../obj_s/filter.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,261 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp - -I../test -DHAVE_CONFIG_H -I. C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,261 NFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-sc -o ../obj_s/filter.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,364 -param max-inline-insns-single=1200 -o echochar ../obj_s/echochar.o -Wl,-search_paths_first -I. -I.-I../include -D_DARWIN_gcc -I. -I. -I../test -DHAVE_COingle=1200 -dynamic -c ../test/filter.gcc -O2 -no-cpp-precomp --param max-inline-insns-I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-p-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncursnel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,364 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:15,365 -single=1200 -o filter ../obj_s/filter.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H recomp --param max-inlinees " | sed -e 's/-lform.*-lpagcc -I. -I. -I../test -DHAVE_CONFIG_H -00 -dynamic -c ../test/firework.c -o ../obj_s/firework.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,465 -single=1200 -o filter ../obj_s/filter.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H recomp --param max-inlinees " | sed -e 's/-lform.*-lpagcc -I. -I. -I../test -DHAVE_CONFIG_H -00 -dynamic -c ../test/firework.c -o ../obj_s/firework.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,465 I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=12gcc -O2 -no-cpp-precomp - -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,465 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:15,559 -param max-inline-insns-single=1200 -o firework ../obj_s/firework.o -Wl,-search_paths_first -I. -I.comp --param max-inline-i-search_paths_first -I. -I. -I.. -I../include -D_DARWIN_C_SOURCE -DNam max-inline-insns-single=1200 -dynamic -L../-lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,569 gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-prensns-single=1200 -dynamic -c ../test/firstlast.c -o ../obj_s/firstlast.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,569 -param max-inline-insns-single=1200 -o firework ../obj_s/firework.o -Wl,-search_paths_first -I. -I.comp --param max-inline-i-search_paths_first -I. -I. -I.. -I../include -D_DARWIN_C_SOURCE -DNam max-inline-insns-single=1200 -dynamic -L../-lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,569 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,672 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o firstlast ../obj_s/firstlast.o -Wl,./test -DHAVE_CONFIG_H -IDEBUG -O2 -no-cpp-precomp --parlib -lform -lmenu -lpanel -lncurses gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/foldkeys.c -o ../obj_s/foldkeys.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,672 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:15,701 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp - -I../test -DHAVE_CONFIG_H -I. C_SOURCE -DNDEBUG -O2 -no-cpp-precomp -1200 -dynamic `echo "-L../lib -lform -lmenu -l*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,777 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp - -I../test -DHAVE_CONFIG_H -I. C_SOURCE -DNDEBUG -O2 -no-cpp-precomp -1200 -dynamic `echo "-L../lib -lform -lmenu -l*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,777 -param max-inline-insns-single=1200 -o foldkeys ../obj_s/foldkeys.o -Wl,-search_paths_first -I. -I.-I../include -D_DARWIN_-param max-inline-insns-single=panel -lncurses " | sed -e 's/-lform.gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../ir_w.c -o ../obj_s/form_driver_w.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,777 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:15,800 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../test/form_drivew.o -Wl,-search_paths_first -I.FIG_H -I. -I../include -D_DARWIN_C_SOmp --param max-inline-insns-single=1200 -dynamirses -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,881 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../test/form_drivew.o -Wl,-search_paths_first -I.FIG_H -I. -I../include -D_DARWIN_C_SOmp --param max-inline-insns-single=1200 -dynamirses -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,881 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o form_driver_w ../obj_s/form_driver_ -I. -I../test -DHAVE_CONURCE -DNDEBUG -O2 -no-cpp-precoc -L../lib -lform -lmenu -lpanel -lncugcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/gdc.c -o ../obj_s/gdc.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:15,881 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:16,046 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynas_first -I. -I. -I../test/include -D_DARWIN_C_SOURCE -aram max-inline-insns-single=1200 -dynanel -lncurses " | sed -e 's/-lform.*-lpanel[^gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_st/hanoi.c -o ../obj_s/hanoi.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,087 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o gdc ../obj_s/gdc.o -Wl,-search_path -DHAVE_CONFIG_H -I. -I..DNDEBUG -O2 -no-cpp-precomp --pamic `echo "-L../lib -lform -lmenu -lp ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,088 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynas_first -I. -I. -I../test/include -D_DARWIN_C_SOURCE -aram max-inline-insns-single=1200 -dynanel -lncurses " | sed -e 's/-lform.*-lpanel[^gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_st/hanoi.c -o ../obj_s/hanoi.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,088 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,191 DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../tegcc -O2 -no-cpp-precomp -test -DHAVE_CONFIG_H -I. -I../iCE -DNDEBUG -O2 -no-cpp-precomp --param-dynamic `echo "-L../lib -lform -lmenu -lpanel el[^ ]*//'` -lutil install_environment.STDOUT DEBUG 2017-11-18 16:59:16,221 -param max-inline-insns-single=1200 -o hanoi ../obj_s/hanoi.o -Wl,-search_paths_first -I. -I. -I../nclude -D_DARWIN_C_SOUR max-inline-insns-single=1200 -lncurses " | sed -e 's/-lform.*-lpangcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/hashtest.c -o ../obj_s/hashtest.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,294 -param max-inline-insns-single=1200 -o hanoi ../obj_s/hanoi.o -Wl,-search_paths_first -I. -I. -I../nclude -D_DARWIN_C_SOUR max-inline-insns-single=1200 -lncurses " | sed -e 's/-lform.*-lpangcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/hashtest.c -o ../obj_s/hashtest.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,294 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:16,357 -param max-inline-insns-single=1200 -o hashtest ../obj_s/hashtest.o -Wl,-search_paths_first -I. -I.comp --param max-inline-insns-single=1200 -dynamic -c ../test/inch_wide.c -o ../obj_s/inch_wide.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,399 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp - -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,399 -param max-inline-insns-single=1200 -o hashtest ../obj_s/hashtest.o -Wl,-search_paths_first -I. -I.comp --param max-inline-insns-single=1200 -dynamic -c ../test/inch_wide.c -o ../obj_s/inch_wide.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,399 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,500 gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-pregcc -O2 -no-cpp-precomp -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,501 gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-prensns-single=1200 -dynamis/inchs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,501 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,601 ine-insns-single=1200 -o inchs ../obj_s/inchs.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CODEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,601 gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-prest/ins_wide.c -o ../obj_s/ins_wide.o install_environment.STDOUT DEBUG 2017-11-18 16:59:16,665 -param max-inline-insns-single=1200 -o inch_wide ../obj_s/inch_wide.o -Wl,-search_paths_first -I. -comp --param max-inline-ic -c ../test/inchs.c -o ../obj_gcc -O2 -no-cpp-precomp --param max-inlNFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNcomp --param max-inline-insns-single=1200 -dynamic -c ../tegcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o ins_wide .ARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `enu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil 127.0.0.1 - - [18/Nov/2017:16:59:16 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,702 -param max-inline-insns-single=1200 -o inch_wide ../obj_s/inch_wide.o -Wl,-search_paths_first -I. -comp --param max-inline-ic -c ../test/inchs.c -o ../obj_gcc -O2 -no-cpp-precomp --param max-inlNFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNcomp --param max-inline-insns-single=1200 -dynamic -c ../tegcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o ins_wide .ARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `enu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,702 ./obj_s/ins_wide.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_Dcho "-L../lib -lform -lmegcc -I. -I. -I../test -DHAVE_COingle=1200 -dynamic -c ../test/insdello tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,703 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,804 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:16,817 NFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-sn.c -o ../obj_s/insdelln.gcc -O2 -no-cpp-precomp --paramtest -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,908 NFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-sn.c -o ../obj_s/insdelln.gcc -O2 -no-cpp-precomp --paramtest -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,908 max-inline-insns-single=1200 -o insdelln ../obj_s/insdelln.o -Wl,-search_paths_first -I. -I. -I../gcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c .j_s/inserts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:16,908 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:16,995 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-i./test/inserts.c -o ../obgcc -O2 -no-cpp-precomp --paramst -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,013 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-i./test/inserts.c -o ../obgcc -O2 -no-cpp-precomp --paramst -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,118 max-inline-insns-single=1200 -o inserts ../obj_s/inserts.o -Wl,-search_paths_first -I. -I. -I../tegcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c .obj_s/key_names.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,118 max-inline-insns-single=1200 -o key_names ../obj_s/key_names.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,118 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,220 gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-pre00 -dynamic -c ../test/keynames.c -o ../obj_s/keynames.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,220 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o keynames ../obj_s/keynames.o -Wl,-sG_H -I. -I../include -Dline-insns-single=1200 -dynami-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,220 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,322 pp-precomp --param max-inline-insns-single=1200 -dynamic -c ../test/knight.c -o ../obj_s/knight.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,322 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:17,478 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-i./test/key_names.c -o ../gcc -O2 -no-cpp-precomp --paramcomp --param max-inline-insns-single=12earch_paths_first -I. -I. -I../test -DHAVE_CONFI_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inc `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cgcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o knight ../obj_s/knight.o -Wl,-search_paths_first -I. aram max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,527 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-i./test/key_names.c -o ../gcc -O2 -no-cpp-precomp --paramcomp --param max-inline-insns-single=12earch_paths_first -I. -I. -I../test -DHAVE_CONFI_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inc `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cgcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o knight ../obj_s/knight.o -Wl,-search_paths_first -I. aram max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,527 -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --pgcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c ../test/lrtest.c -o ../obj_s/lrtest.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,631 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o lrtest ../obj_s/lrtest.o -Wl,-searc./test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,631 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,735 gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-preingle=1200 -dynamic -c ../test/movewindow.c -o ../obj_s/movewindow.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,735 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:17,821 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-ih_paths_first -I. -I. -I.comp --param max-inline-insns-sl,-search_paths_first -I. -I. -I../test/include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cnsns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -l*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,838 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-ih_paths_first -I. -I. -I.comp --param max-inline-insns-sl,-search_paths_first -I. -I. -I../test/include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cnsns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -l*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,938 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o movewindow ../obj_s/movewindow.o -W -DHAVE_CONFIG_H -I. -I..pp-precomp --param max-inline-ipanel -lncurses " | sed -e 's/-lform.gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/ncurses.c -o ../obj_s/ncurses.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:17,938 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:18,972 -param max-inline-insns-single=1200 -o ncurses ../obj_s/ncurses.o -Wl,-search_paths_first -I. -I. -../include -D_DARWIN_C_aram max-inline-insns-single=12curses -lutil install_environment.STDOUT DEBUG 2017-11-18 16:59:18,993 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp -I../test -DHAVE_CONFIG_H -I. -ISOURCE -DNDEBUG -O2 -no-cpp-precomp --p00 -dynamic -L../lib -lform -lmenu -lpanel -lngcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_st/newdemo.c -o ../obj_s/newdemo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,077 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp -I../test -DHAVE_CONFIG_H -I. -ISOURCE -DNDEBUG -O2 -no-cpp-precomp --p00 -dynamic -L../lib -lform -lmenu -lpanel -lngcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_st/newdemo.c -o ../obj_s/newdemo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,077 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:19,171 -param max-inline-insns-single=1200 -o newdemo ../obj_s/newdemo.o -Wl,-search_paths_first -I. -I. -../include -D_DARWIN_C_aram max-inline-insns-single=12nel -lncurses " | sed -e 's/-lform.*-gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/railroad.c -o ../obj_s/railroad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,181 DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../tegcc -O2 -no-cpp-precomp -I../test -DHAVE_CONFIG_H -I. -ISOURCE -DNDEBUG -O2 -no-cpp-precomp --p00 -dynamic `echo "-L../lib -lform -lmenu -lpalpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,181 -param max-inline-insns-single=1200 -o newdemo ../obj_s/newdemo.o -Wl,-search_paths_first -I. -I. -../include -D_DARWIN_C_aram max-inline-insns-single=12nel -lncurses " | sed -e 's/-lform.*-gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/railroad.c -o ../obj_s/railroad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,284 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp -t -I. -I. -I../test -DHAVE_CONFD_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-s-single=1200 -dynamic -lncurses -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,284 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,389 I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=12o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,389 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,494 -o rain ../obj_s/rain.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include-single=1200 -dynamic ` tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,494 nline-insns-single=1200 -dynamic -c ../test/redraw.c -o ../obj_s/redraw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,494 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:19,539 -param max-inline-insns-single=1200 -o railroad ../obj_s/railroad.o -L../lib -Wl,-search_paths_firsIG_H -I. -I../include -precomp --param max-inline-insngcc -I. -I. -I../test -DHAVE_CONFIG_H -00 -dynamic -c ../test/rain.c -o ../obj_s/rain.gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insnsecho "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutilgcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-igcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o redraw ../obj_s/redraw.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,596 -param max-inline-insns-single=1200 -o railroad ../obj_s/railroad.o -L../lib -Wl,-search_paths_firsIG_H -I. -I../include -precomp --param max-inline-insngcc -I. -I. -I../test -DHAVE_CONFIG_H -00 -dynamic -c ../test/rain.c -o ../obj_s/rain.gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insnsecho "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutilgcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-igcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o redraw ../obj_s/redraw.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,596 -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=gcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c ../test/savescreen.c -o ../obj_s/savescreen.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,596 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:19,745 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-il,-search_paths_first -I.comp --param max-inline-insns-s./test/tclock.c -o ../obj_s/tclock.o 127.0.0.1 - - [18/Nov/2017:16:59:19 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,801 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o savescreen ../obj_s/savescreen.o -W -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,801 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-il,-search_paths_first -I.comp --param max-inline-insns-s./test/tclock.c -o ../obj_s/tclock.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,801 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:19,848 max-inline-insns-single=1200 -o tclock ../obj_s/tclock.o -Wl,-search_paths_first -I. -I. -I../testDARWIN_C_SOURCE -DNDEBUG gle=1200 -dynamic `echo "-L..*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,902 max-inline-insns-single=1200 -o tclock ../obj_s/tclock.o -Wl,-search_paths_first -I. -I. -I../testDARWIN_C_SOURCE -DNDEBUG gle=1200 -dynamic `echo "-L..*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,902 gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-preingle=1200 -dynamic -c .gcc -O2 -no-cpp-precomp --param -DHAVE_CONFIG_H -I. -I../include -D_-O2 -no-cpp-precomp --param max-inline-insns-sin/lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCEstr.c -o ../obj_s/test_add_wchstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:19,902 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:19,988 -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../test/test_add_wchchstr.o -Wl,-search_paths-DHAVE_CONFIG_H -I. -I../includ -O2 -no-cpp-precomp --param max-inline../lib -lform -lmenu -lpanel -lncurses " | sedgcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_st/test_addchstr.c -o ../obj_s/test_addchstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,005 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o test_add_wchstr ../obj_s/test_add_w_first -I. -I. -I../test e -D_DARWIN_C_SOURCE -DNDEBUG-insns-single=1200 -dynamic `echo "-L -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,005 -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../test/test_add_wchchstr.o -Wl,-search_paths-DHAVE_CONFIG_H -I. -I../includ -O2 -no-cpp-precomp --param max-inline../lib -lform -lmenu -lpanel -lncurses " | sedgcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_st/test_addchstr.c -o ../obj_s/test_addchstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,005 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:20,203 -param max-inline-insns-single=1200 -o test_addchstr ../obj_s/test_addchstr.o -Wl,-search_paths_firFIG_H -I. -I../include -precomp --param max-inline-ins -lmenu -lpanel -lncurses " | sed -e gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/test_addstr.c -o ../obj_s/test_addstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,209 DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../tegcc -O2 -no-cpp-precomp -st -I. -I. -I../test -DHAVE_CON-D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cppns-single=1200 -dynamic `echo "-L../lib -lform's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,210 -param max-inline-insns-single=1200 -o test_addchstr ../obj_s/test_addchstr.o -Wl,-search_paths_firFIG_H -I. -I../include -precomp --param max-inline-ins -lmenu -lpanel -lncurses " | sed -e gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/test_addstr.c -o ../obj_s/test_addstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,310 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:20,359 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o test_addstr ../obj_s/test_addstr.o I. -I. -I../test -DHAVE_CARWIN_C_SOURCE -DNDEBUG -O2 -noingle=1200 -dynamic `echo "-L../lib -lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,412 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o test_addstr ../obj_s/test_addstr.o I. -I. -I../test -DHAVE_CARWIN_C_SOURCE -DNDEBUG -O2 -noingle=1200 -dynamic `echo "-L../lib -lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,412 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dyna-Wl,-search_paths_first -ONFIG_H -I. -I../include -D_D-cpp-precomp --param max-inline-insns-slform -lmenu -lpanel -lncurses " | sed -e 's/-gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_st/test_addwstr.c -o ../obj_s/test_addwstr.o install_environment.STDOUT DEBUG 2017-11-18 16:59:20,497 DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../teo -Wl,-search_paths_first_CONFIG_H -I. -I../include -Dno-cpp-precomp --param max-inline-insns -lform -lmenu -lpanel -lncurses " | sed -e 'sgcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_st/test_arrays.c -o ../obj_s/test_arrays.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,513 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o test_addwstr ../obj_s/test_addwstr. -I. -I. -I../test -DHAVE_DARWIN_C_SOURCE -DNDEBUG -O2 --single=1200 -dynamic `echo "-L../lib/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,514 DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../teo -Wl,-search_paths_first_CONFIG_H -I. -I../include -Dno-cpp-precomp --param max-inline-insns -lform -lmenu -lpanel -lncurses " | sed -e 'sgcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_st/test_arrays.c -o ../obj_s/test_arrays.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,514 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,514 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:20,564 -param max-inline-insns-single=1200 -o test_arrays ../obj_s/test_arrays.o -L../lib -Wl,-search_pathE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -lncurses -lutil install_environment.STDOUT DEBUG 2017-11-18 16:59:20,590 I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=12j_s/test_get_wstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,615 -param max-inline-insns-single=1200 -o test_arrays ../obj_s/test_arrays.o -L../lib -Wl,-search_pathE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -lncurses -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,615 I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=12j_s/test_get_wstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,615 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:20,659 -o test_get_wstr ../obj_s/test_get_wstr.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_m max-inline-insns-singleel[^ ]*//'` -lutil install_environment.STDOUT DEBUG 2017-11-18 16:59:20,696 nline-insns-single=1200 -dynamic -c ../test/test_getstr.c -o ../obj_s/test_getstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,716 -o test_get_wstr ../obj_s/test_get_wstr.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_m max-inline-insns-singleel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,716 nline-insns-single=1200 -dynamic -c ../test/test_getstr.c -o ../obj_s/test_getstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,717 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,818 DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../tegcc -O2 -no-cpp-precomp -s_first -I. -I. -I../test -DHAVgcc -I. -I. -I../test -DHAVE_CONFIG_H -00 -dynamic -c ../test/test_get_wstr.c -o ../obgcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --para=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpangcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-igcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o test_getstr ../obj_s/test_getstr.o -Wl,-search_paths_first -I. -I. -I../test -DHAVns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,918 AVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-i./test/test_instr.c -o ../obj_s/test_instr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:20,919 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,024 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o test_instr ../obj_s/test_instr.o -W -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,024 gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-premic -c ../test/test_inwstr.c -o ../obj_s/test_inwstr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,024 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:21,033 E_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insgcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c .l,-search_paths_first -I. -I. -I../testcomp --param max-inline-insns-single=1200 -dyna-Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H -IN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=120form -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil install_environment.STDOUT DEBUG 2017-11-18 16:59:21,076 I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=12s/test_opaque.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,129 E_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insgcc -I. -I. -I../test -DHnsns-single=1200 -dynamic -c .l,-search_paths_first -I. -I. -I../testcomp --param max-inline-insns-single=1200 -dyna-Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H -IN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=120form -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,130 I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=12s/test_opaque.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,130 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:21,225 -o test_opaque ../obj_s/test_opaque.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H -Ix-inline-insns-single=120 ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,232 -o test_opaque ../obj_s/test_opaque.o -Wl,-search_paths_first -I. -I. -I../test -DHAVE_CONFIG_H -Ix-inline-insns-single=120 ]*//'` -lutil install_environment.STDOUT DEBUG 2017-11-18 16:59:21,264 nline-insns-single=1200 -dynamic -c ../test/test_setupterm.c -o ../obj_s/test_setupterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,336 nline-insns-single=1200 -dynamic -c ../test/test_setupterm.c -o ../obj_s/test_setupterm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,336 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,440 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o test_inwstr ../obj_s/test_inwstr.o . -I../include -D_DARWI0 -dynamic `echo "-L../lib -lgcc -I. -I. -I../test -DHAVE_CONFIG_H -00 -dynamic -c ../test/test_opaque.c -o ../obj_gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param ma0 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-igcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o test_setupterm ../obj_s/test_setupterm.o -Wl,-search_paths_first -I. -I. -I../testne-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,441 gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-prensns-single=1200 -dynamic -c ../test/test_vid_puts.c -o ../obj_s/test_vid_puts.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,441 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:21,495 -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inlicomp --param max-inline-is.o -Wl,-search_paths_first -I.FIG_H -I. -I../include -D_DARWIN_C_SOmp --param max-inline-insns-single=1200 -dynamil -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE.c -o ../obj_s/test_vidputs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,545 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o test_vid_puts ../obj_s/test_vid_put -I. -I../test -DHAVE_CONURCE -DNDEBUG -O2 -no-cpp-precoc `echo "-L../lib -lform -lmenu -lpane tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,545 -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inlicomp --param max-inline-is.o -Wl,-search_paths_first -I.FIG_H -I. -I../include -D_DARWIN_C_SOmp --param max-inline-insns-single=1200 -dynamil -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE.c -o ../obj_s/test_vidputs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,545 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:21,605 -param max-inline-insns-single=1200 -o test_vidputs ../obj_s/test_vidputs.o -Wl,-search_paths_firstG_H -I. -I../include -Drecomp --param max-inline-insnslmenu -lpanel -lncurses " | sed -e 'sgcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/testaddch.c -o ../obj_s/testaddch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,650 -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic -c ../test/test_vidputsgcc -O2 -no-cpp-precomp - -I. -I. -I../test -DHAVE_CONFI_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-p-single=1200 -dynamic `echo "-L../lib -lform -/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,650 -param max-inline-insns-single=1200 -o test_vidputs ../obj_s/test_vidputs.o -Wl,-search_paths_firstG_H -I. -I../include -Drecomp --param max-inline-insnslmenu -lpanel -lncurses " | sed -e 'sgcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/testaddch.c -o ../obj_s/testaddch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,650 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:21,718 -param max-inline-insns-single=1200 -o testaddch ../obj_s/testaddch.o -Wl,-search_paths_first -I. -. -I../include -D_DARWI --param max-inline-insns-singl-lpanel -lncurses " | sed -e 's/-lforgcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/testcurs.c -o ../obj_s/testcurs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,755 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp -I. -I../test -DHAVE_CONFIG_H -IN_C_SOURCE -DNDEBUG -O2 -no-cpp-precompe=1200 -dynamic `echo "-L../lib -lform -lmenu m.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,756 -param max-inline-insns-single=1200 -o testaddch ../obj_s/testaddch.o -Wl,-search_paths_first -I. -. -I../include -D_DARWI --param max-inline-insns-singl-lpanel -lncurses " | sed -e 's/-lforgcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/testcurs.c -o ../obj_s/testcurs.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,756 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:21,914 -param max-inline-insns-single=1200 -o testcurs ../obj_s/testcurs.o -Wl,-search_paths_first -I. -I.-I../include -D_DARWIN_-param max-inline-insns-single=panel -lncurses " | sed -e 's/-lform.gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/testscanw.c -o ../obj_s/testscanw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,961 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp - -I../test -DHAVE_CONFIG_H -I. C_SOURCE -DNDEBUG -O2 -no-cpp-precomp -1200 -dynamic `echo "-L../lib -lform -lmenu -l*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,962 -param max-inline-insns-single=1200 -o testcurs ../obj_s/testcurs.o -Wl,-search_paths_first -I. -I.-I../include -D_DARWIN_-param max-inline-insns-single=panel -lncurses " | sed -e 's/-lform.gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/testscanw.c -o ../obj_s/testscanw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:21,962 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:22,021 -param max-inline-insns-single=1200 -o testscanw ../obj_s/testscanw.o -Wl,-search_paths_first -I. -. -I../include -D_DARWI --param max-inline-insns-singl-lpanel -lncurses " | sed -e 's/-lforgcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/view.c -o ../obj_s/view.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,062 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp -I. -I../test -DHAVE_CONFIG_H -IN_C_SOURCE -DNDEBUG -O2 -no-cpp-precompe=1200 -dynamic `echo "-L../lib -lform -lmenu m.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,063 -param max-inline-insns-single=1200 -o testscanw ../obj_s/testscanw.o -Wl,-search_paths_first -I. -. -I../include -D_DARWI --param max-inline-insns-singl-lpanel -lncurses " | sed -e 's/-lforgcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/view.c -o ../obj_s/view.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,063 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,166 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp -st -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil install_environment.STDOUT DEBUG 2017-11-18 16:59:22,202 -param max-inline-insns-single=1200 -o view ../obj_s/view.o -Wl,-search_paths_first -I. -I. -I../tecomp --param max-inline-i/worm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,270 -param max-inline-insns-single=1200 -o view ../obj_s/view.o -Wl,-search_paths_first -I. -I. -I../tecomp --param max-inline-i/worm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,270 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:22,369 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o worm ../obj_s/worm.o -Wl,-search_paIG_H -I. -I../include --param max-inline-insns-single=ses " | sed -e 's/-lform.*-lpanel[^ ]gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/xmas.c -o ../obj_s/xmas.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,371 gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-prensns-single=1200 -dynamic -c ../test/worm.c -o ../obj_sths_first -I. -I. -I../test -DHAVE_CONFD_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp -1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncur*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,371 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -o worm ../obj_s/worm.o -Wl,-search_paIG_H -I. -I../include --param max-inline-insns-single=ses " | sed -e 's/-lform.*-lpanel[^ ]gcc -I. -I. -I../test -DHAVE_CONFIG_H -I. -I../imic -c ../test/xmas.c -o ../obj_s/xmas.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,476 clang: warning: argument unused during compilation: '--param max-inline-insns-single=1200' install_environment.STDOUT DEBUG 2017-11-18 16:59:22,743 -param max-inline-insns-single=1200 -o xmas ../obj_s/xmas.o -Wl,-search_paths_first -I. -I. -I../te/database/dependencies/ncrses_6_0/0efde9889efd/lib" all install_environment.STDOUT DEBUG 2017-11-18 16:59:22,748 XTERM_KBS=BS \ install_environment.STDOUT DEBUG 2017-11-18 16:59:22,759 ** adjusting tabset paths tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,780 nclude -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynagcc -O2 -no-cpp-precomp -st -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamic `echo "-L../lib -lform -lmenu -lpanel -lncurses " | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,782 -param max-inline-insns-single=1200 -o xmas ../obj_s/xmas.o -Wl,-search_paths_first -I. -I. -I../te/database/dependencies/ncrses_6_0/0efde9889efd/lib" all tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,784 cd misc && /Library/Developer/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxyurses/6.0/iuc/package_ncuWHICH_XTERM=xterm-new \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,787 datadir=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,787 /bin/sh ./gen_edit.sh >run_tic.sed tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,787 XTERM_KBS=BS \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,787 echo '** adjusting tabset paths' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,787 ** adjusting tabset paths tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,788 sed -f run_tic.sed ../misc/terminfo.src >terminfo.tmp install_environment.STDOUT DEBUG 2017-11-18 16:59:22,805 cd c++ && /Library/Developer/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/cp ./etip.h.in etip.h install_environment.STDOUT DEBUG 2017-11-18 16:59:22,812 substituting autoconf'd values from ../include/ncurses_cfg.h into etip.h 127.0.0.1 - - [18/Nov/2017:16:59:22 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:59:22,861 ... CPP_HAS_STATIC_CAST 1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,888 database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib" all tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,888 cd c++ && /Library/Developer/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/cp ./etip.h.in etip.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,888 sh ./edit_cfg.sh ../include/ncurses_cfg.h etip.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,888 substituting autoconf'd values from ../include/ncurses_cfg.h into etip.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,888 ... CPP_HAS_PARAM_INIT 0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,888 ... CPP_HAS_STATIC_CAST 1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,889 ... ETIP_NEEDS_MATH_EXCEPTION 0 install_environment.STDOUT DEBUG 2017-11-18 16:59:22,896 ... ETIP_NEEDS_MATH_H 0 install_environment.STDOUT DEBUG 2017-11-18 16:59:22,933 ... HAVE_GPP_BUILTIN_H 0 install_environment.STDOUT DEBUG 2017-11-18 16:59:22,968 ... HAVE_IOSTREAM 1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,989 ... ETIP_NEEDS_MATH_H 0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,990 ... HAVE_BUILTIN_H 0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,990 ... HAVE_GPP_BUILTIN_H 0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,990 ... HAVE_GXX_BUILTIN_H 0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:22,990 ... HAVE_IOSTREAM 1 install_environment.STDOUT DEBUG 2017-11-18 16:59:23,008 ... HAVE_VALUES_H 0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:23,091 ... HAVE_TYPEINFO 1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:23,091 ... HAVE_VALUES_H 0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:23,091 ... IOSTREAM_NAMESPACE 1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:23,091 cursesf.cc -o ../obj_s/cursesf.o install_environment.STDOUT DEBUG 2017-11-18 16:59:23,223 /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -dynamic -c ../c++//usr/bin/g++ -DHAVE_CONFIrsesm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:23,301 /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -dynamic -c ../c++//usr/bin/g++ -DHAVE_CONFIrsesm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:23,401 G_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -dynamic -c ../c++/cursesm.cc -o ../obj_s/cu/usr/bin/g++ -DHAVE_CONFIrsesw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:23,605 /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -dynamic -c ../c++/cursespad.o install_environment.STDOUT DEBUG 2017-11-18 16:59:23,696 G_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -dynamic -c ../c++/cursesw.cc -o ../obj_s/cucursespad.cc -o ../obj_s//usr/bin/g++ -DHAVE_CONFIG_H -Io tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:23,708 G_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -dynamic -c ../c++/cursesw.cc -o ../obj_s/cucursespad.cc -o ../obj_s//usr/bin/g++ -DHAVE_CONFIG_H -Io tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:23,810 . -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -dynamic -c ../c++/cursesp.cc -o ../obj_s/cursesp./usr/bin/g++ -DHAVE_CONFIrsslk.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,018 /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -dynamic -c ../c++/cursesapp.o install_environment.STDOUT DEBUG 2017-11-18 16:59:24,062 G_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -dynamic -c ../c++/cursslk.cc -o ../obj_s/cucursesapp.cc -o ../obj_s//usr/bin/g++ -DHAVE_CONFIG_H -Ismain.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,122 G_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -dynamic -c ../c++/cursslk.cc -o ../obj_s/cucursesapp.cc -o ../obj_s//usr/bin/g++ -DHAVE_CONFIG_H -Ismain.o install_environment.STDOUT DEBUG 2017-11-18 16:59:24,466 s++.a ../obj_s/cursesf.o ../obj_s/cursesm.o ../obj_s/cursesw.o ../obj_s/cursespad.o ../obj_s/cursespa - ../obj_s/cursesm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,541 . -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -dynamic -c ../c++/cursesmain.cc -o ../obj_s/cursear -curv ../lib/libncurse.o ../obj_s/cursslk.o ../obj_s/cursesapp.o ../obj_s/cursesmain.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,541 a - ../obj_s/cursesf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,541 a - ../obj_s/cursesw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,541 a - ../obj_s/cursespad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,541 a - ../obj_s/cursesp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,541 a - ../obj_s/cursslk.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,541 a - ../obj_s/cursesapp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,542 a - ../obj_s/cursesmain.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,542 s++.a ../obj_s/cursesf.o ../obj_s/cursesm.o ../obj_s/cursesw.o ../obj_s/cursespad.o ../obj_s/cursespa - ../obj_s/cursesm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,542 ranlib ../lib/libncurses++.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,542 +/cursesf.cc -o ../obj_g/cursesf.o install_environment.STDOUT DEBUG 2017-11-18 16:59:24,679 /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -g -DTRACE -c ../c+/usr/bin/g++ -DHAVE_CONFIcursesm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,744 /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -g -DTRACE -c ../c+/usr/bin/g++ -DHAVE_CONFIcursesm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:24,948 G_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -g -DTRACE -c ../c++/cursesm.cc -o ../obj_g//usr/bin/g++ -DHAVE_CONFIcursesw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:25,048 /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -g -DTRACE -c ../c+g/cursespad.o install_environment.STDOUT DEBUG 2017-11-18 16:59:25,199 G_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -g -DTRACE -c ../c++/cursesw.cc -o ../obj_g/+/cursespad.cc -o ../obj_/usr/bin/g++ -DHAVE_CONFIG_H -Ip.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:25,259 G_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -g -DTRACE -c ../c++/cursesw.cc -o ../obj_g/+/cursespad.cc -o ../obj_/usr/bin/g++ -DHAVE_CONFIG_H -Ip.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:25,363 . -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -g -DTRACE -c ../c++/cursesp.cc -o ../obj_g/curses/usr/bin/g++ -DHAVE_CONFIcursslk.o install_environment.STDOUT DEBUG 2017-11-18 16:59:25,475 G_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -g -DTRACE -c ../c++/cursslk.cc -o ../obj_g//usr/bin/g++ -DHAVE_CONFIg/cursesapp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:25,572 G_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -g -DTRACE -c ../c++/cursslk.cc -o ../obj_g//usr/bin/g++ -DHAVE_CONFIg/cursesapp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:25,677 G_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -g -DTRACE -c ../c++/cursesapp.cc -o ../obj_/usr/bin/g++ -DHAVE_CONFI_g/cursesmain.o 127.0.0.1 - - [18/Nov/2017:16:59:25 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:59:25,974 G_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -g -DTRACE -c ../c++/cursesmain.cc -o ../objar -curv ../lib/libncursesp.o ../obj_g/cursslk.o ../obj_rsesmain.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:25,982 G_H -I. -I../include -D_DARWIN_C_SOURCE -DNDEBUG -O2 -g -DTRACE -c ../c++/cursesmain.cc -o ../objar -curv ../lib/libncursesp.o ../obj_g/cursslk.o ../obj_rsesmain.o install_environment.STDOUT DEBUG 2017-11-18 16:59:25,989 a - ../obj_g/cursesm.o install_environment.STDOUT DEBUG 2017-11-18 16:59:26,001 compiling demo (obj_s) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,084 s++_g.a ../obj_g/cursesf.o ../obj_g/cursesm.o ../obj_g/cursesw.o ../obj_g/cursespad.o ../obj_g/curseg/cursesapp.o ../obj_g/cua - ../obj_g/cursesf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,084 a - ../obj_g/cursesw.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,084 a - ../obj_g/cursespad.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,085 a - ../obj_g/cursesp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,085 a - ../obj_g/cursslk.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,085 a - ../obj_g/cursesapp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,085 a - ../obj_g/cursesmain.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,085 a - ../obj_g/cursesm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,085 ranlib ../lib/libncurses++_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,085 compiling demo (obj_s) install_environment.STDOUT DEBUG 2017-11-18 16:59:26,367 -Wl,-search_paths_first -lutil -lstdc++ -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE cd man && /Library/Develorses/6.0/iuc/package_ncurses_6_ll install_environment.STDOUT DEBUG 2017-11-18 16:59:26,375 base/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,395 /usr/bin/g++ -o demo ../obj_s/demo.o -L../lib -lncurses++ -L../lib -lform -lmenu -lpanel -lncurses -DNDEBUG -O2 -dynamic tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,395 -Wl,-search_paths_first -lutil -lstdc++ -DHAVE_CONFIG_H -I. -I../include -D_DARWIN_C_SOURCE cd man && /Library/Develorses/6.0/iuc/package_ncurses_6_ll tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,395 base/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,395 per/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/ncu0/0efde9889efd/lib" instamkdir -p /galaxydir/galaxy/datash ../edit_man.sh normal installing /garminfo.5 *-config.1 ./*.[0-9]* tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,396 ...made /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdpbWHCP/ncurses-6.0-20150725/man_alias.sed install_environment.STDOUT DEBUG 2017-11-18 16:59:26,486 laxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man . teinstalling /galaxydir/gal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,499 laxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man . teinstalling /galaxydir/gal install_environment.STDOUT DEBUG 2017-11-18 16:59:26,591 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man1/ncurses6-cinstalling /galaxydir/gal1m tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,601 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man5/terminfo.5installing /galaxydir/galonfig.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,601 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man1/ncurses6-cinstalling /galaxydir/gal1m install_environment.STDOUT DEBUG 2017-11-18 16:59:26,640 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man1/clear.1 install_environment.STDOUT DEBUG 2017-11-18 16:59:26,696 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/curs_add_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,705 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man1/clear.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,705 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/curs_add_wch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,715 .. installing alias echo_wchar.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,721 .. installing alias mvwadd_wch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,726 .. installing alias wecho_wchar.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,764 share/man/man3/curs_add_wchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,777 chnstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,780 3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,785 .. installing alias mvadd_wchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,789 .. installing alias mvwadd_wchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,794 .. installing alias wadd_wchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,809 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man1/captoinfo.installing /galaxydir/galinstalling /galaxydir/galaxy/da.. installing alias add_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,809 .. installing alias echo_wchar.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,809 .. installing alias mvadd_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,809 .. installing alias mvwadd_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,809 .. installing alias wadd_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,809 .. installing alias wecho_wchar.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,809 share/man/man3/curs_add_wchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,810 chnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,810 3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,810 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias add_w.. installing alias add_wchstr... installing alias mvadd_wchnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,810 .. installing alias mvadd_wchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,811 .. installing alias mvwadd_wchnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,811 .. installing alias mvwadd_wchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,811 .. installing alias wadd_wchnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,811 .. installing alias wadd_wchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,831 share/man/man3/curs_addch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,846 .3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,852 install_environment.STDOUT DEBUG 2017-11-18 16:59:26,859 .. installing alias mvwaddch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,864 .. installing alias wechochar.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,901 share/man/man3/curs_addchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,912 share/man/man3/curs_addch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,912 nstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:26,912 .3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,914 install_environment.STDOUT DEBUG 2017-11-18 16:59:26,921 .. installing alias mvaddchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,925 .. installing alias mvwaddchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,930 .. installing alias waddchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,966 share/man/man3/curs_addstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,980 tr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,985 .. installing alias mvaddnstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,991 .. installing alias mvwaddnstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:26,997 .. installing alias waddnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,014 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias addch.. installing alias echochar.3x.. installing alias mvaddch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,015 .. installing alias mvwaddch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,015 .. installing alias waddch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,015 .. installing alias wechochar.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,015 share/man/man3/curs_addchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,015 nstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,050 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias addnw.. installing alias addwstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,058 .. installing alias mvaddwstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,064 .. installing alias mvwaddwstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,072 .. installing alias waddwstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,111 share/man/man3/curs_attr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,118 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias addch.. installing alias addchstr.3x.. installing alias mvaddchnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,118 .. installing alias mvaddchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,118 .. installing alias mvwaddchnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,118 .. installing alias mvwaddchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,119 .. installing alias waddchnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,119 .. installing alias waddchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,119 share/man/man3/curs_addstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,119 tr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,120 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias addns.. installing alias addstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,120 .. installing alias mvaddnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,120 .. installing alias mvaddstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,121 .. installing alias mvwaddnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,121 .. installing alias mvwaddstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,121 .. installing alias waddnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,121 .. installing alias waddstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,121 share/man/man3/curs_addwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,121 str.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,121 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias addnw.. installing alias addwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,121 .. installing alias mvaddnwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,122 .. installing alias mvaddwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,122 .. installing alias mvwaddnwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,122 .. installing alias mvwaddwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,122 .. installing alias waddnwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,122 .. installing alias waddwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,122 share/man/man3/curs_attr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,124 NUMBER.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,128 install_environment.STDOUT DEBUG 2017-11-18 16:59:27,132 .. installing alias attr_on.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,139 .. installing alias attroff.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,144 .. installing alias attrset.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,148 .. installing alias color_set.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,154 .. installing alias mvwchgat.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,158 .. installing alias standout.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,165 .. installing alias wattr_off.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,171 .. installing alias wattr_set.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,177 .. installing alias wattron.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,182 .. installing alias wchgat.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,189 .. installing alias wstandend.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,225 NUMBER.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,243 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias beep... installing alias flash.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,276 share/man/man3/curs_bkgd.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,287 3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,292 .. installing alias getbkgd.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,298 .. installing alias wbkgdset.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,326 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias PAIR_.. installing alias attr_get.3x.. installing alias attr_off.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,327 .. installing alias attr_on.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,327 .. installing alias attr_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,327 .. installing alias attroff.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,327 .. installing alias attron.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,327 .. installing alias attrset.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,327 .. installing alias chgat.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,327 .. installing alias color_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,327 .. installing alias mvchgat.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,328 .. installing alias mvwchgat.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,328 .. installing alias standend.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,328 .. installing alias standout.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,328 .. installing alias wattr_get.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,328 .. installing alias wattr_off.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,328 .. installing alias wattr_on.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,328 .. installing alias wattr_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,328 .. installing alias wattroff.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,328 .. installing alias wattron.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,329 .. installing alias wattrset.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,329 .. installing alias wchgat.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,329 .. installing alias wcolor_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,329 .. installing alias wstandend.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,329 .. installing alias wstandout.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,329 share/man/man3/curs_beep.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,329 3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,329 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias beep... installing alias flash.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,330 share/man/man3/curs_bkgd.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,330 3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,330 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias bkgd... installing alias bkgdset.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,330 .. installing alias getbkgd.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,330 .. installing alias wbkgd.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,330 .. installing alias wbkgdset.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,331 share/man/man3/curs_bkgrnd.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,344 d.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,349 .. installing alias bkgrndset.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,354 x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,364 .. installing alias wbkgrndset.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,417 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias borde.. installing alias box.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,424 .. installing alias mvhline.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,430 .. installing alias mvwhline.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,433 share/man/man3/curs_bkgrnd.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,433 d.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,433 .. installing alias bkgrndset.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,433 x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,433 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias bkgrn.. installing alias getbkgrnd.3.. installing alias wbkgrnd.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,434 .. installing alias wbkgrndset.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,434 .. installing alias wgetbkgrnd.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,434 share/man/man3/curs_border.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,434 r.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,434 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias borde.. installing alias box.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,434 .. installing alias hline.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,434 .. installing alias mvhline.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,434 .. installing alias mvvline.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,434 .. installing alias mvwhline.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,435 .. installing alias mvwvline.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,438 .. installing alias vline.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,446 .. installing alias whline.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,513 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias borde.. installing alias box_set.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,518 .. installing alias mvhline_set.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,522 .. installing alias mvwhline_set.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,528 .. installing alias vline_set.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,532 .. installing alias whline_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,538 .. installing alias vline.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,538 .. installing alias wborder.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,538 .. installing alias whline.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,538 .. installing alias wvline.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,538 share/man/man3/curs_border_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,538 r_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,538 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias borde.. installing alias box_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,538 .. installing alias hline_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,538 .. installing alias mvhline_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,538 .. installing alias mvvline_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,539 .. installing alias mvwhline_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,539 .. installing alias mvwvline_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,539 .. installing alias vline_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,539 .. installing alias wborder_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,539 .. installing alias whline_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,539 .. installing alias wvline_set.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,583 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias clear.. installing alias clrtobot.3x.. installing alias clrtoeol.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,589 .. installing alias wclear.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,594 .. installing alias wclrtoeol.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,639 share/man/man3/curs_clear.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,640 .3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,652 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias COLOR.. installing alias can_change_.. installing alias color_content.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,657 .. installing alias init_color.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,662 .. installing alias pair_content.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,717 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias delch.. installing alias mvdelch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,723 .. installing alias wdelch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,741 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias clear.. installing alias clrtobot.3x.. installing alias clrtoeol.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,741 .. installing alias erase.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,741 .. installing alias wclear.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,742 .. installing alias wclrtobot.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,742 .. installing alias wclrtoeol.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,742 .. installing alias werase.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,742 share/man/man3/curs_color.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,742 _PAIR.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,742 color.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,742 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias COLOR.. installing alias can_change_.. installing alias color_content.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,742 .. installing alias has_colors.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,742 .. installing alias init_color.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,743 .. installing alias init_pair.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,743 .. installing alias pair_content.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,743 .. installing alias start_color.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,743 share/man/man3/curs_delch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,743 .3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,743 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias delch.. installing alias mvdelch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,743 .. installing alias mvwdelch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,743 .. installing alias wdelch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,760 share/man/man3/curs_deleteln.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,774 eln.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,778 install_environment.STDOUT DEBUG 2017-11-18 16:59:27,787 .. installing alias wdeleteln.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,794 .. installing alias winsertln.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,827 share/man/man3/curs_extend.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,846 share/man/man3/curs_deleteln.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,846 eln.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,846 s_version.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,849 d_names.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,897 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/curs_get_wch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,912 .. installing alias mvget_wch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,917 .. installing alias unget_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,946 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias delet.. installing alias insdelln.3x.. installing alias insertln.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,946 .. installing alias wdeleteln.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,946 .. installing alias winsdelln.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,947 .. installing alias winsertln.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,947 share/man/man3/curs_extend.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,947 s_version.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,947 d_names.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,947 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/curs_get_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,947 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias curse.. installing alias use_extendeinstalling /galaxydir/galaxy/database/d.. installing alias get_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,947 .. installing alias mvget_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,947 .. installing alias mvwget_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,947 .. installing alias unget_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:27,947 .. installing alias wget_wch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,974 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias get_w.. installing alias getn_wstr.3.. installing alias mvget_wstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,979 .. installing alias mvwget_wstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:27,985 .. installing alias wget_wstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,049 share/man/man3/curs_get_wstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,050 str.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,050 x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,050 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias get_w.. installing alias getn_wstr.3.. installing alias mvget_wstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,050 .. installing alias mvgetn_wstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,050 .. installing alias mvwget_wstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,050 .. installing alias mvwgetn_wstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,050 .. installing alias wget_wstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,050 .. installing alias wgetn_wstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,050 share/man/man3/curs_getcchar.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,050 har.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,099 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias getcc.. installing alias setcchar.3xinstalling /galaxydir/galaxy/database/d.. installing alias getch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,104 .. installing alias mvgetch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,111 .. installing alias ungetch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,151 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/curs_getch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,152 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias getcc.. installing alias setcchar.3xinstalling /galaxydir/galaxy/database/d.. installing alias getch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,152 .. installing alias has_key.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,152 .. installing alias mvgetch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,152 .. installing alias mvwgetch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,152 .. installing alias ungetch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,152 .. installing alias wgetch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,153 share/man/man3/curs_getstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,166 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias getns.. installing alias getstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,174 .. installing alias mvgetstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,178 .. installing alias mvwgetstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,183 .. installing alias wgetstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,215 share/man/man3/curs_getyx.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,227 gyx.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,229 install_environment.STDOUT DEBUG 2017-11-18 16:59:28,234 .. installing alias getyx.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,254 tr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,256 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias getns.. installing alias getstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,256 .. installing alias mvgetnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,256 .. installing alias mvgetstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,256 .. installing alias mvwgetnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,256 .. installing alias mvwgetstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,256 .. installing alias wgetnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,256 .. installing alias wgetstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,257 share/man/man3/curs_getyx.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,257 gyx.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,268 share/man/man3/curs_in_wch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,282 h.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,285 install_environment.STDOUT DEBUG 2017-11-18 16:59:28,292 .. installing alias win_wch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,331 share/man/man3/curs_in_wchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,345 hnstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,349 x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,356 .. installing alias mvin_wchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,361 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias getbe.. installing alias getmaxyx.3x.. installing alias getparyx.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,361 .. installing alias getyx.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,361 share/man/man3/curs_in_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,361 h.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,363 .. installing alias mvwin_wchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,369 .. installing alias win_wchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,406 share/man/man3/curs_inch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,419 3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,425 .. installing alias mvwinch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,461 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias in_wc.. installing alias mvin_wch.3x.. installing alias mvwin_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,462 .. installing alias win_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,462 share/man/man3/curs_in_wchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,462 hnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,462 x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,462 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias in_wc.. installing alias in_wchstr.3.. installing alias mvin_wchnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,462 .. installing alias mvin_wchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,462 .. installing alias mvwin_wchnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,462 .. installing alias mvwin_wchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,462 .. installing alias win_wchnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,462 .. installing alias win_wchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,463 share/man/man3/curs_inch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,463 3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,463 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias inch... installing alias mvinch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,463 .. installing alias mvwinch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,463 .. installing alias winch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,463 share/man/man3/curs_inchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,477 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias inchn.. installing alias inchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,482 .. installing alias mvinchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,487 .. installing alias mvwinchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,496 .. installing alias winchstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,539 share/man/man3/curs_initscr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,552 reen.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,559 .. installing alias initscr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,564 .. installing alias newterm.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,564 str.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,564 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias inchn.. installing alias inchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,564 .. installing alias mvinchnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,564 .. installing alias mvinchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,565 .. installing alias mvwinchnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,565 .. installing alias mvwinchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,565 .. installing alias winchnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,565 .. installing alias winchstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,565 share/man/man3/curs_initscr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,565 reen.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,565 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias delsc.. installing alias endwin.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,565 .. installing alias initscr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,565 .. installing alias isendwin.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,565 .. installing alias newterm.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,618 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias cbrea.. installing alias echo.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,623 .. installing alias intrflush.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,628 .. installing alias meta.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,633 .. installing alias nodelay.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,637 .. installing alias noqiflush.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,642 .. installing alias notimeout.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,647 .. installing alias raw.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,652 .. installing alias typeahead.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,670 .. installing alias set_term.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,671 share/man/man3/curs_inopts.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,671 k.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,671 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias cbrea.. installing alias echo.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,671 .. installing alias halfdelay.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,671 .. installing alias intrflush.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,671 .. installing alias keypad.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,671 .. installing alias meta.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,671 .. installing alias nocbreak.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,671 .. installing alias nodelay.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,671 .. installing alias noecho.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,671 .. installing alias noqiflush.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,671 .. installing alias noraw.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,672 .. installing alias notimeout.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,672 .. installing alias qiflush.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,672 .. installing alias raw.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,672 .. installing alias timeout.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,672 .. installing alias typeahead.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,672 .. installing alias wtimeout.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,708 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias ins_w.. installing alias mvins_wch.3.. installing alias mvwins_wch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,759 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias ins_n.. installing alias ins_wstr.3x.. installing alias mvins_nwstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,763 .. installing alias mvwins_nwstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,769 .. installing alias wins_nwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,773 share/man/man3/curs_ins_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,774 ch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,774 x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,774 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias ins_w.. installing alias mvins_wch.3.. installing alias mvwins_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,775 .. installing alias wins_wch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,775 share/man/man3/curs_ins_wstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,775 wstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,818 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias insch.. installing alias mvinsch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,824 .. installing alias winsch.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,854 share/man/man3/curs_insstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,869 tr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,877 .. installing alias mvinsnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,880 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias ins_n.. installing alias ins_wstr.3x.. installing alias mvins_nwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,880 .. installing alias mvins_wstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,880 .. installing alias mvwins_nwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,880 .. installing alias mvwins_wstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,880 .. installing alias wins_nwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,881 .. installing alias wins_wstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,881 share/man/man3/curs_insch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,881 .3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,881 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias insch.. installing alias mvinsch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,881 .. installing alias mvwinsch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,881 .. installing alias winsch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,881 share/man/man3/curs_insstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,881 tr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,881 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias insns.. installing alias insstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,881 .. installing alias mvinsnstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,884 .. installing alias mvwinsnstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,889 .. installing alias winsnstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,944 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias innst.. installing alias instr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,957 .. installing alias mvinstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:28,961 .. installing alias winnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,986 .. installing alias mvinsstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,987 .. installing alias mvwinsnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,987 .. installing alias mvwinsstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,987 .. installing alias winsnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,987 .. installing alias winsstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,987 share/man/man3/curs_instr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,987 r.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,987 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias innst.. installing alias instr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,987 .. installing alias mvinnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,987 .. installing alias mvwinnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,987 .. installing alias mvinstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,988 .. installing alias mvwinstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,988 .. installing alias winnstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:28,988 .. installing alias winstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,027 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias innws.. installing alias inwstr.3x 127.0.0.1 - - [18/Nov/2017:16:59:28 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:59:29,038 .. installing alias mvinwstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,045 .. installing alias mvwinwstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,049 .. installing alias winwstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,085 share/man/man3/curs_kernel.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,090 share/man/man3/curs_inwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,090 tr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,090 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias innws.. installing alias inwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,090 .. installing alias mvinnwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,090 .. installing alias mvinwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,091 .. installing alias mvwinnwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,091 .. installing alias mvwinwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,091 .. installing alias winnwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,091 .. installing alias winwstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,091 share/man/man3/curs_kernel.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,099 set.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,102 de.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,109 .. installing alias getsyx.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,116 .. installing alias reset_prog_mode.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,122 .. installing alias resetty.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,128 .. installing alias savetty.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,182 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias getat.. installing alias getbegx.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,187 .. installing alias getcurx.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,192 .. installing alias getmaxx.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,195 set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,195 de.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,195 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias curs_.. installing alias def_prog_mo.. installing alias def_shell_mode.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,195 .. installing alias getsyx.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,195 .. installing alias napms.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,195 .. installing alias reset_prog_mode.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,195 .. installing alias reset_shell_mode.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,196 .. installing alias resetty.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,196 .. installing alias ripoffline.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,196 .. installing alias savetty.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,196 .. installing alias setsyx.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,196 share/man/man3/curs_legacy.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,196 trs.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,196 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias getat.. installing alias getbegx.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,196 .. installing alias getbegy.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,196 .. installing alias getcurx.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,196 .. installing alias getcury.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,196 .. installing alias getmaxx.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,196 .. installing alias getmaxy.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,198 .. installing alias getparx.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,291 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias _nc_f.. installing alias _nc_freeallinstalling /galaxydir/galaxy/database/d.. installing alias getmouse.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,296 .. installing alias mouse_trafo.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,298 .. installing alias getparx.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,298 .. installing alias getpary.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,298 share/man/man3/curs_memleaks.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,299 ree_and_exit.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,299 .3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,299 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/curs_mouse.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,299 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias _nc_f.. installing alias _nc_freeallinstalling /galaxydir/galaxy/database/d.. installing alias getmouse.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,299 .. installing alias has_mouse.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,299 .. installing alias mouse_trafo.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,299 .. installing alias mouseinterval.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,301 .. installing alias mousemask.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,305 .. installing alias wenclose.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,355 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias move... installing alias wmove.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,386 share/man/man3/curs_opaque.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,400 eared.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,404 .. installing alias mousemask.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,404 .. installing alias ungetmouse.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,404 .. installing alias wenclose.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,404 .. installing alias wmouse_trafo.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,404 share/man/man3/curs_move.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,404 3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,405 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias move... installing alias wmove.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,405 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,405 share/man/man3/curs_opaque.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,405 eared.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,414 .. installing alias is_immedok.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,419 .. installing alias is_nodelay.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,425 .. installing alias is_pad.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,430 .. installing alias is_subwin.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,435 .. installing alias wgetdelay.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,441 .. installing alias wgetscrreg.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,475 share/man/man3/curs_outopts.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,486 ok.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,492 .. installing alias idlok.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,497 .. installing alias leaveok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,510 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias is_cl.. installing alias is_idcok.3x.. installing alias is_idlok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,510 .. installing alias is_keypad.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,510 .. installing alias is_immedok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,510 .. installing alias is_leaveok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,511 .. installing alias is_nodelay.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,511 .. installing alias is_notimeout.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,511 .. installing alias is_pad.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,511 .. installing alias is_scrollok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,511 .. installing alias is_subwin.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,511 .. installing alias is_syncok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,511 .. installing alias wgetdelay.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,511 .. installing alias wgetparent.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,511 .. installing alias wgetscrreg.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,511 share/man/man3/curs_outopts.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,512 ok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,512 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias clear.. installing alias idcok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,512 .. installing alias idlok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,512 .. installing alias immedok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,512 .. installing alias leaveok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,512 .. installing alias nl.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,510 .. installing alias nonl.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,518 .. installing alias setscrreg.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,521 .. installing alias wsetscrreg.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,550 share/man/man3/curs_overlay.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,563 in.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,570 .. installing alias overwrite.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,600 share/man/man3/curs_pad.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,613 .. installing alias nonl.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,613 .. installing alias setscrreg.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,614 .. installing alias scrollok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,614 .. installing alias wsetscrreg.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,614 share/man/man3/curs_overlay.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,614 in.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,615 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias copyw.. installing alias overlay.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,615 d.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,615 .. installing alias overwrite.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,615 share/man/man3/curs_pad.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,616 d.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,617 .3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,623 .. installing alias pnoutrefresh.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,629 .. installing alias subpad.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,666 share/man/man3/curs_print.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,678 nt.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,709 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/curs_printw.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,717 .3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,717 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias newpa.. installing alias pecho_wchar.. installing alias pechochar.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,718 .. installing alias pnoutrefresh.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,718 .. installing alias prefresh.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,718 .. installing alias subpad.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,718 share/man/man3/curs_print.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,718 nt.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,718 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/curs_printw.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,723 .. installing alias mvwprintw.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,729 .. installing alias vw_printw.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,734 .. installing alias wprintw.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,765 share/man/man3/curs_refresh.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,782 ate.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,786 x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,792 .. installing alias wnoutrefresh.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,799 .. installing alias wrefresh.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,818 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias mcpriinstalling /galaxydir/galaxy/da.. installing alias mvprintw.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,819 .. installing alias mvwprintw.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,819 .. installing alias printw.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,819 .. installing alias vw_printw.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,819 .. installing alias vwprintw.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,819 .. installing alias wprintw.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,819 share/man/man3/curs_refresh.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,819 ate.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,819 x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,819 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias doupd.. installing alias redrawwin.3.. installing alias refresh.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,819 .. installing alias wnoutrefresh.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,819 .. installing alias wredrawln.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,819 .. installing alias wrefresh.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,832 share/man/man3/curs_scanw.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,845 nw.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,848 install_environment.STDOUT DEBUG 2017-11-18 16:59:29,853 .. installing alias vw_scanw.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,858 .. installing alias wscanw.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,891 share/man/man3/curs_scr_dump.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,903 ump.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,906 install_environment.STDOUT DEBUG 2017-11-18 16:59:29,914 .. installing alias scr_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,920 share/man/man3/curs_scanw.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:29,920 nw.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,950 share/man/man3/curs_scroll.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,964 3x install_environment.STDOUT DEBUG 2017-11-18 16:59:29,969 .. installing alias wscrl.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,003 share/man/man3/curs_slk.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,016 ttr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,019 f.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,021 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias mvsca.. installing alias mvwscanw.3x.. installing alias scanw.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,021 .. installing alias vw_scanw.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,021 .. installing alias vwscanw.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,021 .. installing alias wscanw.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,022 share/man/man3/curs_scr_dump.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,022 ump.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,026 .. installing alias slk_attr_set.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,033 .. installing alias slk_attron.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,040 .. installing alias slk_clear.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,047 .. installing alias slk_init.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,055 .. installing alias slk_noutrefresh.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,066 .. installing alias slk_restore.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,073 .. installing alias slk_touch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,125 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias scr_d.. installing alias scr_init.3x.. installing alias scr_restore.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,125 .. installing alias scr_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,125 share/man/man3/curs_scroll.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,125 3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,125 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias scrl... installing alias scroll.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,125 .. installing alias wscrl.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,125 share/man/man3/curs_slk.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,126 ttr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,126 f.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,126 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias slk_a.. installing alias slk_attr_of.. installing alias slk_attr_on.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,126 .. installing alias slk_attr_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,126 .. installing alias slk_attroff.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,126 .. installing alias slk_attron.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,126 .. installing alias slk_attrset.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,126 .. installing alias slk_clear.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,127 .. installing alias slk_color.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,127 .. installing alias slk_init.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,127 .. installing alias slk_label.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,127 .. installing alias slk_noutrefresh.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,127 .. installing alias slk_refresh.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,127 .. installing alias slk_restore.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,128 .. installing alias slk_set.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,128 .. installing alias slk_touch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,128 .. installing alias slk_wset.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,128 share/man/man3/curs_sp_funcs.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,135 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias assum.. installing alias baudrate_sp.. installing alias beep_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,140 .. installing alias cbreak_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,146 .. installing alias color_content_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,150 .. installing alias def_prog_mode_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,155 .. installing alias define_key_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,161 .. installing alias delay_output_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,166 .. installing alias echo_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,174 .. installing alias erasechar_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,181 .. installing alias flash_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,188 .. installing alias get_escdelay_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,194 .. installing alias getwin_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,200 .. installing alias halfdelay_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,210 .. installing alias has_ic_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,218 .. installing alias has_key_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,225 .. installing alias init_color_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,229 e_default_colors_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,229 .3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,229 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias assum.. installing alias baudrate_sp.. installing alias beep_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,230 .. installing alias can_change_color_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,230 .. installing alias cbreak_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,230 .. installing alias ceiling_panel.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,230 .. installing alias color_content_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,230 .. installing alias curs_set_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,230 .. installing alias def_prog_mode_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,230 .. installing alias def_shell_mode_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,231 .. installing alias define_key_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,231 .. installing alias del_curterm_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,231 .. installing alias delay_output_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,231 .. installing alias doupdate_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,231 .. installing alias echo_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,231 .. installing alias endwin_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,231 .. installing alias erasechar_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,231 .. installing alias filter_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,231 .. installing alias flash_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,231 .. installing alias flushinp_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,231 .. installing alias get_escdelay_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,231 .. installing alias getmouse_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,231 .. installing alias getwin_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,231 .. installing alias ground_panel.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,232 .. installing alias halfdelay_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,232 .. installing alias has_colors_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,232 .. installing alias has_ic_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,232 .. installing alias has_il_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,232 .. installing alias has_key_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,232 .. installing alias has_mouse_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,232 .. installing alias init_color_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,232 .. installing alias init_pair_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,233 .. installing alias intrflush_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,238 .. installing alias isendwin_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,243 .. installing alias keybound_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,248 .. installing alias keyok_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,253 .. installing alias mcprint_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,259 .. installing alias mousemask_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,264 .. installing alias napms_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,271 .. installing alias new_menu_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,276 .. installing alias newpad_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,284 .. installing alias newwin_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,289 .. installing alias nocbreak_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,294 .. installing alias nofilter_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,299 .. installing alias noqiflush_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,306 .. installing alias pair_content_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,312 .. installing alias qiflush_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,319 .. installing alias reset_prog_mode_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,325 .. installing alias resetty_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,331 .. installing alias resizeterm_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,334 .. installing alias intrflush_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,334 .. installing alias is_term_resized_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,334 .. installing alias isendwin_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,334 .. installing alias key_defined_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,334 .. installing alias keybound_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias keyname_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias keyok_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias killchar_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias mcprint_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias mouseinterval_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias mousemask_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias mvcur_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias napms_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias new_form_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias new_menu_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias new_prescr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias newpad_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias newterm_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias newwin_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,335 .. installing alias nl_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,336 .. installing alias nocbreak_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,336 .. installing alias noecho_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,336 .. installing alias nofilter_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,336 .. installing alias nonl_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,336 .. installing alias noqiflush_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,336 .. installing alias noraw_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,336 .. installing alias pair_content_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,336 .. installing alias putp_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,336 .. installing alias qiflush_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,336 .. installing alias raw_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,336 .. installing alias reset_prog_mode_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,336 .. installing alias reset_shell_mode_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,336 .. installing alias resetty_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,336 .. installing alias resize_term_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,337 .. installing alias resizeterm_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,337 .. installing alias restartterm_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,337 .. installing alias ripoffline_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,343 .. installing alias scr_init_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,348 .. installing alias scr_set_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,354 .. installing alias set_escdelay_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,359 .. installing alias slk_attr_set_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,365 .. installing alias slk_attroff_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,370 .. installing alias slk_attrset_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,375 .. installing alias slk_color_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,381 .. installing alias slk_label_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,386 .. installing alias slk_refresh_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,391 .. installing alias slk_set_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,399 .. installing alias start_color_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,404 .. installing alias termattrs_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,411 .. installing alias tgetent_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,417 .. installing alias tgetnum_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,422 .. installing alias tigetflag_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,429 .. installing alias tigetstr_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,439 .. installing alias ripoffline_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,439 .. installing alias typeahead_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,439 .. installing alias savetty_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,445 .. installing alias scr_init_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,445 .. installing alias scr_restore_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,445 .. installing alias scr_set_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,445 .. installing alias set_curterm_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,445 .. installing alias set_escdelay_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,445 .. installing alias set_tabsize_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,445 .. installing alias slk_attr_set_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,445 .. installing alias slk_attr_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,446 .. installing alias slk_attroff_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,446 .. installing alias slk_attron_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,446 .. installing alias slk_attrset_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,446 .. installing alias slk_clear_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,446 .. installing alias slk_color_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,446 .. installing alias slk_init_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,446 .. installing alias slk_label_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,446 .. installing alias slk_noutrefresh_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,446 .. installing alias slk_refresh_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,446 .. installing alias slk_restore_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,446 .. installing alias slk_set_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,447 .. installing alias slk_touch_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,447 .. installing alias start_color_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,447 .. installing alias term_attrs_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,447 .. installing alias termattrs_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,447 .. installing alias termname_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,447 .. installing alias tgetent_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,447 .. installing alias tgetflag_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,447 .. installing alias tgetnum_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,447 .. installing alias tgetstr_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,447 .. installing alias tigetflag_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,447 .. installing alias tigetnum_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,448 .. installing alias tigetstr_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,448 .. installing alias tputs_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,448 .. installing alias unctrl_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,448 .. installing alias unget_wch_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,448 .. installing alias typeahead_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,452 .. installing alias ungetmouse_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,462 .. installing alias use_default_colors_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,470 .. installing alias use_legacy_coding_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,477 .. installing alias vid_puts_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,484 .. installing alias vidputs_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,542 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias erase.. installing alias erasewchar... installing alias has_ic.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,547 .. installing alias killchar.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,552 .. installing alias ungetch_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,552 .. installing alias ungetmouse_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,552 .. installing alias update_panels_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,552 .. installing alias use_default_colors_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,553 .. installing alias use_env_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,553 .. installing alias use_legacy_coding_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,553 .. installing alias vid_attr_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,553 .. installing alias vid_puts_sp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,553 .. installing alias longname.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,553 .. installing alias vidattr_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,553 .. installing alias vidputs_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,553 .. installing alias wunctrl_sp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,553 share/man/man3/curs_termattrs.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,554 .. installing alias baudrate.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,554 char.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,554 3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,554 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias erase.. installing alias erasewchar... installing alias has_ic.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,554 .. installing alias has_il.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,554 .. installing alias killchar.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,554 .. installing alias killwchar.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,554 .. installing alias longname.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,558 .. installing alias termattrs.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,613 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias BC.3x.. installing alias PC.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,619 .. installing alias ospeed.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,624 .. installing alias tgetflag.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,631 .. installing alias tgetstr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,636 .. installing alias tputs.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,656 .. installing alias term_attrs.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,657 .. installing alias termattrs.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,657 .. installing alias termname.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,657 share/man/man3/curs_termcap.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,679 share/man/man3/curs_terminfo.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,691 urterm.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,697 .. installing alias putp.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,703 .. installing alias set_curterm.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,709 .. installing alias setupterm.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,715 .. installing alias tigetnum.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,720 .. installing alias tiparm.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,730 .. installing alias tputs.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,738 .. installing alias vid_puts.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,744 .. installing alias vidputs.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,760 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias BC.3x.. installing alias PC.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,760 .. installing alias UP.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,760 .. installing alias ospeed.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,760 .. installing alias tgetent.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,761 .. installing alias tgetflag.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,761 .. installing alias tgetnum.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,761 .. installing alias tgetstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,761 .. installing alias tgoto.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,761 .. installing alias tputs.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,761 share/man/man3/curs_terminfo.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,761 urterm.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,761 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias del_c.. installing alias mvcur.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,761 .. installing alias putp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,761 .. installing alias restartterm.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,761 .. installing alias set_curterm.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,762 .. installing alias setterm.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,762 .. installing alias setupterm.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,762 .. installing alias tigetflag.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,762 .. installing alias tigetnum.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,762 .. installing alias tigetstr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,762 .. installing alias tiparm.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,762 .. installing alias tparm.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,762 .. installing alias tputs.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,762 .. installing alias vid_attr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,762 .. installing alias vid_puts.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,762 .. installing alias vidattr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,762 .. installing alias vidputs.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,789 share/man/man3/curs_threads.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,801 scdelay.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,803 y.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,810 .. installing alias use_screen.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,863 share/man/man3/curs_threads.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,863 scdelay.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,864 y.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,864 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias get_e.. installing alias set_escdela.. installing alias set_tabsize.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,864 .. installing alias use_screen.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,864 .. installing alias use_window.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,864 share/man/man3/curs_touch.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,864 netouched.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,868 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias is_li.. installing alias is_wintouch.. installing alias touchline.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,873 .. installing alias untouchwin.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,933 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias _nc_t.. installing alias _traceattr... installing alias _traceattr2.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,938 .. installing alias _tracecchar_t2.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,943 .. installing alias _tracechtype.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,949 .. installing alias _tracedump.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:30,954 .. installing alias _tracemouse.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,965 ed.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,965 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias is_li.. installing alias is_wintouch.. installing alias touchline.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,965 .. installing alias touchwin.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,965 .. installing alias untouchwin.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,965 .. installing alias wtouchln.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,965 share/man/man3/curs_trace.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,965 racebits.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,965 3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,965 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias _nc_t.. installing alias _traceattr... installing alias _traceattr2.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,965 .. installing alias _tracecchar_t.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,965 .. installing alias _tracecchar_t2.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,966 .. installing alias _tracechar.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,966 .. installing alias _tracechtype.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,966 .. installing alias _tracechtype2.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,966 .. installing alias _tracedump.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,966 .. installing alias _tracef.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,966 .. installing alias _tracemouse.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:30,966 .. installing alias trace.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,008 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias delay.. installing alias filter.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,013 .. installing alias getwin.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,017 .. installing alias keyname.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,022 .. installing alias putwin.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,027 .. installing alias use_env.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,033 .. installing alias wunctrl.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,067 share/man/man3/curs_util.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,067 _output.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,067 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias delay.. installing alias filter.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,067 .. installing alias flushinp.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,067 .. installing alias getwin.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,067 .. installing alias key_name.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,067 .. installing alias keyname.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,068 .. installing alias nofilter.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,068 .. installing alias putwin.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,068 .. installing alias unctrl.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,068 .. installing alias use_env.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,068 .. installing alias use_tioctl.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,068 .. installing alias wunctrl.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,070 share/man/man3/curs_variables.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,081 S.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,084 .3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,089 .. installing alias ESCDELAY.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,094 .. installing alias TABSIZE.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,100 .. installing alias newscr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,157 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias delwi.. installing alias derwin.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,163 .. installing alias mvderwin.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,168 .. installing alias newwin.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,173 share/man/man3/curs_variables.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,173 .. installing alias syncok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,173 S.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,173 .3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,174 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias COLOR.. installing alias COLOR_PAIRS.. installing alias COLS.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,174 .. installing alias ESCDELAY.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,174 .. installing alias LINES.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,174 .. installing alias TABSIZE.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,174 .. installing alias curscr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,174 .. installing alias newscr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,174 .. installing alias stdscr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,174 share/man/man3/curs_window.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,174 n.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,174 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias delwi.. installing alias derwin.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,175 .. installing alias dupwin.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,175 .. installing alias mvderwin.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,175 .. installing alias mvwin.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,175 .. installing alias newwin.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,175 .. installing alias subwin.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,175 .. installing alias syncok.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,179 .. installing alias wsyncdown.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,276 .. installing alias wcursyncup.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,276 .. installing alias wsyncdown.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,276 .. installing alias wsyncup.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,277 share/man/man3/default_colors.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,277 e_default_colors.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,277 _colors.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,277 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/define_key.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,367 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias assum.. installing alias use_defaultinstalling /galaxydir/galaxy/database/dinstalling /galaxydir/galaxy/database/dependenciinstalling /galaxydir/galaxy/database/dependencies/ncurses/6.. installing alias pos_form_cursor.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,380 es/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/form.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,380 .0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/form_cursor.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,381 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias assum.. installing alias use_defaultinstalling /galaxydir/galaxy/database/dinstalling /galaxydir/galaxy/database/dependenciinstalling /galaxydir/galaxy/database/dependencies/ncurses/6.. installing alias pos_form_cursor.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,399 share/man/man3/form_data.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,413 ahead.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,416 .3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,467 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/form_driver.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,483 share/man/man3/form_data.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,483 ahead.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,483 .3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,484 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/form_driver.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,518 es/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/form_field.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,537 .. installing alias form_fields.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,542 .. installing alias set_form_fields.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,576 share/man/man3/form_field_attributes.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,584 es/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/form_field.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,584 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias data_.. installing alias data_behindinstalling /galaxydir/galaxy/database/dinstalling /galaxydir/galaxy/database/dependenci.. installing alias field_count.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,584 .. installing alias form_fields.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,584 .. installing alias move_field.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,584 .. installing alias set_form_fields.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,584 share/man/man3/form_field_attributes.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,591 _back.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,594 3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,604 .. installing alias set_field_back.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,610 .. installing alias set_field_pad.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,652 share/man/man3/form_field_buffer.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,662 _buffer.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,665 s.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,670 install_environment.STDOUT DEBUG 2017-11-18 16:59:31,675 .. installing alias set_max_field.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,689 _back.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,689 3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,690 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias field.. installing alias field_fore... installing alias field_pad.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,690 .. installing alias set_field_back.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,690 .. installing alias set_field_fore.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,690 .. installing alias set_field_pad.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,690 share/man/man3/form_field_buffer.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,690 _buffer.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,690 s.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,709 share/man/man3/form_field_info.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,721 ic_field_info.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,724 3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,761 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/form_field_just.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,779 .. installing alias set_field_just.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,793 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias field.. installing alias field_statu.. installing alias set_field_buffer.3x.. installing alias set_field_status.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,793 .. installing alias set_max_field.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,793 share/man/man3/form_field_info.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,793 ic_field_info.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,793 3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,794 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/form_field_just.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,794 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias dynam.. installing alias field_info.installing /galaxydir/galaxy/database/d.. installing alias field_just.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,794 .. installing alias set_field_just.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,812 share/man/man3/form_field_new.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,824 ield.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,829 3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,836 .. installing alias new_field.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,871 share/man/man3/form_field_opts.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,883 _opts.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,886 off.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,895 .. installing alias set_field_opts.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,898 share/man/man3/form_field_new.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,899 ield.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,899 3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,899 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias dup_f.. installing alias free_field... installing alias link_field.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,899 .. installing alias new_field.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,899 share/man/man3/form_field_opts.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,899 _opts.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,899 off.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,899 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias field.. installing alias field_opts_.. installing alias field_opts_on.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:31,899 .. installing alias set_field_opts.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,934 share/man/man3/form_field_userptr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,945 _userptr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:31,951 serptr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,003 share/man/man3/form_field_userptr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,003 _userptr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,004 serptr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,004 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias field.. installing alias set_field_uinstalling /galaxydir/galaxy/database/d tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,004 .. installing alias field_arg.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,004 _type.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,073 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/form_field_validation.3x.. installing alias field.. installing alias set_field_tinstalling /galaxydir/galaxy/database/d.. installing alias link_fieldtype.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,080 .. installing alias set_fieldtype_arg.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,112 ype.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,113 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/form_fieldtype.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,113 .. installing alias free_fieldtype.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,113 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/form_field_validation.3x.. installing alias field.. installing alias set_field_tinstalling /galaxydir/galaxy/database/d.. installing alias link_fieldtype.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,113 .. installing alias new_fieldtype.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,113 .. installing alias set_fieldtype_arg.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,113 .. installing alias set_fieldtype_choice.3x 127.0.0.1 - - [18/Nov/2017:16:59:32 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:59:32,161 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias field.. installing alias field_term... installing alias form_init.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,167 .. installing alias set_field_init.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,172 .. installing alias set_form_init.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,215 share/man/man3/form_hook.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,215 _init.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,216 3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,216 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias field.. installing alias field_term... installing alias form_init.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,216 .. installing alias form_term.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,216 .. installing alias set_field_init.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,216 .. installing alias set_field_term.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,216 .. installing alias set_form_init.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,216 .. installing alias set_form_term.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,216 share/man/man3/form_new.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,269 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias free_.. installing alias new_form.3xinstalling /galaxydir/galaxy/database/d.. installing alias new_page.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,318 form.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,331 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias form_.. installing alias form_opts_o.. installing alias set_form_opts.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,364 share/man/man3/form_page.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,377 nt_field.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,379 .3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,387 x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,418 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/form_new_page.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,419 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias free_.. installing alias new_form.3xinstalling /galaxydir/galaxy/database/d.. installing alias new_page.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,419 .. installing alias set_new_page.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,419 share/man/man3/form_opts.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,419 opts_off.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,419 n.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,419 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias form_.. installing alias form_opts_o.. installing alias set_form_opts.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,419 share/man/man3/form_page.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,419 nt_field.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,419 .3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,420 x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,420 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias curre.. installing alias field_index.. installing alias set_current_field.3.. installing alias set_form_page.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,493 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias post_.. installing alias unpost_forminstalling /galaxydir/galaxy/database/d.. installing alias form_request_by_name.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,520 share/man/man3/form_post.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,521 form.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,521 .3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,521 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/form_requestname.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,521 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias post_.. installing alias unpost_forminstalling /galaxydir/galaxy/database/d.. installing alias form_request_by_name.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,521 .. installing alias form_request_name.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,581 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias set_finstalling /galaxydir/galaxy/dax install_environment.STDOUT DEBUG 2017-11-18 16:59:32,595 ALNUM.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,597 3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,603 .. installing alias TYPE_INTEGER.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,608 .. installing alias TYPE_NUMERIC.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,621 share/man/man3/form_userptr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,621 orm_userptr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,622 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias set_finstalling /galaxydir/galaxy/dax tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,622 ALNUM.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,622 3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,622 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/form_variables.3.. installing alias TYPE_.. installing alias TYPE_ALPHA... installing alias TYPE_ENUM.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,622 .. installing alias TYPE_INTEGER.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,622 .. installing alias TYPE_IPV4.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,622 .. installing alias TYPE_NUMERIC.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,622 .. installing alias TYPE_REGEXP.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,666 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias form_.. installing alias scale_form... installing alias set_form_sub.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,722 share/man/man3/form_win.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,723 sub.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,723 3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,723 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias form_.. installing alias scale_form... installing alias set_form_sub.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,723 .. installing alias set_form_win.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,723 share/man/man1/infocmp.1m install_environment.STDOUT DEBUG 2017-11-18 16:59:32,769 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/installing /galaxydir/gal1m tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,825 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/installing /galaxydir/gal1m tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,825 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man1/infotocap.installing /galaxydir/gald.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:32,870 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/key_defineinstalling /galaxydir/galx install_environment.STDOUT DEBUG 2017-11-18 16:59:32,915 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/keyok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,929 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/key_defineinstalling /galaxydir/galx tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:32,929 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/keyok.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,030 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/keybound.3installing /galaxydir/galinstalling /galaxydir/galaxy/da tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,030 egacy_coding.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,030 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/menu.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,068 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/legacy_coding.3x.. installing alias use_linstalling /galaxydir/galaxy/dainstalling /galaxydir/galaxy/database/d.. installing alias menu_back.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,074 .. installing alias menu_grey.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,080 .. installing alias set_menu_back.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,087 .. installing alias set_menu_grey.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,134 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/menu_attributes.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,134 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/legacy_coding.3x.. installing alias use_linstalling /galaxydir/galaxy/dainstalling /galaxydir/galaxy/database/d.. installing alias menu_back.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,134 .. installing alias menu_fore.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,135 .. installing alias menu_grey.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,135 .. installing alias menu_pad.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,135 .. installing alias set_menu_back.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,136 .. installing alias set_menu_fore.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,136 .. installing alias set_menu_grey.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,136 .. installing alias set_menu_pad.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,136 share/man/man3/menu_cursor.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,137 enu_cursor.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,225 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias pos_minstalling /galaxydir/galaxy/dainstalling /galaxydir/galaxy/database/d.. installing alias set_menu_format.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,237 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/menu_driver.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,238 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/menu_format.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,238 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias pos_minstalling /galaxydir/galaxy/dainstalling /galaxydir/galaxy/database/d.. installing alias set_menu_format.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,254 share/man/man3/menu_hook.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,267 init.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,270 x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,279 .. installing alias menu_term.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,284 .. installing alias set_item_term.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,291 .. installing alias set_menu_term.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,323 share/man/man3/menu_items.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,340 share/man/man3/menu_hook.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,341 init.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,341 x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,341 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias item_.. installing alias item_term.3.. installing alias menu_init.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,341 .. installing alias menu_term.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,341 .. installing alias set_item_init.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,341 .. installing alias set_item_term.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,341 count.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,341 .. installing alias set_menu_init.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,342 .. installing alias set_menu_term.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,342 share/man/man3/menu_items.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,349 ems.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,380 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/menu_mark.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,442 count.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,442 ems.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,442 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/menu_mark.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,442 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias item_.. installing alias set_menu_itinstalling /galaxydir/galaxy/database/d.. installing alias set_menu_mark.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,442 share/man/man3/menu_new.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,442 menu.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,488 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias free_.. installing alias new_menu.3xinstalling /galaxydir/galaxy/database/d.. installing alias menu_opts_off.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,495 .. installing alias set_menu_opts.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,549 share/man/man3/menu_pattern.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,549 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/menu_opts.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,549 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias free_.. installing alias new_menu.3xinstalling /galaxydir/galaxy/database/d.. installing alias menu_opts_off.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,549 .. installing alias menu_opts_on.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,550 .. installing alias set_menu_opts.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,550 share/man/man3/menu_pattern.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,563 enu_pattern.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,651 enu_pattern.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,651 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias set_mshare/man/man3/menu_post.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,651 menu.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,651 .3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,668 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias post_.. installing alias unpost_menuinstalling /galaxydir/galaxy/database/d.. installing alias menu_request_by_name.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,746 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/installing /galaxydir/galtr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,752 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/menu_requestname.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,752 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias post_.. installing alias unpost_menuinstalling /galaxydir/galaxy/database/d.. installing alias menu_request_by_name.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,752 .. installing alias menu_request_name.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,752 share/man/man3/menu_spacing.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,752 .. installing alias set_menu_spacing.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,753 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/installing /galaxydir/galtr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,760 enu_userptr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,792 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/menu_win.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,810 .. installing alias scale_menu.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,816 .. installing alias set_menu_win.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,853 enu_userptr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,853 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/menu_win.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,853 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/menu_userp.. installing alias set_minstalling /galaxydir/galaxy/da.. installing alias menu_sub.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,854 .. installing alias scale_menu.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,854 .. installing alias set_menu_sub.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,854 .. installing alias set_menu_win.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,858 share/man/man3/mitem_current.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,870 nt_item.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,872 3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,877 install_environment.STDOUT DEBUG 2017-11-18 16:59:33,882 .. installing alias top_row.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,916 share/man/man3/mitem_name.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,926 description.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,929 x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,957 share/man/man3/mitem_current.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,958 nt_item.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:33,958 3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,963 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/mitem_new.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:33,985 .. installing alias new_item.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,026 share/man/man3/mitem_opts.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,037 opts.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,040 ff.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,047 .. installing alias set_item_opts.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,060 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias curre.. installing alias item_index... installing alias set_current_item.3x.. installing alias set_top_row.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,060 .. installing alias top_row.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,062 share/man/man3/mitem_name.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,062 description.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,063 x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,063 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/mitem_new.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,063 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias item_.. installing alias item_name.3installing /galaxydir/galaxy/database/d.. installing alias free_item.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,063 .. installing alias new_item.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,063 share/man/man3/mitem_opts.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,063 opts.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,063 ff.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,063 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias item_.. installing alias item_opts_o.. installing alias item_opts_on.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,063 .. installing alias set_item_opts.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,079 share/man/man3/mitem_userptr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,090 userptr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,096 erptr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,131 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/mitem_value.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,150 .. installing alias set_item_value.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,168 share/man/man3/mitem_userptr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,168 userptr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,168 erptr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,168 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/mitem_value.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,168 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias item_.. installing alias set_item_usinstalling /galaxydir/galaxy/database/d.. installing alias item_value.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,168 .. installing alias set_item_value.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,183 share/man/man3/mitem_visible.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,196 visible.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,265 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/ncurses.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,268 share/man/man3/mitem_visible.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,269 visible.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,269 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/ncurses.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,369 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias item_installing /galaxydir/galaxy/da.. installing alias curses.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,369 share/man/man1/ncurses6-config.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,369 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/panel.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,382 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/installing /galaxydir/gal.. installing alias bottom_pane.. installing alias del_panel.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,390 .. installing alias move_panel.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,399 .. installing alias panel_above.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,404 .. installing alias panel_hidden.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,411 .. installing alias panel_window.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,418 .. installing alias set_panel_userptr.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,424 .. installing alias top_panel.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,470 l.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,471 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/installing /galaxydir/gal.. installing alias bottom_pane.. installing alias del_panel.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,471 .. installing alias hide_panel.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,471 .. installing alias move_panel.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,471 .. installing alias new_panel.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,471 .. installing alias panel_above.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,471 .. installing alias panel_below.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,472 .. installing alias panel_hidden.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,472 .. installing alias panel_userptr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,472 .. installing alias panel_window.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,472 .. installing alias replace_panel.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,472 .. installing alias set_panel_userptr.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,473 .. installing alias show_panel.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,473 .. installing alias top_panel.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,473 .. installing alias update_panels.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,473 share/man/man3/resizeterm.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,575 rm_resized.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,575 .3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,575 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man1/tabs.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,575 es/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man5/term.5 install_environment.STDOUT DEBUG 2017-11-18 16:59:34,667 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias is_te.. installing alias resize_terminstalling /galaxydir/galaxy/database/dinstalling /galaxydir/galaxy/database/dependenciinstalling /galaxydir/galaxy/database/dependencies/ncurses/6share/man/man3/term_variables.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,677 .0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man7/term.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,677 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias is_te.. installing alias resize_terminstalling /galaxydir/galaxy/database/dinstalling /galaxydir/galaxy/database/dependenciinstalling /galaxydir/galaxy/database/dependencies/ncurses/6share/man/man3/term_variables.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,680 install_environment.STDOUT DEBUG 2017-11-18 16:59:34,685 .. installing alias boolcodes.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,690 .. installing alias boolnames.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,695 .. installing alias numcodes.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,700 .. installing alias numnames.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,708 .. installing alias strfnames.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,713 .. installing alias ttytype.3x install_environment.STDOUT DEBUG 2017-11-18 16:59:34,815 share/man/man5/terminfo.5 install_environment.STDOUT DEBUG 2017-11-18 16:59:34,875 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man1/tic.1m tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,882 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias SP.3x.. installing alias acs_map.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,883 .. installing alias boolcodes.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,883 .. installing alias boolfnames.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,883 .. installing alias boolnames.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,883 .. installing alias cur_term.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,883 .. installing alias numcodes.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,883 .. installing alias numfnames.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,883 .. installing alias numnames.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,883 .. installing alias strcodes.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,883 .. installing alias strfnames.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,883 .. installing alias strnames.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,883 .. installing alias ttytype.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,884 share/man/man5/terminfo.5 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,884 axy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man1/tic.1m install_environment.STDOUT DEBUG 2017-11-18 16:59:34,930 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man1/toe.1m tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:34,986 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man1/toe.1m install_environment.STDOUT DEBUG 2017-11-18 16:59:34,987 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man1/tput.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:35,088 ependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man1/tput.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:35,088 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/installing /galaxydir/galinstalling /galaxydir/galaxy/dainstalling /galaxydir/galaxy/database/d.. installing alias reset.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:35,089 share/man/man1/tset.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:35,089 .1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:35,190 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/man/man3/wresize.3x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:35,191 dLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/ncurses/6.0/i tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:35,191 /iuc/package_ncurses_6_0/0efde9889efd/include/ncurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:35,191 iuc/package_ncurses_6_0/0efde9889efd/include/ncurses 127.0.0.1 - - [18/Nov/2017:16:59:35 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:59:35,314 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias resetinstalling /galaxydir/galaxy/dacd include && /Library/Developer/Commanuc/package_ncurses_6_0/0efde9889efd/lib" installmkdir -p /galaxydir/galaxy/database/dependencies/ncurses/6.0installing curses.h in /galaxydir/galaxy/database/dependencies/ncurses/6.0/efde9889efd/include/ncurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:35,394 installing /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/.. installing alias resetinstalling /galaxydir/galaxy/dacd include && /Library/Developer/Commanuc/package_ncurses_6_0/0efde9889efd/lib" installmkdir -p /galaxydir/galaxy/database/dependencies/ncurses/6.0installing curses.h in /galaxydir/galaxy/database/dependencies/ncurses/6.0/efde9889efd/include/ncurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:35,499 installing unctrl.h in /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0installing ncurses_dll.h ncurses install_environment.STDOUT DEBUG 2017-11-18 16:59:35,535 in /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/installing term.h in /gal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:35,603 in /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/installing term.h in /gal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:35,708 axydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses0efde9889efd/include/ncurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:35,808 installing ./tic.h in /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0es install_environment.STDOUT DEBUG 2017-11-18 16:59:35,891 installing termcap.h in /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/fde9889efd/include/ncurseinstalling ./term_entry.h in /ges tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:35,913 installing termcap.h in /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/fde9889efd/include/ncurseinstalling ./term_entry.h in /ges tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,016 alaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncursinstalling ./nc_tparm.h icurses install_environment.STDOUT DEBUG 2017-11-18 16:59:36,178 n /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncd ncurses && /Library/De/ncurses/6.0/iuc/package_ncursenstall install_environment.STDOUT DEBUG 2017-11-18 16:59:36,215 base/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,220 n /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncd ncurses && /Library/De/ncurses/6.0/iuc/package_ncursenstall tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,220 base/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib install_environment.STDOUT DEBUG 2017-11-18 16:59:36,240 ndencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libncurses.6.dylib install_environment.STDOUT DEBUG 2017-11-18 16:59:36,240 -single=1200 -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/packadatabase/dependencies/ncuatibility_version 6 -current_ve89efd/lib/libncurses.6.dylib ../obj_s/hbj_s/lib_box.o ../obj_s/lib_chgat.o ../obj_s/libj_s/lib_delwin.o ../obj_s/lib_echo.o ../obj_s/lib_endwin.o .nitscr.o ../obj_s/lib_insch.o ../obj_s/lib_insdel.o ../obj_s/lib_insnstr.o rlay.o ../obj_s/lib_pad.o ../obj_s/lib_printw.o ../obj_s/lib_redrawln.o ../obj_s/lib_refresh.oib_slkattr.o ../obj_s/lib_slkclear.o ../obj_s/lib_slkcolor.o ../obj_s/lib_slkinit.o ../obj_s/lib_slklab.o ../obj_s/lib../obj_s/lib_freeall.o ../obj_s/expanded.o ../obj_s/legacy_coding.o ../obj_s/lib_dft_fgbg.o ../obj_s/lib_print.o ../obj_s/resizeterm.o ../obj_s/usedata.o ../obj_s/lib_has_cap.o ../obj_s/lib_kernel.o ../obj_s/lib_keyname.o ../obj_s/lib_longname.o ../obj_s/lib_napms.o ../obj_s/lib_options.o ../obj_s/lib_raw.o ../obj_s/lib_setup.o .e_key.o ../obj_s/hashed_db.o ../obj_s/key_defined.o ../obj_s/keybound.o ../obj_s/keyok.o ../obj_s/version.o -L../lib -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,322 ndencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libncurses.6.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,322 -single=1200 -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/packadatabase/dependencies/ncuatibility_version 6 -current_ve89efd/lib/libncurses.6.dylib ../obj_s/hbj_s/lib_box.o ../obj_s/lib_chgat.o ../obj_s/libj_s/lib_delwin.o ../obj_s/lib_echo.o ../obj_s/lib_endwin.o .nitscr.o ../obj_s/lib_insch.o ../obj_s/lib_insdel.o ../obj_s/lib_insnstr.o rlay.o ../obj_s/lib_pad.o ../obj_s/lib_printw.o ../obj_s/lib_redrawln.o ../obj_s/lib_refresh.oib_slkattr.o ../obj_s/lib_slkclear.o ../obj_s/lib_slkcolor.o ../obj_s/lib_slkinit.o ../obj_s/lib_slklab.o ../obj_s/lib../obj_s/lib_freeall.o ../obj_s/expanded.o ../obj_s/legacy_coding.o ../obj_s/lib_dft_fgbg.o ../obj_s/lib_print.o ../obj_s/resizeterm.o ../obj_s/usedata.o ../obj_s/lib_has_cap.o ../obj_s/lib_kernel.o ../obj_s/lib_keyname.o ../obj_s/lib_longname.o ../obj_s/lib_napms.o ../obj_s/lib_options.o ../obj_s/lib_raw.o ../obj_s/lib_setup.o .e_key.o ../obj_s/hashed_db.o ../obj_s/key_defined.o ../obj_s/keybound.o ../obj_s/keyok.o ../obj_s/version.o -L../lib -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,322 veloper/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependenciess_6_0/0efde9889efd/lib" imkdir -p /galaxydir/galaxy/datalinking /galaxydir/galaxy/database/depegcc -O2 -no-cpp-precomp --param max-inline-insnsge_ncurses_6_0/0efde9889efd/lib/`basename /galaxydir/galaxy/rses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libncurses.6.dylib` -comprsion 6 -o /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde98ardscroll.o ../obj_s/hashmap.o ../obj_s/lib_addch.o ../obj_s/lib_addstr.o ../obj_s/lib_beep.o ../obj_s/lib_bkgd.o ../o_clear.o ../obj_s/lib_clearok.o ../obj_s/lib_clrbot.o ../obj_s/lib_clreol.o ../obj_s/lib_color.o ../obj_s/lib_colorset.o ../obj_s/lib_delch.o ../ob./obj_s/lib_erase.o ../obj_s/lib_flash.o ../obj_s/lib_gen.o ../obj_s/lib_getch.o ../obj_s/lib_getstr.o ../obj_s/lib_hline.o ../obj_s/lib_immedok.o ../obj_s/lib_inchstr.o ../obj_s/lib_i../obj_s/lib_instr.o ../obj_s/lib_isendwin.o ../obj_s/lib_leaveok.o ../obj_s/lib_mouse.o ../obj_s/lib_move.o ../obj_s/lib_mvcur.o ../obj_s/lib_mvwin.o ../obj_s/lib_newterm.o ../obj_s/lib_newwin.o ../obj_s/lib_nl.o ../obj_s/lib_ove ../obj_s/lib_restart.o ../obj_s/lib_scanw.o ../obj_s/lib_screen.o ../obj_s/lib_scroll.o ../obj_s/lib_scrollok.o ../obj_s/lib_scrreg.o ../obj_s/lib_set_term.o ../obj_s/lib_slk.o ../obj_s/lib_slkatr_set.o ../obj_s/lib_slkatrof.o ../obj_s/lib_slkatron.o ../obj_s/lib_slkatrset.o ../obj_s/l_slkrefr.o ../obj_s/lib_slkset.o ../obj_s/lib_slktouch.o ../obj_s/lib_touch.o ../obj_s/lib_tstp.o ../obj_s/lib_ungetch.o ../obj_s/lib_vidattr.o ../obj_s/lib_vline.o ../obj_s/lib_wattroff.o ../obj_s/lib_wattron.o ../obj_s/lib_winch.o ../obj_s/lib_window.o ../obj_s/nc_panel.o ../obj_s/safe_sprintf.o ../obj_s/tty_update.o ../obj_s/varargs.o ../obj_s/vsscanf.o _screen.o ../obj_s/use_window.o ../obj_s/wresize.o ../obj_s/access.o ../obj_s/add_tries.o ../obj_s/alloc_ttype.o ../obj_s/codes.o ../obj_s/comp_captab.o ../obj_s/comp_error.o ../obj_s/comp_hash.o ../obj_s/db_iterator.o ../obj_s/doalloc.o ../obj_s/entries.o ../obj_s/fallback.o ../obj_s/free_ttype.o ../obj_s/getenv_num.o ../obj_s/home_terminfo.o ../obj_s/init_keytry.o ../obj_s/lib_acs.o ../obj_s/lib_baudrate.o ../obj_s/lib_cur_term.o ../obj_s/lib_./obj_s/lib_termcap.o ../obj_s/lib_termname.o ../obj_s/lib_tgoto.o ../obj_s/lib_ti.o ../obj_s/lib_tparm.o ../obj_s/lib_tputs.o ../obj_s/lib_trace.o ../obj_s/lib_ttyflags.o ../obj_s/lib_twait.o ../obj_s/name_match.o ../obj_s/names.o ../obj_s/obsolete.o ../obj_s/read_entry.o ../obj_s/read_termcap.o ../obj_s/strings.o ../obj_s/tries.o ../obj_s/trim_sgr0.o ../obj_s/unctrl.o ../obj_s/visbuf.o ../obj_s/alloc_entry.o ../obj_s/captoinfo.o ../obj_s/comp_expand.o ../obj_s/comp_parse.o ../obj_s/comp_scan.o ../obj_s/parse_entry.o ../obj_s/write_entry.o ../obj_s/defincd /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib && (ln -s -f libncurses.6.dylib libncurses.dylib; ) install_environment.STDOUT DEBUG 2017-11-18 16:59:36,340 installing ../lib/libncurses.a as /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_nc/usr/bin/install -c -m 64fde9889efd/lib/libncurses.a install_environment.STDOUT DEBUG 2017-11-18 16:59:36,346 database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libncurses.a install_environment.STDOUT DEBUG 2017-11-18 16:59:36,399 a as /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/li/usr/bin/install -c -m 640efde9889efd/lib/libncurses_g.aranlib /galaxydir/galaxy/database/depencd progs && /Library/Developer/CommandLineTools/ncurses_6_0/0efde9889efd/lib" install install_environment.STDOUT DEBUG 2017-11-18 16:59:36,412 y/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin install_environment.STDOUT DEBUG 2017-11-18 16:59:36,419 laxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin/`echo tic|$//'` tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,427 urses_6_0/0efde9889efd/lib/libncurses.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,427 installing ../lib/libncurses.a as /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_nc/usr/bin/install -c -m 64fde9889efd/lib/libncurses.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,427 database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libncurses.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,427 4 ../lib/libncurses.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0eranlib /galaxydir/galaxy/installing ../lib/libncurses_g.bncurses_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,427 4 ../lib/libncurses_g.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,427 dencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libncurses_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,427 a as /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/li/usr/bin/install -c -m 640efde9889efd/lib/libncurses_g.aranlib /galaxydir/galaxy/database/depencd progs && /Library/Developer/CommandLineTools/ncurses_6_0/0efde9889efd/lib" install tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,427 y/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,427 laxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin/`echo tic|$//'` install_environment.STDOUT DEBUG 2017-11-18 16:59:36,487 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin/`echo toe| sed 's/$//linking infotocap to tic tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,529 usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_mkdir -p /galaxydir/galax/usr/bin/install -c tic /ga sed 's/$//'|sed 's,x,x,'|sed 's//usr/bin/install -c toe /galaxydir/galaxy/da'|sed 's,x,x,'|sed 's/$//'` tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,529 tabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin/`echo toe| sed 's/$//linking infotocap to tic tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,529 (cd /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin && x,x,'|sed 's/$//'`) install_environment.STDOUT DEBUG 2017-11-18 16:59:36,536 ln -s -f `echo tic| sed 's/$//'|sed 's,x,x,'|sed 's/$//'` `echo infotocap| sed 's/$//'|sed 's,linking captoinfo to tic install_environment.STDOUT DEBUG 2017-11-18 16:59:36,574 ln -s -f `echo tic| sed 's/$//'|sed 's,x,x,'|sed 's/$//'` `echo captoinfo| sed 's/$//'|sed 's,/usr/bin/install -c infoco infocmp| sed 's/$//'|sed 's/usr/bin/install -c clear /galaxydir/ed 's/$//'|sed 's,x,x,'|sed 's/$//'` install_environment.STDOUT DEBUG 2017-11-18 16:59:36,589 /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin/`ech,x,x,'|sed 's/$//'` tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,631 ln -s -f `echo tic| sed 's/$//'|sed 's,x,x,'|sed 's/$//'` `echo infotocap| sed 's/$//'|sed 's,linking captoinfo to tic tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,632 (cd /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin && x,x,'|sed 's/$//'`) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,632 mp /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin/`ech,x,x,'|sed 's/$//'` tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,632 ln -s -f `echo tic| sed 's/$//'|sed 's,x,x,'|sed 's/$//'` `echo captoinfo| sed 's/$//'|sed 's,/usr/bin/install -c infoco infocmp| sed 's/$//'|sed 's/usr/bin/install -c clear /galaxydir/ed 's/$//'|sed 's,x,x,'|sed 's/$//'` tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,632 /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin/`ech,x,x,'|sed 's/$//'` tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,633 galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin/`echo clear| s/usr/bin/install -c tabs o tabs| sed 's/$//'|sed 's/usr/bin/install -c tput /galaxydir/ed 's/$//'|sed 's,x,x,'|sed 's/$//'` tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,633 /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin/`echo tset| sed 's/$//'|sed 's,x,x,'|sed 's/$//'` install_environment.STDOUT DEBUG 2017-11-18 16:59:36,656 galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin/`echo tput| s/usr/bin/install -c tset (cd /galaxydir/galaxy/database/s/$//'|sed 's,x,x,'|sed 's/$//'` `echo d 's,x,x,'|sed 's/$//'`) install_environment.STDOUT DEBUG 2017-11-18 16:59:36,688 CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/ncursesgcc -O2 -no-cpp-precomp -s/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/`basename ../lib/libpanel.6.dylib` -compatibility_version 6 -current_version 6 -o ../lib/libpanel.6.dylib ../obj_s/panel.o ../obj_s/p_above.o ../obj_s/p_below.o ../obj_s/p_bottom.o ../obj_s/p_delete.o ../obj_s/p_hide.o ../obj_s/p_hidden.o ../obj_s/p_move.o ../obj_s/p_new.o ../obj_s/p_replace.o ../obj_s/p_show.o ../obj_s/p_top.o ../obj_s/p_update.o ../obj_s/p_user.o ../obj_s/p_win.o -L../lib -lncurses -Wl,-search_paths_first install_environment.STDOUT DEBUG 2017-11-18 16:59:36,722 bpanel.6.dylib libpanel.dylib; ) install_environment.STDOUT DEBUG 2017-11-18 16:59:36,732 ase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libpanel.6.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,734 linking reset to tset tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,734 galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin/`echo tput| s/usr/bin/install -c tset (cd /galaxydir/galaxy/database/s/$//'|sed 's,x,x,'|sed 's/$//'` `echo d 's,x,x,'|sed 's/$//'`) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,734 dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin && ln -s -f `echo tset| sed 'reset| sed 's/$//'|secd panel && /Library/Developer//6.0/iuc/package_ncurses_6_0/0efde9889efd/lib" install tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,734 linking ../lib/libpanel.6.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,734 CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/ncursesgcc -O2 -no-cpp-precomp -s/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/`basename ../lib/libpanel.6.dylib` -compatibility_version 6 -current_version 6 -o ../lib/libpanel.6.dylib ../obj_s/panel.o ../obj_s/p_above.o ../obj_s/p_below.o ../obj_s/p_bottom.o ../obj_s/p_delete.o ../obj_s/p_hide.o ../obj_s/p_hidden.o ../obj_s/p_move.o ../obj_s/p_new.o ../obj_s/p_replace.o ../obj_s/p_show.o ../obj_s/p_top.o ../obj_s/p_update.o ../obj_s/p_user.o ../obj_s/p_win.o -L../lib -lncurses -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,734 bpanel.6.dylib libpanel.dylib; ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,735 ase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libpanel.6.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,735 -param max-inline-insns-single=1200 -dynamiclib -install_name /galaxydir/galaxy/database/dependenciecd ../lib && (ln -s -f lilinking /galaxydir/galaxy/databgcc -O2 -no-cpp-precomp --param max-inliuc/package_ncurses_6_0/0efde9889efd/lib/`basenabase/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9ompatibility_version 6 -current_version 6 -o /galaxydir/galaxy/database/depes_6_0/0efde9889efd/lib/libpanel.6.dylib ../obj_s/panel.o ../obj_s/p_above.o ../obj_s/p_below._s/p_hide.o ../obj_s/p_hidden.o ../obj_s/p_move.o ../obj_s/p_new.o ../obj_s/p_replace.o ../obj_s/p_show.o ../obj_s/p_t-L../lib -lncurses -Wl,-search_paths_first install_environment.STDOUT DEBUG 2017-11-18 16:59:36,788 ine-insns-single=1200 -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/ncurses/6.0/me /galaxydir/galaxy/data889efd/lib/libpanel.6.dylib` -cendencies/ncurses/6.0/iuc/package_ncurso ../obj_s/p_bottom.o ../obj_s/p_delete.o ../objop.o ../obj_s/p_update.o ../obj_s/p_user.o ../obj_s/p_win.o cd /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_installing ../lib/libpanel.a as /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/packag/usr/bin/install -c -m 644 ../lib/libpanel.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6ranlib /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libpanel.a install_environment.STDOUT DEBUG 2017-11-18 16:59:36,797 urses_6_0/0efde9889efd/lib/libpanel_g.a install_environment.STDOUT DEBUG 2017-11-18 16:59:36,797 4 ../lib/libpanel_g.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libpanel_g.a install_environment.STDOUT DEBUG 2017-11-18 16:59:36,826 ranlib /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/installing ./panel.h in /ses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,838 6_0/0efde9889efd/lib && (ln -s -f libpanel.6.dylib libpanel.dylib; ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,838 e_ncurses_6_0/0efde9889efd/lib/libpanel.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,839 _0/0efde9889efd/lib/libpanel.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,839 ine-insns-single=1200 -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/ncurses/6.0/me /galaxydir/galaxy/data889efd/lib/libpanel.6.dylib` -cendencies/ncurses/6.0/iuc/package_ncurso ../obj_s/p_bottom.o ../obj_s/p_delete.o ../objop.o ../obj_s/p_update.o ../obj_s/p_user.o ../obj_s/p_win.o cd /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_installing ../lib/libpanel.a as /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/packag/usr/bin/install -c -m 644 ../lib/libpanel.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6ranlib /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libpanel.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,842 urses_6_0/0efde9889efd/lib/libpanel_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,842 4 ../lib/libpanel_g.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libpanel_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,843 installing ../lib/libpanel_g.a as /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_nc/usr/bin/install -c -m 64libpanel_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,843 ranlib /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/installing ./panel.h in /ses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,843 /Library/Developer/CommandLineTools/usr/bin/ranlib: file: /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libpanel.a(panel.o) has no symbols tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:36,944 galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurcd menu && /Library/Develurses/6.0/iuc/package_ncurses_6all install_environment.STDOUT DEBUG 2017-11-18 16:59:36,949 oper/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/nc_0/0efde9889efd/lib" instlinking ../lib/libmenu.6.dylib install_environment.STDOUT DEBUG 2017-11-18 16:59:36,949 laxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/`basename ../lib/libity_version 6 -current_veib ../obj_s/m_attribs.o ../obj__s/m_format.o ../obj_s/m_global.o ../obem_nam.o ../obj_s/m_item_new.o ../obj_s/m_item_oitem_val.o ../obj_s/m_item_vis.o ../obj_s/m_items.o ../obj_s_post.o ../obj_s/m_req_name.o ../obj_s/m_scale.o ../obj_s/m_spacing.o ../ob install_environment.STDOUT DEBUG 2017-11-18 16:59:36,999 linking /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/libgcc -O2 -no-cpp-precomp -s/ncurses/6.0/iuc/package_ncursbasename /galaxydir/galaxy/database/depge_ncurses_6_0/0efde9889efd/lib/libmenu.6.dylib`ion 6 -o /galaxydir/galaxy/database/dependencies/ncurses/6.0u.6.dylib ../obj_s/m_attribs.o ../obj_s/m_cursor.o ../obj_s/m_driver.o ../o_s/m_item_cur.o ../obj_s/m_item_nam.o ../obj_s/m_item_new.o ../obj_s/m_item_opt.o ../obj_s/m_i ../obj_s/m_items.o ../obj_s/m_new.o ../obj_s/m_opts.o ../obj_s/m_pad.o ../obj_s/m_pattern.o ../obj_s/m_post.o ../obj_./obj_s/m_win.o -L../lib -lncurses -Wl,-search_paths_first install_environment.STDOUT DEBUG 2017-11-18 16:59:37,036 .dylib libmenu.dylib; ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,046 oper/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/nc_0/0efde9889efd/lib" instlinking ../lib/libmenu.6.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,046 laxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/`basename ../lib/libity_version 6 -current_veib ../obj_s/m_attribs.o ../obj__s/m_format.o ../obj_s/m_global.o ../obem_nam.o ../obj_s/m_item_new.o ../obj_s/m_item_oitem_val.o ../obj_s/m_item_vis.o ../obj_s/m_items.o ../obj_s_post.o ../obj_s/m_req_name.o ../obj_s/m_scale.o ../obj_s/m_spacing.o ../ob tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,046 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamiclib -install_name /galaxydir/gamenu.6.dylib` -compatibilrsion 6 -o ../lib/libmenu.6.dyls/m_cursor.o ../obj_s/m_driver.o ../objj_s/m_hook.o ../obj_s/m_item_cur.o ../obj_s/m_itpt.o ../obj_s/m_item_top.o ../obj_s/m_item_use.o ../obj_s/m_/m_new.o ../obj_s/m_opts.o ../obj_s/m_pad.o ../obj_s/m_pattern.o ../obj_s/mj_s/m_sub.o ../obj_s/m_userptr.o ../obj_s/m_win.o -L../lib -lncurses -Wl,-search_paths_first cd ../lib && (ln -s -f libmenu.6.dylib libmenu.dylib; ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,047 /libmenu.6.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,047 linking /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/libgcc -O2 -no-cpp-precomp -s/ncurses/6.0/iuc/package_ncursbasename /galaxydir/galaxy/database/depge_ncurses_6_0/0efde9889efd/lib/libmenu.6.dylib`ion 6 -o /galaxydir/galaxy/database/dependencies/ncurses/6.0u.6.dylib ../obj_s/m_attribs.o ../obj_s/m_cursor.o ../obj_s/m_driver.o ../o_s/m_item_cur.o ../obj_s/m_item_nam.o ../obj_s/m_item_new.o ../obj_s/m_item_opt.o ../obj_s/m_i ../obj_s/m_items.o ../obj_s/m_new.o ../obj_s/m_opts.o ../obj_s/m_pad.o ../obj_s/m_pattern.o ../obj_s/m_post.o ../obj_./obj_s/m_win.o -L../lib -lncurses -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,047 .dylib libmenu.dylib; ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,047 -param max-inline-insns-single=1200 -dynamiclib -install_name /galaxydir/galaxy/database/dependenciees_6_0/0efde9889efd/lib/`endencies/ncurses/6.0/iuc/packa -compatibility_version 6 -current_vers/iuc/package_ncurses_6_0/0efde9889efd/lib/libmenbj_s/m_format.o ../obj_s/m_global.o ../obj_s/m_hook.o ../objtem_top.o ../obj_s/m_item_use.o ../obj_s/m_item_val.o ../obj_s/m_item_vis.os/m_req_name.o ../obj_s/m_scale.o ../obj_s/m_spacing.o ../obj_s/m_sub.o ../obj_s/m_userptr.o .cd /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib && (ln -s -f libmenu.6installing ../lib/libmenu.a as /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libmenu.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,048 package_ncurses_6_0/0efde9889efd/lib/libmenu.a install_environment.STDOUT DEBUG 2017-11-18 16:59:37,064 /usr/bin/install -c -m 644 ../lib/libmenu.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/ranlib /galaxydir/galaxy/installing ../lib/libmenu_g.a anu_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,149 database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libmenu.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,149 /usr/bin/install -c -m 644 ../lib/libmenu.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/ranlib /galaxydir/galaxy/installing ../lib/libmenu_g.a anu_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,149 s /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libme/usr/bin/install -c -m 64de9889efd/lib/libmenu_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,149 database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libmenu_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,149 r/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,249 y/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses install_environment.STDOUT DEBUG 2017-11-18 16:59:37,320 4 ../lib/libmenu_g.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efranlib /galaxydir/galaxy/installing ./eti.h in /galaxydiinstalling ./menu.h in /galaxydir/galaxcd form && /Library/Developer/CommandLineTools/ucurses_6_0/0efde9889efd/lib" install install_environment.STDOUT DEBUG 2017-11-18 16:59:37,332 dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,350 4 ../lib/libmenu_g.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efranlib /galaxydir/galaxy/installing ./eti.h in /galaxydiinstalling ./menu.h in /galaxydir/galaxcd form && /Library/Developer/CommandLineTools/ucurses_6_0/0efde9889efd/lib" install tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,351 dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,351 sr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_nlinking ../lib/libform.6.gcc -O2 -no-cpp-precomp --parammax.o ../obj_s/fld_move.o ../obj_s/fld_newftyp.o ../obj_s/fld_opts.o ../obj_s/fld_pad.o ../obj_s/fld_page.o ../obj_s/fld_stat.o ../obj_s/fld_type.o ../obj_s/fld_user.o ../obj_s/frm_cursor.o ../obj_s/frm_data.o ../obj_s/frm_def.o ../obj_s/frm_driver.o ../obj_s/frm_hook.o ../obj_s/frm_opts.o ../obj_s/frm_page.o ../obj_s/frm_post.o ../obj_s/frm_req_name.o ../obj_s/frm_scale.o ../obj_s/frm_sub.o ../obj_s/frm_user.o ../obj_s/frm_win.o ../obj_s/fty_alnum.o ../obj_s/fty_alpha.o ../obj_s/fty_enum.o ../obj_s/fty_generic.o ../obj_s/fty_int.o ../obj_s/fty_ipv4.o ../obj_s/fty_num.o ../obj_s/fty_regex.o -L../lib -lncurses -Wl,-search_paths_first install_environment.STDOUT DEBUG 2017-11-18 16:59:37,388 max-inline-insns-single=1200 -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/`basename ../lib/libform.6.dylib` -compatibility_version 6 -current_version 6 -o ../lib/libform.6.dylib ../obj_s/fld_arg.o ../obj_s/fld_attr.o ../obj_s/fld_current.o ../obj_s/fld_def.o ../obj_s/fld_dup.o ../obj_s/fld_ftchoice.o ../obj_s/fld_ftlink.o ../obj_s/fld_info.o ../obj_s/fld_just.o ../obj_s/fld_link.o ../obj_s/fld_linking /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libform.6.dylib install_environment.STDOUT DEBUG 2017-11-18 16:59:37,430 laxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/`basename /galaxydircies/ncurses/6.0/iuc/packb/libform.6.dylib` -compatibiliaxydir/galaxy/database/dependencies/ncub/libform.6.dylib ../obj_s/fld_arg.o ../obj_s/flfld_dup.o ../obj_s/fld_ftchoice.o ../obj_s/fld_ftlink.o ../o../obj_s/fld_move.o ../obj_s/fld_newftyp.o ../obj_s/fld_opts.o ../obj_s/flds/frm_cursor.o ../obj_s/frm_data.o ../obj_s/frm_def.o ../obj_s/frm_driver.o ../obj_s/frm_hook.m_sub.o ../obj_s/frm_user.o ../obj_s/frm_win.o ../obj_s/fty_alnum.o ../obj_s/fty_alpha.o ../obj_s/fty_enum.o ../obj_s/cd /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib && (ln -s -f libform.6.dylib libform.dylib; ) install_environment.STDOUT DEBUG 2017-11-18 16:59:37,437 es_6_0/0efde9889efd/lib/libform.a install_environment.STDOUT DEBUG 2017-11-18 16:59:37,451 4 ../lib/libform.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efderanlib /galaxydir/galaxy/installing ../lib/libform_g.a arm_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,454 cd ../lib && (ln -s -f libform.6.dylib libform.dylib; ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,454 max-inline-insns-single=1200 -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/`basename ../lib/libform.6.dylib` -compatibility_version 6 -current_version 6 -o ../lib/libform.6.dylib ../obj_s/fld_arg.o ../obj_s/fld_attr.o ../obj_s/fld_current.o ../obj_s/fld_def.o ../obj_s/fld_dup.o ../obj_s/fld_ftchoice.o ../obj_s/fld_ftlink.o ../obj_s/fld_info.o ../obj_s/fld_just.o ../obj_s/fld_link.o ../obj_s/fld_linking /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libform.6.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,454 gcc -O2 -no-cpp-precomp --param max-inline-insns-single=1200 -dynamiclib -install_name /galaxydir/ga/galaxy/database/dependenage_ncurses_6_0/0efde9889efd/lity_version 6 -current_version 6 -o /galrses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lid_attr.o ../obj_s/fld_current.o ../obj_s/fld_def.o ../obj_s/bj_s/fld_info.o ../obj_s/fld_just.o ../obj_s/fld_link.o ../obj_s/fld_max.o _pad.o ../obj_s/fld_page.o ../obj_s/fld_stat.o ../obj_s/fld_type.o ../obj_s/fld_user.o ../obj_o ../obj_s/frm_opts.o ../obj_s/frm_page.o ../obj_s/frm_post.o ../obj_s/frm_req_name.o ../obj_s/frm_scale.o ../obj_s/frfty_generic.o ../obj_s/fty_int.o ../obj_s/fty_ipv4.o ../obj_s/fty_num.o ../obj_s/fty_regex.o -L../lib -lncurses -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,454 laxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/`basename /galaxydircies/ncurses/6.0/iuc/packb/libform.6.dylib` -compatibiliaxydir/galaxy/database/dependencies/ncub/libform.6.dylib ../obj_s/fld_arg.o ../obj_s/flfld_dup.o ../obj_s/fld_ftchoice.o ../obj_s/fld_ftlink.o ../o../obj_s/fld_move.o ../obj_s/fld_newftyp.o ../obj_s/fld_opts.o ../obj_s/flds/frm_cursor.o ../obj_s/frm_data.o ../obj_s/frm_def.o ../obj_s/frm_driver.o ../obj_s/frm_hook.m_sub.o ../obj_s/frm_user.o ../obj_s/frm_win.o ../obj_s/fty_alnum.o ../obj_s/fty_alpha.o ../obj_s/fty_enum.o ../obj_s/cd /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib && (ln -s -f libform.6.dylib libform.dylib; ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,455 es_6_0/0efde9889efd/lib/libform.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,455 installing ../lib/libform.a as /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurs/usr/bin/install -c -m 649889efd/lib/libform.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,455 database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libform.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,455 4 ../lib/libform.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efderanlib /galaxydir/galaxy/installing ../lib/libform_g.a arm_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,455 s /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libfo/usr/bin/install -c -m 64de9889efd/lib/libform_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,557 database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libform_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,558 ir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses install_environment.STDOUT DEBUG 2017-11-18 16:59:37,590 4 ../lib/libform_g.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efranlib /galaxydir/galaxy/installing ./form.h in /galaxydcd test && /Library/Developer/CommandLipackage_ncurses_6_0/0efde9889efd/lib" install install_environment.STDOUT DEBUG 2017-11-18 16:59:37,603 ne for `install'. install_environment.STDOUT DEBUG 2017-11-18 16:59:37,604 ommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/ncurses/d/lib" install install_environment.STDOUT DEBUG 2017-11-18 16:59:37,611 /ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/tabset install_environment.STDOUT DEBUG 2017-11-18 16:59:37,613 prefix=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd \ install_environment.STDOUT DEBUG 2017-11-18 16:59:37,634 Running sh ./shlib tic to install /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_nc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,658 4 ../lib/libform_g.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efranlib /galaxydir/galaxy/installing ./form.h in /galaxydcd test && /Library/Developer/CommandLipackage_ncurses_6_0/0efde9889efd/lib" install tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,658 ne for `install'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,658 ommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/ncurses/d/lib" install tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,661 /ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/tabset tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,661 neTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/make[1]: Nothing to be docd misc && /Library/Developer/C6.0/iuc/package_ncurses_6_0/0efde9889efmkdir -p /galaxydir/galaxy/database/dependenciesDESTDIR= \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,661 exec_prefix=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,661 bindir=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/bin \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,662 top_srcdir=.. \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,662 srcdir=. \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,662 datadir=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,662 ticdir=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/terminfo \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,662 source=terminfo.tmp \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,662 cross_compiling=no \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,662 /bin/sh ./run_tic.sh tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,662 prefix=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,662 ** Building terminfo database, please wait... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,662 urses_6_0/0efde9889efd/share/terminfo ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,662 You may see messages regarding extended capabilities, e.g., AX. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,662 These are extended terminal capabilities which are compiled tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,663 using tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,663 tic -x tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,663 If you have ncurses 4.2 applications, you should read the INSTALL tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,663 document, and install the terminfo without the -x option. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:37,764 Running sh ./shlib tic to install /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_nc 127.0.0.1 - - [18/Nov/2017:16:59:38 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:59:38 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/datasets/error?dataset_id=a799d38679e985db&__identifer=9nms4ovms1v" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:59:38 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:59:38 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:59:39,071 d/share/terminfo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,108 d/share/terminfo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,108 1667 entries written to /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/share/terminfo install_environment.STDOUT DEBUG 2017-11-18 16:59:39,126 galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/terminfo for compainstalling std install_environment.STDOUT DEBUG 2017-11-18 16:59:39,139 installing vt100 install_environment.STDOUT DEBUG 2017-11-18 16:59:39,158 /usr/bin/install -c ncurses-config /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncd c++ && /Library/Develoses_6_0/0efde9889efd/lib" install install_environment.STDOUT DEBUG 2017-11-18 16:59:39,178 a as /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libncurses++.a install_environment.STDOUT DEBUG 2017-11-18 16:59:39,182 libncurses++.a install_environment.STDOUT DEBUG 2017-11-18 16:59:39,201 ses++_g.a as /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889ef.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libncurses++_g.a install_environment.STDOUT DEBUG 2017-11-18 16:59:39,207 database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libncurses++_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,209 ** built new /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889ef** sym-linked /galaxydir/tibility tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,209 galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/terminfo for compainstalling std tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,210 installing stdcrt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,210 installing vt100 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,210 installing vt300 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,210 curses_6_0/0efde9889efd/bin/ncurses6-config tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,210 /usr/bin/install -c ncurses-config /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncd c++ && /Library/Develoses_6_0/0efde9889efd/lib" install tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,210 per/CommandLineTools/usr/bin/make DESTDIR="" RPATH_LIST="/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurinstalling ../lib/libncurses++./usr/bin/install -c -m 644 ../lib/libncurses++.a /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libncurses++.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,210 a as /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libncurses++.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,210 libncurses++.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,210 ranlib /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/installing ../lib/libncurd/lib/libncurses++_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,211 ses++_g.a as /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889ef.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libncurses++_g.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,211 database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/libncurses++_g.a 127.0.0.1 - - [18/Nov/2017:16:59:39 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,311 /usr/bin/install -c -m 644 ../lib/libncurses++_g.a /galaxydir/galaxy/database/dependencies/ncurses/6ranlib /galaxydir/galaxy/installing ./cursesapp.h in /gas 127.0.0.1 - - [18/Nov/2017:16:59:39 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,516 /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses install_environment.STDOUT DEBUG 2017-11-18 16:59:39,688 laxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurseinstalling ./cursesf.h in0/0efde9889efd/include/ncurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,719 laxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurseinstalling ./cursesf.h in0/0efde9889efd/include/ncurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:39,920 installing ./cursesm.h in /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_installing ./cursesp.h inurses install_environment.STDOUT DEBUG 2017-11-18 16:59:40,079 /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncinstalling ./cursesw.h inurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:40,122 /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncinstalling ./cursesw.h inurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:40,323 /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncinstalling ./cursslk.h inurses install_environment.STDOUT DEBUG 2017-11-18 16:59:40,462 /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncinstalling etip.h in /gal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:40,526 /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncinstalling etip.h in /gal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:ncurses DEBUG 2017-11-18 16:59:40,732 axydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment WARNING 2017-11-18 16:59:40,845 Length of stdout > 32K, so only a portion will be saved in the database. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment WARNING 2017-11-18 16:59:40,845 Length of stderr > 32K, so only a portion will be saved in the database. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 16:59:41,177 Changing status for tool dependency ncurses from Installing to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:59:41,179 Updating an existing record for version 6.0 of tool dependency ncurses for revision 0efde9889efd of repository package_ncurses_6_0 by updating the status from Installing to Installed. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 16:59:41,238 Tool dependency ncurses version 6.0 has been installed in /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd. 127.0.0.1 - - [18/Nov/2017:16:59:41 -0400] "GET /admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:16:59:41 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:59:43,912 Creating a new record for version 2.4 of tool dependency libtool for revision 944f93d45594 of repository package_xz_5_0_5. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:59:43,962 Creating a new record for version 5.0.5 of tool dependency xz for revision 944f93d45594 of repository package_xz_5_0_5. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:59:44,175 Updating an existing record for version 2.4 of tool dependency libtool for revision 944f93d45594 of repository package_xz_5_0_5 by updating the status from Never installed to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 16:59:44,255 Updating an existing record for version 5.0.5 of tool dependency xz for revision 944f93d45594 of repository package_xz_5_0_5 by updating the status from Never installed to Installing. tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 16:59:44,329 Attempting to download via url: https://github.com/bgruening/download_store/raw/master/xz/xz-5.0.5.tar.bz2 127.0.0.1 - - [18/Nov/2017:16:59:44 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 16:59:45,850 Successfully downloaded from url: https://github.com/bgruening/download_store/raw/master/xz/xz-5.0.5.tar.bz2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:45,859 + PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin:$PATH; export PATH BZLIB_LIB_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib; export BZLIB_LIB_DIR BZLIB_INCLUDE_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include; export BZLIB_INCLUDE_DIR BZLIB_SOURCE_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source; export BZLIB_SOURCE_DIR LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib:$LIBRARY_PATH; export LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source:$LIBRARY_PATH; export LIBRARY_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH BZLIB_ROOT_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595; export BZLIB_ROOT_DIR ./configure --prefix=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594 && make && make install install_environment.STDOUT DEBUG 2017-11-18 16:59:46,229 XZ Utils 5.0.5 install_environment.STDOUT DEBUG 2017-11-18 16:59:46,396 checking host system type... x86_64-apple-darwin15.6.0 install_environment.STDOUT DEBUG 2017-11-18 16:59:46,396 Configure options: install_environment.STDOUT DEBUG 2017-11-18 16:59:46,404 checking which encoders to build... lzma1 lzma2 delta x86 powerpc ia64 arm armthumb sparc install_environment.STDOUT DEBUG 2017-11-18 16:59:46,420 checking which match finders to build... hc3 hc4 bt2 bt3 bt4 install_environment.STDOUT DEBUG 2017-11-18 16:59:46,427 checking if assembler optimizations should be used... no install_environment.STDOUT DEBUG 2017-11-18 16:59:46,428 checking if threading support is wanted... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:46,438 install_environment.STDOUT DEBUG 2017-11-18 16:59:46,450 install_environment.STDOUT DEBUG 2017-11-18 16:59:46,476 checking for a BSD-compatible install... /usr/bin/install -c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,487 System type: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,487 XZ Utils 5.0.5 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,487 checking build system type... x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,487 checking host system type... x86_64-apple-darwin15.6.0 install_environment.STDOUT DEBUG 2017-11-18 16:59:46,506 checking for a thread-safe mkdir -p... build-aux/install-sh -c -d install_environment.STDOUT DEBUG 2017-11-18 16:59:46,507 checking for mawk... no install_environment.STDOUT DEBUG 2017-11-18 16:59:46,509 checking for awk... awk install_environment.STDOUT DEBUG 2017-11-18 16:59:46,554 checking whether make supports nested variables... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:46,585 checking for style of include used by make... GNU tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,589 Configure options: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,589 checking if debugging code should be compiled... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,589 checking which encoders to build... lzma1 lzma2 delta x86 powerpc ia64 arm armthumb sparc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,589 checking which decoders to build... lzma1 lzma2 delta x86 powerpc ia64 arm armthumb sparc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,589 checking which match finders to build... hc3 hc4 bt2 bt3 bt4 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,589 checking which integrity checks to build... crc32 crc64 sha256 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,590 checking if assembler optimizations should be used... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,590 checking if small size is preferred over speed... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,590 checking if threading support is wanted... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,590 checking how much RAM to assume if the real amount is unknown... 128 MiB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,690 checking for a shell that conforms to POSIX... /bin/sh install_environment.STDOUT DEBUG 2017-11-18 16:59:46,781 checking whether the C compiler works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,794 Initializing Automake: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,794 checking for a BSD-compatible install... /usr/bin/install -c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,794 checking whether build environment is sane... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,794 checking for a thread-safe mkdir -p... build-aux/install-sh -c -d tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,794 checking for gawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,794 checking for mawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,794 checking for nawk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,795 checking for awk... awk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,795 checking whether make sets $(MAKE)... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,795 checking whether make supports nested variables... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,795 checking whether ln -s works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,795 checking for style of include used by make... GNU tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,795 checking for gcc... gcc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,795 checking whether the C compiler works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,795 checking for C compiler default output file name... a.out install_environment.STDOUT DEBUG 2017-11-18 16:59:46,831 checking for suffix of executables... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,897 checking for suffix of executables... install_environment.STDOUT DEBUG 2017-11-18 16:59:46,946 checking for suffix of object files... o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,998 checking whether we are cross compiling... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,998 checking for suffix of object files... o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:46,998 checking whether we are using the GNU C compiler... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:47,031 checking whether gcc accepts -g... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:47,100 checking whether gcc accepts -g... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:47,201 checking for gcc option to accept ISO C89... none needed install_environment.STDOUT DEBUG 2017-11-18 16:59:47,203 checking whether gcc understands -c and -o together... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:47,305 checking whether gcc understands -c and -o together... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:47,409 checking dependency style of gcc... gcc3 install_environment.STDOUT DEBUG 2017-11-18 16:59:47,447 checking for gcc option to accept ISO C99... none needed tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:47,512 checking for gcc option to accept ISO C99... none needed tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:47,616 checking dependency style of gcc... gcc3 install_environment.STDOUT DEBUG 2017-11-18 16:59:47,670 checking how to run the C preprocessor... gcc -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:47,719 checking how to run the C preprocessor... gcc -E 127.0.0.1 - - [18/Nov/2017:16:59:47 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:59:48,043 checking for egrep... /usr/bin/grep -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:48,137 checking for grep that handles long lines and -e... /usr/bin/grep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:48,138 checking for egrep... /usr/bin/grep -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:48,344 checking for ANSI C header files... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:48,402 checking for sys/types.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:48,448 checking for sys/types.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:48,550 checking for sys/stat.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:48,579 checking for stdlib.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:48,650 checking for stdlib.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:48,651 checking for string.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:48,724 checking for memory.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:48,753 checking for memory.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:48,855 checking for strings.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:48,872 checking for inttypes.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:48,959 checking for inttypes.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:48,959 checking for stdint.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:49,027 checking for unistd.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,062 checking for unistd.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:49,161 checking minix/config.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,170 checking minix/config.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,171 checking minix/config.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,175 checking for minix/config.h... no install_environment.STDOUT DEBUG 2017-11-18 16:59:49,229 checking whether it is safe to define __EXTENSIONS__... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:49,232 Threading support: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,277 checking whether it is safe to define __EXTENSIONS__... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,378 Threading support: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,378 checking whether pthreads work with -pthread... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:49,393 checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE install_environment.STDOUT DEBUG 2017-11-18 16:59:49,469 checking for PTHREAD_PRIO_INHERIT... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:49,471 Initializing Libtool: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,480 checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,480 checking if more special flags are required for pthreads... -D_THREAD_SAFE tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,481 checking for PTHREAD_PRIO_INHERIT... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,582 Initializing Libtool: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,582 checking how to print strings... printf install_environment.STDOUT DEBUG 2017-11-18 16:59:49,702 checking for a sed that does not truncate output... /usr/bin/sed install_environment.STDOUT DEBUG 2017-11-18 16:59:49,733 checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld install_environment.STDOUT DEBUG 2017-11-18 16:59:49,787 checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,788 checking for a sed that does not truncate output... /usr/bin/sed tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,788 checking for fgrep... /usr/bin/grep -F tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,788 checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,788 checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,788 checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B install_environment.STDOUT DEBUG 2017-11-18 16:59:49,855 checking the maximum length of command line arguments... 196608 install_environment.STDOUT DEBUG 2017-11-18 16:59:49,860 checking whether the shell understands "+="... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:49,871 func_convert_file_noop install_environment.STDOUT DEBUG 2017-11-18 16:59:49,871 86_64-apple-darwin15.6.0 file names to toolchain format... func_convert_file_noop install_environment.STDOUT DEBUG 2017-11-18 16:59:49,872 /CommandLineTools/usr/bin/ld option to reload object files... -r install_environment.STDOUT DEBUG 2017-11-18 16:59:49,874 checking how to recognize dependent libraries... pass_all install_environment.STDOUT DEBUG 2017-11-18 16:59:49,876 checking how to associate runtime and link libraries... printf %s\n tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,892 checking the name lister (/usr/bin/nm -B) interface... BSD nm tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,892 checking the maximum length of command line arguments... 196608 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,893 checking whether the shell understands some XSI constructs... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,894 checking whether the shell understands "+="... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,894 func_convert_file_noop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,894 86_64-apple-darwin15.6.0 file names to toolchain format... func_convert_file_noop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,894 /CommandLineTools/usr/bin/ld option to reload object files... -r tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,894 checking how to convert x86_64-apple-darwin15.6.0 file names to x86_64-apple-darwin15.6.0 format... checking how to convert xchecking for /Library/Developerchecking for objdump... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,894 checking how to recognize dependent libraries... pass_all tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,894 checking for dlltool... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,894 checking how to associate runtime and link libraries... printf %s\n tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,894 checking for ar... ar install_environment.STDOUT DEBUG 2017-11-18 16:59:49,940 checking for archiver @FILE support... no install_environment.STDOUT DEBUG 2017-11-18 16:59:49,942 checking for ranlib... ranlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,995 checking for archiver @FILE support... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,996 checking for strip... strip tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:49,996 checking for ranlib... ranlib install_environment.STDOUT DEBUG 2017-11-18 16:59:50,175 checking for sysroot... no install_environment.STDOUT DEBUG 2017-11-18 16:59:50,187 checking if : is a manifest tool... no install_environment.STDOUT DEBUG 2017-11-18 16:59:50,192 checking for nmedit... nmedit tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,199 checking command to parse /usr/bin/nm -B output from gcc object... ok tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,199 checking for sysroot... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,199 checking for mt... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,199 checking if : is a manifest tool... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,199 checking for dsymutil... dsymutil tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,199 checking for lipo... lipo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,201 checking for otool... otool tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,204 checking for nmedit... nmedit tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,204 checking for otool64... no install_environment.STDOUT DEBUG 2017-11-18 16:59:50,260 checking for -single_module linker flag... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,305 checking for -single_module linker flag... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,407 checking for -exported_symbols_list linker flag... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:50,451 checking for -force_load linker flag... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,512 checking for -force_load linker flag... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:50,536 checking for objdir... .libs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,612 checking for dlfcn.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,612 checking for objdir... .libs install_environment.STDOUT DEBUG 2017-11-18 16:59:50,710 checking for gcc option to produce PIC... -fno-common -DPIC tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,716 checking if gcc supports -fno-rtti -fno-exceptions... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,716 checking for gcc option to produce PIC... -fno-common -DPIC tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,820 checking if gcc PIC flag -fno-common -DPIC works... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:50,833 checking if gcc static flag -static works... no 127.0.0.1 - - [18/Nov/2017:16:59:50 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:59:50,916 checking if gcc supports -c -o file.o... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,921 checking if gcc static flag -static works... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,921 checking if gcc supports -c -o file.o... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,921 checking if gcc supports -c -o file.o... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:50,921 checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:50,971 checking dynamic linker characteristics... darwin15.6.0 dyld install_environment.STDOUT DEBUG 2017-11-18 16:59:50,978 checking whether stripping libraries is possible... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:50,979 checking whether to build shared libraries... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:50,982 checking for windres... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,022 checking dynamic linker characteristics... darwin15.6.0 dyld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,022 checking how to hardcode library paths into programs... immediate tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,022 checking whether stripping libraries is possible... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,022 checking if libtool supports shared libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,022 checking whether to build shared libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,022 checking whether to build static libraries... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,022 checking for windres... no install_environment.STDOUT DEBUG 2017-11-18 16:59:51,059 Initializing gettext: install_environment.STDOUT DEBUG 2017-11-18 16:59:51,069 checking for msgfmt... no install_environment.STDOUT DEBUG 2017-11-18 16:59:51,089 checking for xgettext... no install_environment.STDOUT DEBUG 2017-11-18 16:59:51,139 checking for ld used by GCC... /Library/Developer/CommandLineTools/usr/bin/ld install_environment.STDOUT DEBUG 2017-11-18 16:59:51,204 checking for shared library run path origin... done tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,231 Initializing gettext: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,231 checking whether NLS is requested... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,231 checking for msgfmt... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,231 checking for gmsgfmt... : tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,232 checking for xgettext... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,232 checking for msgmerge... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,232 checking for ld used by GCC... /Library/Developer/CommandLineTools/usr/bin/ld tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,232 checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,232 checking for shared library run path origin... done tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,333 checking for CFPreferencesCopyAppValue... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:51,416 checking for CFLocaleCopyCurrent... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,438 checking for CFLocaleCopyCurrent... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,542 checking for GNU gettext in libc... no install_environment.STDOUT DEBUG 2017-11-18 16:59:51,638 checking for iconv... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,643 checking for iconv... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:51,729 checking how to link with libiconv... -liconv tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,745 checking for working iconv... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,746 checking how to link with libiconv... -liconv install_environment.STDOUT DEBUG 2017-11-18 16:59:51,848 checking whether to use NLS... no install_environment.STDOUT DEBUG 2017-11-18 16:59:51,849 System headers and functions: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,850 checking for GNU gettext in libintl... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,850 checking whether to use NLS... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,956 System headers and functions: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:51,956 checking fcntl.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:51,972 checking fcntl.h presence... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:52,054 checking limits.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,058 checking fcntl.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,058 checking for fcntl.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,059 checking limits.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:52,096 checking for limits.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,160 checking limits.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,160 checking for limits.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:52,229 checking sys/time.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,262 checking sys/time.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,262 checking sys/time.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,262 checking for sys/time.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:52,301 checking for stdbool.h that conforms to C99... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,367 checking for stdbool.h that conforms to C99... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,470 checking for _Bool... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:52,516 checking for uint8_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,574 checking for uint8_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,679 checking for uint16_t... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:52,721 checking for int32_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,783 checking for int32_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,885 checking for uint32_t... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:52,925 checking for int64_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:52,988 checking for int64_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:53,088 checking for uint64_t... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:53,133 checking for uintptr_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:53,189 checking for uintptr_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:53,294 checking size of size_t... 8 install_environment.STDOUT DEBUG 2017-11-18 16:59:53,398 checking for struct stat.st_atim.tv_nsec... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:53,499 checking for struct stat.st_atim.tv_nsec... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:53,499 checking for struct stat.st_atimespec.tv_nsec... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:53,607 checking for struct stat.st_atimensec... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:53,700 checking for struct stat.st_atimensec... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:53,804 checking for struct stat.st_uatime... no 127.0.0.1 - - [18/Nov/2017:16:59:53 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:59:53,942 checking for struct stat.st_atim.st__tim.tv_nsec... no install_environment.STDOUT DEBUG 2017-11-18 16:59:53,992 checking for _FILE_OFFSET_BITS value needed for large files... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,011 checking for struct stat.st_atim.st__tim.tv_nsec... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,011 checking for special C compiler options needed for large files... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,011 checking for _FILE_OFFSET_BITS value needed for large files... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,216 checking whether byte ordering is bigendian... no install_environment.STDOUT DEBUG 2017-11-18 16:59:54,222 checking getopt.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:54,272 checking for getopt.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,322 checking getopt.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,322 checking getopt.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,322 checking for getopt.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,427 checking for getopt_long... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:54,441 checking whether optreset is declared... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,527 checking whether optreset is declared... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:54,615 checking for futimes... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,631 checking for futimens... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,631 checking for futimes... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,733 checking whether program_invocation_name is declared... no install_environment.STDOUT DEBUG 2017-11-18 16:59:54,777 checking byteswap.h usability... no install_environment.STDOUT DEBUG 2017-11-18 16:59:54,831 checking for byteswap.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,835 checking byteswap.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,835 checking byteswap.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,835 checking for byteswap.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:54,939 checking sys/endian.h usability... no install_environment.STDOUT DEBUG 2017-11-18 16:59:54,956 checking sys/endian.h presence... no install_environment.STDOUT DEBUG 2017-11-18 16:59:55,034 checking sys/byteorder.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,042 checking sys/endian.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,042 checking for sys/endian.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,042 checking sys/byteorder.h usability... no install_environment.STDOUT DEBUG 2017-11-18 16:59:55,092 checking for sys/byteorder.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,143 checking sys/byteorder.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,143 checking for sys/byteorder.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,143 checking if unaligned memory access should be used... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:55,168 checking sys/param.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:55,221 checking for sys/param.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,244 checking sys/param.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,244 checking sys/param.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,244 checking for sys/param.h... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:55,388 checking for sys/param.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,456 checking how to detect the amount of physical memory... sysconf tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,456 checking for sys/param.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,557 checking how to detect the number of available CPU cores... sysctl install_environment.STDOUT DEBUG 2017-11-18 16:59:55,562 checking whether mbrtowc and mbstate_t are properly declared... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:55,640 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,665 checking whether mbrtowc and mbstate_t are properly declared... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,665 checking for wcwidth... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,665 GCC extensions: install_environment.STDOUT DEBUG 2017-11-18 16:59:55,727 checking for simple visibility declarations... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,768 checking whether the -Werror option is usable... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,768 checking for simple visibility declarations... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:55,821 checking if gcc accepts -Wextra... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,868 checking if gcc accepts -Wall... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,869 checking if gcc accepts -Wextra... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:55,913 checking if gcc accepts -Wformat=2... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,969 checking if gcc accepts -Wvla... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,969 checking if gcc accepts -Wformat=2... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:55,969 checking if gcc accepts -Winit-self... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:56,009 checking if gcc accepts -Wmissing-include-dirs... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,073 checking if gcc accepts -Wmissing-include-dirs... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,074 checking if gcc accepts -Wstrict-aliasing... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:56,106 checking if gcc accepts -Wfloat-equal... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,175 checking if gcc accepts -Wfloat-equal... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,175 checking if gcc accepts -Wundef... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:56,193 checking if gcc accepts -Wshadow... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:56,275 checking if gcc accepts -Wbad-function-cast... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,279 checking if gcc accepts -Wshadow... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,279 checking if gcc accepts -Wpointer-arith... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,279 checking if gcc accepts -Wbad-function-cast... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:56,377 checking if gcc accepts -Wlogical-op... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,380 checking if gcc accepts -Wwrite-strings... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,380 checking if gcc accepts -Wlogical-op... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:56,477 checking if gcc accepts -Wstrict-prototypes... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,482 checking if gcc accepts -Waggregate-return... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,482 checking if gcc accepts -Wstrict-prototypes... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,584 checking if gcc accepts -Wold-style-definition... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:56,587 checking if gcc accepts -Wmissing-prototypes... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:56,673 checking if gcc accepts -Wmissing-noreturn... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,687 checking if gcc accepts -Wmissing-prototypes... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,688 checking if gcc accepts -Wmissing-declarations... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,688 checking if gcc accepts -Wmissing-noreturn... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:56,719 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,789 checking if gcc accepts -Wredundant-decls... yes install_environment.STDOUT DEBUG 2017-11-18 16:59:56,794 configure: creating ./config.status tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,894 checking that generated files are newer than configure... done tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:56,894 configure: creating ./config.status 127.0.0.1 - - [18/Nov/2017:16:59:56 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 16:59:58,190 config.status: creating Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,225 config.status: creating Doxyfile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,226 config.status: creating Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,226 config.status: creating po/Makefile.in install_environment.STDOUT DEBUG 2017-11-18 16:59:58,265 config.status: creating lib/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,327 config.status: creating lib/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,327 config.status: creating src/Makefile install_environment.STDOUT DEBUG 2017-11-18 16:59:58,358 config.status: creating src/liblzma/liblzma.pc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,441 config.status: creating src/liblzma/liblzma.pc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,441 config.status: creating src/liblzma/Makefile install_environment.STDOUT DEBUG 2017-11-18 16:59:58,498 config.status: creating src/liblzma/api/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,541 config.status: creating src/liblzma/api/Makefile install_environment.STDOUT DEBUG 2017-11-18 16:59:58,601 config.status: creating src/xzdec/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,644 config.status: creating src/xz/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,644 config.status: creating src/xzdec/Makefile install_environment.STDOUT DEBUG 2017-11-18 16:59:58,694 config.status: creating src/scripts/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,745 config.status: creating src/lzmainfo/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,745 config.status: creating src/scripts/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,745 config.status: creating tests/Makefile install_environment.STDOUT DEBUG 2017-11-18 16:59:58,783 config.status: creating debug/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,846 config.status: creating debug/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,846 config.status: creating src/scripts/xzdiff install_environment.STDOUT DEBUG 2017-11-18 16:59:58,867 config.status: creating src/scripts/xzgrep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,948 config.status: creating src/scripts/xzgrep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:58,948 config.status: creating src/scripts/xzmore install_environment.STDOUT DEBUG 2017-11-18 16:59:58,948 config.status: creating src/scripts/xzless install_environment.STDOUT DEBUG 2017-11-18 16:59:59,027 config.status: executing depfiles commands tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:59,050 config.status: creating src/scripts/xzless tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:59,050 config.status: creating config.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:59,051 config.status: executing depfiles commands tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 16:59:59,974 config.status: executing libtool commands 127.0.0.1 - - [18/Nov/2017:17:00:00 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:00:00,202 config.status: executing po-directories commands install_environment.STDOUT DEBUG 2017-11-18 17:00:00,227 config.status: creating po/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,277 config.status: executing po-directories commands tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,277 config.status: creating po/POTFILES tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,277 config.status: creating po/Makefile install_environment.STDOUT DEBUG 2017-11-18 17:00:00,349 Making all in src tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,379 /Library/Developer/CommandLineTools/usr/bin/make all-recursive tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,379 Making all in src tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,379 Making all in liblzma install_environment.STDOUT DEBUG 2017-11-18 17:00:00,394 Making all in api install_environment.STDOUT DEBUG 2017-11-18 17:00:00,418 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nMF .deps/liblzma_la-tuklib_physmem.Tpo -c -o liblzma_la-tuklib_physmem.lo `test -f '../../src/common/tuklib_physmem.c' || echo './'`../../src/common/tuklib_physmem.c install_environment.STDOUT DEBUG 2017-11-18 17:00:00,461 /common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-tuklib_physmem.lo -MD -MP -MF .deps/liblzma_la-tuklib_physmem.Tpo -c ../../src/common/tuklib_physmem.c -fno-common -DPIC -o .libs/liblzma_la-tuklib_physmem.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,483 Making all in api tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,483 make[4]: Nothing to be done for `all'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,483 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nMF .deps/liblzma_la-tuklib_physmem.Tpo -c -o liblzma_la-tuklib_physmem.lo `test -f '../../src/common/tuklib_physmem.c' || echo './'`../../src/common/tuklib_physmem.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,483 /common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-tuklib_physmem.lo -MD -MP -MF .deps/liblzma_la-tuklib_physmem.Tpo -c ../../src/common/tuklib_physmem.c -fno-common -DPIC -o .libs/liblzma_la-tuklib_physmem.o install_environment.STDOUT DEBUG 2017-11-18 17:00:00,526 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-pv/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,585 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-pv/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,585 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,585 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:00,638 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_Ste-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-common.lo -MD -MP -MF .deps/liblzma_la-common.Tpo -c -o liblzma_la-common.lo `test -f 'common/common.c' || echo './'`commn -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../srcc/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-trict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-ping-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-common.lo -MD -MP -MF .deps/liblzma_la-common.Tpo -c common/common.c -fno-common -DPIC -o .libs/liblzma_la-common.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,688 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-tuklib_physmem.lo -MD -MP -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmalibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-tuklib_physmem.lo -MD -MP -MF .deps/liblzma_la-tuklib_physmem.Tpo -c ../../src/common/tuklib_physmem.c -o liblzma_la-tuklib_physmem.o >/demv -f .deps/liblzma_la-tuklib_physmem.Tpo .deps/liblzma_la-tuklib_physmem.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,688 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregaon/common.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,689 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_Ste-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-common.lo -MD -MP -MF .deps/liblzma_la-common.Tpo -c -o liblzma_la-common.lo `test -f 'common/common.c' || echo './'`commn -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../srcc/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-trict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-ping-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-common.lo -MD -MP -MF .deps/liblzma_la-common.Tpo -c common/common.c -fno-common -DPIC -o .libs/liblzma_la-common.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,689 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,791 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commo/liblzma/delta -I../../srself -Wmissing-include-dirs -Wsrototypes -Wmissing-declarations -Wmisslibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-common.lo -MD -MP -MF .deps/liblzma_la-common.Tpo -c common/common.c -o liblzma_la-common.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,791 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,893 mv -f .deps/liblzma_la-common.Tpo .deps/liblzma_la-common.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,893 tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmack -I../../src/liblzma/lz/src/liblzma/lzma -I../../src/lsrc/common -DTUKLIB_SYMBOL_PREFIX=lzma_-Wvla -Wformat=2 -Winit-self -Wmissing-include-dfunction-cast -Wwrite-strings -Wlogical-op -Waggregate-retursing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_util.lo -MD -MP/block_util.c install_environment.STDOUT DEBUG 2017-11-18 17:00:00,908 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma//bin/sh ../../libtool --/common -I../../src/liblzma/che -I../../src/liblzma/rangecoder -I../..iblzma/delta -I../../src/liblzma/simple -I../../ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra irs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-n -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmis -MF .deps/liblzma_la-block_util.Tpo -c -o liblzma_la-block_util.lo `test -f 'common/block_util.c' || echo './'`commonlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliaf -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT P -MF .deps/liblzma_la-block_util.Tpo -c common/block_util.c -fno-common -DPIC -o .libs/liblzma_la-block_util.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,997 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma//bin/sh ../../libtool --/common -I../../src/liblzma/che -I../../src/liblzma/rangecoder -I../..iblzma/delta -I../../src/liblzma/simple -I../../ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra irs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-n -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmis -MF .deps/liblzma_la-block_util.Tpo -c -o liblzma_la-block_util.lo `test -f 'common/block_util.c' || echo './'`commonlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliaf -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT P -MF .deps/liblzma_la-block_util.Tpo -c common/block_util.c -fno-common -DPIC -o .libs/liblzma_la-block_util.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,997 /lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/lising -Wfloat-equal -Wundeliblzma_la-block_util.lo -MD -Mlibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_util.lo -MD -MP -MF .deps/liblzma_la-block_util.Tpo -c common/block_util.c -o liblzma_la-block_util.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,997 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:00,997 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:01,068 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../srcmv -f .deps/liblzma_la-bl/bin/sh ../../libtool --tag=CCn -I../../src/liblzma/check -I../../srciblzma/rangecoder -I../../src/liblzma/lzma -I../c/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lity=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_preset.lo -MD -MP -MF .deps/liblzmpreset.c' || echo './'`common/easy_preset.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,100 ock_util.Tpo .deps/liblzma_la-block_util.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,100 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../srcmv -f .deps/liblzma_la-bl/bin/sh ../../libtool --tag=CCn -I../../src/liblzma/check -I../../srciblzma/rangecoder -I../../src/liblzma/lzma -I../c/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lity=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_preset.lo -MD -MP -MF .deps/liblzmpreset.c' || echo './'`common/easy_preset.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,202 --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commo/liblzma/lz -I../../src/l../src/liblzma/delta -I../../srzma_ -D_THREAD_SAFE -pthread -fvisibils -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadt-prototypes -Wold-style-definition -Wmissing-prototypes -Wma_la-easy_preset.Tpo -c -o liblzma_la-easy_preset.lo `test -f 'common/easy_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmaliblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_Tibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -ngs -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-eala-easy_preset.Tpo -c common/easy_preset.c -fno-common -DPIC -o .libs/liblzma_la-easy_preset.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,203 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/I../../src/liblzma/delta -D_THREAD_SAFE -pthread -fvisibng -Wfloat-equal -Wundef -Wshadow -Wpoiion -Wmissing-prototypes -Wmissing-declarations iblzma_la-easy_preset.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,203 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,203 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:01,255 /common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/HREAD_SAFE -pthread -fvisWbad-function-cast -Wwrite-strisy_preset.lo -MD -MP -MF .deps/liblzma_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_preset.lo -MD -MP -MF .deps/liblzma_la-easy_preset.Tpo -c common/easy_preset.c -o lmv -f .deps/liblzma_la-easy_preset.Tpo .deps/liblzma_la-easy_preset.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:01,258 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_common.lo -MD -MP -M_common.c' || echo './'`common/filter_common.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,303 /common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/HREAD_SAFE -pthread -fvisWbad-function-cast -Wwrite-strisy_preset.lo -MD -MP -MF .deps/liblzma_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_preset.lo -MD -MP -MF .deps/liblzma_la-easy_preset.Tpo -c common/easy_preset.c -o lmv -f .deps/liblzma_la-easy_preset.Tpo .deps/liblzma_la-easy_preset.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,304 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_common.lo -MD -MP -M_common.c' || echo './'`common/filter_common.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,304 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nF .deps/liblzma_la-filter_common.Tpo -c -o liblzma_la-filter_common.lo `test -f 'common/filterlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_common.lo -MD -MP -MF .deps/liblzma_la-filter_common.Tpo -c common/filter_common.c -fno-common -DPIC -o .libs/liblzma_la-filter_common.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,409 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,513 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commock -I../../src/liblzma/lz -I../../src/liblzma/lzma -I../a/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_common.lo -MD -MP -MF .deps/liblzma_la-filter_common.Tpo -c common/filter_common.c -o liblzma_la-filter_common.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,513 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:01,562 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../srcn -I../../src/liblzma/che -I../../src/liblzma/rangecoder../src/liblzma/delta -I../../src/liblzm/bin/sh ../../libtool --tag=CC --mode=compilelzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangeclzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/commo -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissoat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-hardware_physmem.lo -MD -MP -MF .deps/liblzma_la-hardwar'common/hardware_physmem.c' || echo './'`common/hardware_physmem.c install_environment.STDOUT DEBUG 2017-11-18 17:00:01,603 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangrc/common -DTUKLIB_SYMBOL-dirs -Wstrict-aliasing -Wfloation -Wmissing-prototypes -Wmissing-declC -o .libs/liblzma_la-hardware_physmem.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,614 mv -f .deps/liblzma_la-filter_common.Tpo .deps/liblzma_la-filter_common.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,614 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../srcn -I../../src/liblzma/che -I../../src/liblzma/rangecoder../src/liblzma/delta -I../../src/liblzm/bin/sh ../../libtool --tag=CC --mode=compilelzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangeclzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/commo -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissoat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-hardware_physmem.lo -MD -MP -MF .deps/liblzma_la-hardwar'common/hardware_physmem.c' || echo './'`common/hardware_physmem.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,614 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangrc/common -DTUKLIB_SYMBOL-dirs -Wstrict-aliasing -Wfloation -Wmissing-prototypes -Wmissing-declC -o .libs/liblzma_la-hardware_physmem.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,715 gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liboder -I../../src/liblzma/n -DTUKLIB_SYMBOL_PREFIX=lzma_ ing-include-dirs -Wstrict-aliasing -Wflt-prototypes -Wold-style-definition -Wmissing-pre_physmem.Tpo -c -o liblzma_la-hardware_physmem.lo `test -f libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../s_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definitarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-hardware_physmem.lo -MD -MP -MF .deps/liblzma_la-hardware_physmem.Tpo -c common/hardware_physmem.c -fno-common -DPIlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/deld -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wssing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-hardware_physmem.lo -MD -MP -MF .deps/liblzma_la-hardware_physmem.Tpo -c common/hardware_physmem.c -o liblzma_la-hardware_physmem.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,716 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,716 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:01,733 ta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthreamissing-declarations -Wmimv -f .deps/liblzma_la-hardware/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arl-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissi -MD -MP -MF .deps/liblzma_la-index.Tpo -c -o liblzma_la-index.lo `test -f 'common/index.c' || echo './'`common/index.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,821 _physmem.Tpo .deps/liblzma_la-hardware_physmem.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,821 ta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthreamissing-declarations -Wmimv -f .deps/liblzma_la-hardware/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arl-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissi -MD -MP -MF .deps/liblzma_la-index.Tpo -c -o liblzma_la-index.lo `test -f 'common/index.c' || echo './'`common/index.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,821 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index.lolibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../s_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definitarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index.lo -MD -MP -MF .deps/liblzma_la-index.Tpo -c common/index.c -fno-common -DPIC -o .libs/liblzma_la-index.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:01,822 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,027 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/I../../src/liblzma/delta -D_THREAD_SAFE -pthread -fvisibng -Wfloat-equal -Wundef -Wshadow -Wpoiion -Wmissing-prototypes -Wmissing-declarations >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,027 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:02,244 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangrc/common -DTUKLIB_SYMBOL-dirs -Wstrict-aliasing -Wfloation -Wmissing-prototypes -Wmissing-decllibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index.lo -MD -MP -MF .deps/liblzma_la-index.Tpo -c common/index.c -o liblzma_la-index.o mv -f .deps/liblzma_la-index.Tpo .deps/liblzma_la-index.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:02,247 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_flags_common.lo -MD -f 'common/stream_flags_common.c' || echo './'`common/stream_flags_common.c install_environment.STDOUT DEBUG 2017-11-18 17:00:02,284 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-pblzma_la-stream_flags_common.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,333 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangrc/common -DTUKLIB_SYMBOL-dirs -Wstrict-aliasing -Wfloation -Wmissing-prototypes -Wmissing-decllibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index.lo -MD -MP -MF .deps/liblzma_la-index.Tpo -c common/index.c -o liblzma_la-index.o mv -f .deps/liblzma_la-index.Tpo .deps/liblzma_la-index.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,333 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_flags_common.lo -MD -f 'common/stream_flags_common.c' || echo './'`common/stream_flags_common.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,333 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-pblzma_la-stream_flags_common.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,333 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,433 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-n-MP -MF .deps/liblzma_la-stream_flags_common.Tpo -c -o liblzma_la-stream_flags_common.lo `testlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_flags_common.lo -MD -MP -MF .deps/liblzma_la-stream_flags_common.Tpo -c common/stream_flags_common.c -fno-common -DPIC -o .libs/lilibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIBit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_flags_common.lo -MD -MP -MF .deps/liblzma_la-stream_flags_common.Tpo -c common/stream_flags_common.c -o liblzma_la-stream_flags_common.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,433 mv -f .deps/liblzma_la-stream_flags_common.Tpo .deps/liblzma_la-stream_flags_common.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,434 tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmack -I../../src/liblzma/lz/src/liblzma/lzma -I../../src/lsrc/common -DTUKLIB_SYMBOL_PREFIX=lzma_-Wvla -Wformat=2 -Winit-self -Wmissing-include-dfunction-cast -Wwrite-strings -Wlogical-op -Waggregate-retursing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-vli_size.lo -MD -MP -e.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,434 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:02,469 _SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Win/bin/sh ../../libtool --/common -I../../src/liblzma/che -I../../src/liblzma/rangecoder -I../..iblzma/delta -I../../src/liblzma/simple -I../../ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra irs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-n -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -WmisMF .deps/liblzma_la-vli_size.Tpo -c -o liblzma_la-vli_size.lo `test -f 'common/vli_size.c' || echo './'`common/vli_sizlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliaf -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT -MF .deps/liblzma_la-vli_size.Tpo -c common/vli_size.c -fno-common -DPIC -o .libs/liblzma_la-vli_size.o install_environment.STDOUT DEBUG 2017-11-18 17:00:02,529 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../srcaggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-vli_size.lo -MD -MP -MF .deps/liblzma_la-vli_size.Tpo -c common/vli_size.c -o liblzma_la-vli_size.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,538 _SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Win/bin/sh ../../libtool --/common -I../../src/liblzma/che -I../../src/liblzma/rangecoder -I../..iblzma/delta -I../../src/liblzma/simple -I../../ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra irs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-n -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -WmisMF .deps/liblzma_la-vli_size.Tpo -c -o liblzma_la-vli_size.lo `test -f 'common/vli_size.c' || echo './'`common/vli_sizlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliaf -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT -MF .deps/liblzma_la-vli_size.Tpo -c common/vli_size.c -fno-common -DPIC -o .libs/liblzma_la-vli_size.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,539 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../srcaggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-vli_size.lo -MD -MP -MF .deps/liblzma_la-vli_size.Tpo -c common/vli_size.c -o liblzma_la-vli_size.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,539 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,539 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,642 /lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/lising -Wfloat-equal -Wundeliblzma_la-vli_size.lo -MD -MP libtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Wmv -f .deps/liblzma_la-vli_size.Tpo .deps/liblzma_la-vli_size.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,643 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-alone_encoder.lo -MD -MP -Mencoder.c' || echo './'`common/alone_encoder.c install_environment.STDOUT DEBUG 2017-11-18 17:00:02,726 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nF .deps/liblzma_la-alone_encoder.Tpo -c -o liblzma_la-alone_encoder.lo `test -f 'common/alone_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-alone_encoder.lo -MD -MP -MF .deps/liblzma_la-alone_encoder.Tpo -c common/alone_encoder.c -fno-common -DPIC -o .libs/liblzma_la-alone_enclibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIBit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-alone_encoder.lo -MD -MP -MF .deps/liblzma_la-aloalone_encoder.c -o liblzma_la-alone_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,746 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-poder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,747 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nF .deps/liblzma_la-alone_encoder.Tpo -c -o liblzma_la-alone_encoder.lo `test -f 'common/alone_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-alone_encoder.lo -MD -MP -MF .deps/liblzma_la-alone_encoder.Tpo -c common/alone_encoder.c -fno-common -DPIC -o .libs/liblzma_la-alone_enclibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIBit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-alone_encoder.lo -MD -MP -MF .deps/liblzma_la-aloalone_encoder.c -o liblzma_la-alone_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,747 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,747 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:02,819 coder.Tpo .deps/liblzma_la-alone_encoder.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:02,822 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_bur.c' || echo './'`common/block_buffer_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,851 coder.Tpo .deps/liblzma_la-alone_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,851 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_bur.c' || echo './'`common/block_buffer_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,956 _SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winne_encoder.Tpo -c common/mv -f .deps/liblzma_la-alone_en/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arl-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissiffer_encoder.lo -MD -MP -MF .deps/liblzma_la-block_buffer_encoder.Tpo -c -o liblzma_la-block_buffer_encoder.lo `test -f 'common/block_buffer_encodelibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_buffer_encoder.lo -MD -MP -MF .deps/liblzma_la-block_buffer_encoder.Tpo -c common/block_buffer_encoder.c -fno-common -DPICer_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,956 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:02,957 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:02,958 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggre -o .libs/liblzma_la-block_bufflibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/zma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wform -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite--prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -gs/liblzma_la-block_buffer_encoder.Tpo -c common/block_buffer_encoder.c -o liblzma_la-block_buffer_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,057 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggre -o .libs/liblzma_la-block_bufflibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/zma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wform -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite--prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -gs/liblzma_la-block_buffer_encoder.Tpo -c common/block_buffer_encoder.c -o liblzma_la-block_buffer_encoder.o >/dev/null 2>&1 install_environment.STDOUT DEBUG 2017-11-18 17:00:03,061 er_encoder.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:03,126 liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/TUKLIB_SYMBOL_PREFIX=lzmaundef -Wshadow -Wpointer-arith t-decls -g -O2 -MT liblzma_la-block_enclibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../ma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_encoder.lo -MD -MP -MF .deps/liblzma_la-block_encoder.Tpo -c common/block_encoder.c -fno-common -DPIC -o .libs/liblzma_la-block_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,164 er_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,164 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src../src/liblzma/lzma -I../common -DTUKLIB_SYMBOL_PREFIX=lat=2 -Winit-self -Wmissing-include-dirsstrings -Wlogical-op -Waggregate-return -Wstrict -O2 -MT liblzma_la-block_buffer_encoder.lo -MD -MP -MF .depmv -f .deps/liblzma_la-block_buffer_encoder.Tpo .deps/liblzma_la-block_buff/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -D_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -W-Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundanoder.lo -MD -MP -MF .deps/liblzma_la-block_encoder.Tpo -c -o liblzma_la-block_encoder.lo `test -f 'common/block_encoder.c' || echo './'`common/block_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,165 liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/TUKLIB_SYMBOL_PREFIX=lzmaundef -Wshadow -Wpointer-arith t-decls -g -O2 -MT liblzma_la-block_enclibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../ma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_encoder.lo -MD -MP -MF .deps/liblzma_la-block_encoder.Tpo -c common/block_encoder.c -fno-common -DPIC -o .libs/liblzma_la-block_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,165 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] 127.0.0.1 - - [18/Nov/2017:17:00:03 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,268 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzn -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_encoder.lo -MD -MP -MF .deps/liblzma_la-block_encoder.Tpo -c common/block_encoder.c -o liblzma_la-block_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,268 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,373 mv -f .deps/liblzma_la-block_encoder.Tpo .deps/liblzma_la-block_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,373 tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmack -I../../src/liblzma/lz/src/liblzma/lzma -I../../src/lsrc/common -DTUKLIB_SYMBOL_PREFIX=lzma_-Wvla -Wformat=2 -Winit-self -Wmissing-include-dfunction-cast -Wwrite-strings -Wlogical-op -Waggregate-retursing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_header_encoder.ck_header_encoder.c' || echo './'`common/block_header_encoder.c install_environment.STDOUT DEBUG 2017-11-18 17:00:03,384 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commo/bin/sh ../../libtool --/common -I../../src/liblzma/che -I../../src/liblzma/rangecoder -I../..iblzma/delta -I../../src/liblzma/simple -I../../ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra irs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-n -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmislo -MD -MP -MF .deps/liblzma_la-block_header_encoder.Tpo -c -o liblzma_la-block_header_encoder.lo `test -f 'common/blolibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliaf -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT .lo -MD -MP -MF .deps/liblzma_la-block_header_encoder.Tpo -c common/block_header_encoder.c -fno-common -DPIC -o .libs/liblzma_la-block_header_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,473 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commo/bin/sh ../../libtool --/common -I../../src/liblzma/che -I../../src/liblzma/rangecoder -I../..iblzma/delta -I../../src/liblzma/simple -I../../ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra irs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-n -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmislo -MD -MP -MF .deps/liblzma_la-block_header_encoder.Tpo -c -o liblzma_la-block_header_encoder.lo `test -f 'common/blolibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliaf -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT .lo -MD -MP -MF .deps/liblzma_la-block_header_encoder.Tpo -c common/block_header_encoder.c -fno-common -DPIC -o .libs/liblzma_la-block_header_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,474 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,474 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,577 /lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/lising -Wfloat-equal -Wundeliblzma_la-block_header_encoderlibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/zma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wform -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite--prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -gs/liblzma_la-block_header_encoder.Tpo -c common/block_header_encoder.c -o liblzma_la-block_header_encoder.o >/dev/null 2>&1 install_environment.STDOUT DEBUG 2017-11-18 17:00:03,596 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src../src/liblzma/lzma -I../common -DTUKLIB_SYMBOL_PREFIX=lat=2 -Winit-self -Wmissing-include-dirsstrings -Wlogical-op -Waggregate-return -Wstrict -O2 -MT liblzma_la-block_header_encoder.lo -MD -MP -MF .depmv -f .deps/liblzma_la-block_header_encoder.Tpo .deps/liblzma_la-block_heada/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_buffer_encoder.lo -MD -MP -MF .deps/liblzma_la-easy_buffer_encoder.Tpo -c -o liblzma_la-easy_buffer_encoder.lo `test -f 'common/easy_buffer_encoder.c' || echo './'`common/easy_buffer_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,680 er_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,680 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src../src/liblzma/lzma -I../common -DTUKLIB_SYMBOL_PREFIX=lat=2 -Winit-self -Wmissing-include-dirsstrings -Wlogical-op -Waggregate-return -Wstrict -O2 -MT liblzma_la-block_header_encoder.lo -MD -MP -MF .depmv -f .deps/liblzma_la-block_header_encoder.Tpo .deps/liblzma_la-block_heada/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_buffer_encoder.lo -MD -MP -MF .deps/liblzma_la-easy_buffer_encoder.Tpo -c -o liblzma_la-easy_buffer_encoder.lo `test -f 'common/easy_buffer_encoder.c' || echo './'`common/easy_buffer_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,680 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzmlibtool: compile: gcc -Dck -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/la/simple -I../../src/common -DTUKLIB_SYMBOL_PREFbility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmual -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -We-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls asy_buffer_encoder.Tpo -c common/easy_buffer_encoder.c -fno-common -DPIC -o .libs/liblzma_la-easy_buffer_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,681 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:03,698 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che../src/liblzma/rangecoderiblzma/delta -I../../src/liblzmIX=lzma_ -D_THREAD_SAFE -pthread -fvisiissing-include-dirs -Wstrict-aliasing -Wfloat-eqlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl-g -O2 -MT liblzma_la-easy_buffer_encoder.lo -MD -MP -MF .deps/liblzma_la-elibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmaliblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_Tibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -ngs -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-ealiblzma_la-easy_buffer_encoder.Tpo -c common/easy_buffer_encoder.c -o liblzma_la-easy_buffer_encoder.o >/dev/null 2>&1 install_environment.STDOUT DEBUG 2017-11-18 17:00:03,769 deps/liblzma_la-easy_buffer_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,782 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che../src/liblzma/rangecoderiblzma/delta -I../../src/liblzmIX=lzma_ -D_THREAD_SAFE -pthread -fvisiissing-include-dirs -Wstrict-aliasing -Wfloat-eqlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl-g -O2 -MT liblzma_la-easy_buffer_encoder.lo -MD -MP -MF .deps/liblzma_la-elibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmaliblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_Tibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -ngs -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-ealiblzma_la-easy_buffer_encoder.Tpo -c common/easy_buffer_encoder.c -o liblzma_la-easy_buffer_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,782 deps/liblzma_la-easy_buffer_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,782 /common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/HREAD_SAFE -pthread -fvisWbad-function-cast -Wwrite-strisy_buffer_encoder.lo -MD -MP -MF .deps/mv -f .deps/liblzma_la-easy_buffer_encoder.Tpo ./bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzlta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFEWall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpo-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn oder.lo -MD -MP -MF .deps/liblzma_la-easy_encoder.Tpo -c -o liblzma_la-easy_encoder.lo `test -f 'common/easy_encoder.c' || echo './'`common/easy_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,783 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:03,813 CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -ma -I../../src/liblzma/de -pthread -fvisibility=hidden -inter-arith -Wbad-function-cast -Wwrite-Wredundant-decls -g -O2 -MT liblzma_la-easy_enclibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I-I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast e-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liba_la-easy_encoder.Tpo -c common/easy_encoder.c -fno-common -DPIC -o .libs/liblzma_la-easy_encoder.o install_environment.STDOUT DEBUG 2017-11-18 17:00:03,880 rc/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../s-Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_encoder.lo -MD -MP -MF .deps/liblzma_la-easy_encoder.Tpo -c common/easy_encoder.c -o liblzma_la-easy_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,887 CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -ma -I../../src/liblzma/de -pthread -fvisibility=hidden -inter-arith -Wbad-function-cast -Wwrite-Wredundant-decls -g -O2 -MT liblzma_la-easy_enclibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I-I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast e-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liba_la-easy_encoder.Tpo -c common/easy_encoder.c -fno-common -DPIC -o .libs/liblzma_la-easy_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,887 rc/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../s-Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_encoder.lo -MD -MP -MF .deps/liblzma_la-easy_encoder.Tpo -c common/easy_encoder.c -o liblzma_la-easy_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,887 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,888 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,990 rc/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../s../../src/liblzma/simple all -Wextra -Wvla -Wformat=2 -W-Wwrite-strings -Wlogical-op -Waggregatlzma_la-easy_encoder.lo -MD -MP -MF .deps/liblzmlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition mv -f .deps/liblzma_la-easy_encoder.Tpo .deps/liblzma_la-easy_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:03,990 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_encoder_memusage.lo -M `test -f 'common/easy_encoder_memusage.c' || echo './'`common/easy_encoder_memusage.c install_environment.STDOUT DEBUG 2017-11-18 17:00:04,062 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nD -MP -MF .deps/liblzma_la-easy_encoder_memusage.Tpo -c -o liblzma_la-easy_encoder_memusage.lolibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_encoder_memusage.lo -MD -MP -MF .deps/liblzma_la-easy_encoder_memusage.Tpo -c common/easy_encoder_memusage.c -fno-common -DPIC -o .llibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIBit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_encoder_memusage.lo -MD -MP -MF .deps/liblzme.Tpo -c common/easy_encoder_memusage.c -o liblzma_la-easy_encoder_memusage.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,092 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-pibs/liblzma_la-easy_encoder_memusage.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,093 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nD -MP -MF .deps/liblzma_la-easy_encoder_memusage.Tpo -c -o liblzma_la-easy_encoder_memusage.lolibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_encoder_memusage.lo -MD -MP -MF .deps/liblzma_la-easy_encoder_memusage.Tpo -c common/easy_encoder_memusage.c -fno-common -DPIC -o .llibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIBit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_encoder_memusage.lo -MD -MP -MF .deps/liblzme.Tpo -c common/easy_encoder_memusage.c -o liblzma_la-easy_encoder_memusage.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,095 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,096 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:04,151 oder_memusage.Tpo .deps/liblzma_la-easy_encoder_memusage.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,197 oder_memusage.Tpo .deps/liblzma_la-easy_encoder_memusage.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,197 _SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Wina_la-easy_encoder_memusagmv -f .deps/liblzma_la-easy_enc/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arl-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissiuffer_encoder.lo -MD -MP -MF .deps/liblzma_la-filter_buffer_encoder.Tpo -c -o liblzma_la-filter_buffer_encoder.lo `test -f 'common/filter_buffer_encoder.c' || echo './'`common/filter_buffer_encoder.c install_environment.STDOUT DEBUG 2017-11-18 17:00:04,198 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_blibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../s_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definitarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_buffer_encoder.lo -MD -MP -MF .deps/liblzma_la-filter_buffer_encoder.Tpo -c common/filter_buffer_encoder.c -er_encoder.o install_environment.STDOUT DEBUG 2017-11-18 17:00:04,273 rc/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../s../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_buffer_encoder.lo -MD -MP -MF .deps/liblzma_la-filter_buffer_encoder.Tpo -c common/filter_buffer_encoder.c -o liblzma_la-filter_buffer_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,301 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_blibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../s_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definitarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_buffer_encoder.lo -MD -MP -MF .deps/liblzma_la-filter_buffer_encoder.Tpo -c common/filter_buffer_encoder.c -er_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,301 rc/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../s../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_buffer_encoder.lo -MD -MP -MF .deps/liblzma_la-filter_buffer_encoder.Tpo -c common/filter_buffer_encoder.c -o liblzma_la-filter_buffer_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,301 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,301 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,402 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangrc/common -DTUKLIB_SYMBOL-dirs -Wstrict-aliasing -Wfloation -Wmissing-prototypes -Wmissing-declfno-common -DPIC -o .libs/liblzma_la-filter_bufflibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -Imv -f .deps/liblzma_la-filter_buffer_encoder.Tpo .deps/liblzma_la-filter_buffer_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,402 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_encoder.lo -MD -MP -ter_encoder.c' || echo './'`common/filter_encoder.c install_environment.STDOUT DEBUG 2017-11-18 17:00:04,411 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nMF .deps/liblzma_la-filter_encoder.Tpo -c -o liblzma_la-filter_encoder.lo `test -f 'common/fillibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_encoder.lo -MD -MP -MF .deps/liblzma_la-filter_encoder.Tpo -c common/filter_encoder.c -fno-common -DPIC -o .libs/liblzma_la-filter_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,503 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nMF .deps/liblzma_la-filter_encoder.Tpo -c -o liblzma_la-filter_encoder.lo `test -f 'common/fillibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_encoder.lo -MD -MP -MF .deps/liblzma_la-filter_encoder.Tpo -c common/filter_encoder.c -fno-common -DPIC -o .libs/liblzma_la-filter_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,504 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,608 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../srclibtool: compile: gcc -Dck -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/la/simple -I../../src/common -DTUKLIB_SYMBOL_PREFbility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmual -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -We-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls _encoder.Tpo -c common/filter_encoder.c -o liblzma_la-filter_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,608 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:04,647 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che../src/liblzma/rangecoderiblzma/delta -I../../src/liblzmIX=lzma_ -D_THREAD_SAFE -pthread -fvisiissing-include-dirs -Wstrict-aliasing -Wfloat-eqlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl-g -O2 -MT liblzma_la-filter_encoder.lo -MD -MP -MF .deps/liblzma_la-filtermv -f .deps/liblzma_la-filter_encoder.Tpo .deps/liblzma_la-filter_encoder.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:04,651 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_flags_encoder.lo -MDest -f 'common/filter_flags_encoder.c' || echo './'`common/filter_flags_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,708 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che../src/liblzma/rangecoderiblzma/delta -I../../src/liblzmIX=lzma_ -D_THREAD_SAFE -pthread -fvisiissing-include-dirs -Wstrict-aliasing -Wfloat-eqlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl-g -O2 -MT liblzma_la-filter_encoder.lo -MD -MP -MF .deps/liblzma_la-filtermv -f .deps/liblzma_la-filter_encoder.Tpo .deps/liblzma_la-filter_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,708 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_flags_encoder.lo -MDest -f 'common/filter_flags_encoder.c' || echo './'`common/filter_flags_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,708 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-n -MP -MF .deps/liblzma_la-filter_flags_encoder.Tpo -c -o liblzma_la-filter_flags_encoder.lo `tlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_flags_encoder.lo -MD -MP -MF .deps/liblzma_la-filter_flags_encoder.Tpo -c common/filter_flags_encoder.c -fno-common -DPIC -o .libs/liblzma_la-filter_flags_encoder.o install_environment.STDOUT DEBUG 2017-11-18 17:00:04,759 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../srcn -I../../src/liblzma/che -I../../src/liblzma/rangecoder../src/liblzma/delta -I../../src/liblzmMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-eqrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl -Wredundant-decls -g -O2 -MT liblzma_la-filter_flags_encoder.lo -MD -MP -MF .deps/liblzma_la- >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,810 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../srcn -I../../src/liblzma/che -I../../src/liblzma/rangecoder../src/liblzma/delta -I../../src/liblzmMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-eqrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl -Wredundant-decls -g -O2 -MT liblzma_la-filter_flags_encoder.lo -MD -MP -MF .deps/liblzma_la- >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,810 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,810 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:04,882 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nF .deps/liblzma_la-index_encoder.Tpo -c -o liblzma_la-index_encoder.lo `test -f 'common/index_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index_encoder.lo -MD -MP -MF .deps/liblzma_la-index_encoder.Tpo -c common/index_encoder.c -fno-common -DPIC -o .libs/liblzma_la-index_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,913 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commock -I../../src/liblzma/lz -I../../src/liblzma/lzma -I../a/simple -I../../src/common -DTUKLIB_SYbility=hidden -Wall -Wextra -Wvla -Wformat=2 -Wiual -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwe-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturnfilter_flags_encoder.Tpo -c common/filter_flags_encoder.c -o liblzma_la-filter_flags_encoder.omv -f .deps/liblzma_la-filter_flags_encoder.Tpo .deps/liblzma_la-filter_flags_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,913 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-index_encoder.lo -MD -MP -Mencoder.c' || echo './'`common/index_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,914 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nF .deps/liblzma_la-index_encoder.Tpo -c -o liblzma_la-index_encoder.lo `test -f 'common/index_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index_encoder.lo -MD -MP -MF .deps/liblzma_la-index_encoder.Tpo -c common/index_encoder.c -fno-common -DPIC -o .libs/liblzma_la-index_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:04,914 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:04,969 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rang-MP -MF .deps/liblzma_la-index_encoder.Tpo -c common/index_encoder.c -o liblzma_la-index_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,019 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rang-MP -MF .deps/liblzma_la-index_encoder.Tpo -c common/index_encoder.c -o liblzma_la-index_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,020 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,122 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototyplibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index_encoder.lo -MD mv -f .deps/liblzma_la-index_encoder.Tpo .deps/liblzma_la-index_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,122 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_buffer_encoder.lo -M `test -f 'common/stream_buffer_encoder.c' || echo './'`common/stream_buffer_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,123 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-pibs/liblzma_la-stream_buffer_encoder.o install_environment.STDOUT DEBUG 2017-11-18 17:00:05,192 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nD -MP -MF .deps/liblzma_la-stream_buffer_encoder.Tpo -c -o liblzma_la-stream_buffer_encoder.lolibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_buffer_encoder.lo -MD -MP -MF .deps/liblzma_la-stream_buffer_encoder.Tpo -c common/stream_buffer_encoder.c -fno-common -DPIC -o .llibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIBit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_buffer_encoder.lo -MD -MP -MF .deps/liblzmr.Tpo -c common/stream_buffer_encoder.c -o liblzma_la-stream_buffer_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,226 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nD -MP -MF .deps/liblzma_la-stream_buffer_encoder.Tpo -c -o liblzma_la-stream_buffer_encoder.lolibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_buffer_encoder.lo -MD -MP -MF .deps/liblzma_la-stream_buffer_encoder.Tpo -c common/stream_buffer_encoder.c -fno-common -DPIC -o .llibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIBit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_buffer_encoder.lo -MD -MP -MF .deps/liblzmr.Tpo -c common/stream_buffer_encoder.c -o liblzma_la-stream_buffer_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,227 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,227 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:05,275 uffer_encoder.Tpo .deps/liblzma_la-stream_buffer_encoder.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:05,277 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_e/stream_encoder.c install_environment.STDOUT DEBUG 2017-11-18 17:00:05,318 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggrela-stream_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,329 uffer_encoder.Tpo .deps/liblzma_la-stream_buffer_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,329 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_e/stream_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,329 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggrela-stream_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,429 _SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Wina_la-stream_buffer_encodemv -f .deps/liblzma_la-stream_b/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arl-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissincoder.lo -MD -MP -MF .deps/liblzma_la-stream_encoder.Tpo -c -o liblzma_la-stream_encoder.lo `test -f 'common/stream_encoder.c' || echo './'`commonlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_encoder.lo -MD -MP -MF .deps/liblzma_la-stream_encoder.Tpo -c common/stream_encoder.c -fno-common -DPIC -o .libs/liblzma_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_encoder.lo -MD -MP -MF .deps/liblzma_la-stream_encoder.Tpo -c common/stream_encoder.c -o liblzma_la-stream_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,430 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,430 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,533 mv -f .deps/liblzma_la-stream_encoder.Tpo .deps/liblzma_la-stream_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,533 tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmack -I../../src/liblzma/lz/src/liblzma/lzma -I../../src/lsrc/common -DTUKLIB_SYMBOL_PREFIX=lzma_-Wvla -Wformat=2 -Winit-self -Wmissing-include-dfunction-cast -Wwrite-strings -Wlogical-op -Waggregate-retursing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_flags_encoder.eam_flags_encoder.c' || echo './'`common/stream_flags_encoder.c install_environment.STDOUT DEBUG 2017-11-18 17:00:05,564 Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -/bin/sh ../../libtool --/common -I../../src/liblzma/che -I../../src/liblzma/rangecoder -I../..iblzma/delta -I../../src/liblzma/simple -I../../ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra irs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-n -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmislo -MD -MP -MF .deps/liblzma_la-stream_flags_encoder.Tpo -c -o liblzma_la-stream_flags_encoder.lo `test -f 'common/strlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_flags_encoder.lo -MD -MP -MF .deps/liblzma_la-stream_flags_encoder.Tpo -c common/stream_flags_encoder.c -fno-common -DPIC -o .libs/liblzma_la-stream_flags_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,634 Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -/bin/sh ../../libtool --/common -I../../src/liblzma/che -I../../src/liblzma/rangecoder -I../..iblzma/delta -I../../src/liblzma/simple -I../../ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra irs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-n -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmislo -MD -MP -MF .deps/liblzma_la-stream_flags_encoder.Tpo -c -o liblzma_la-stream_flags_encoder.lo `test -f 'common/strlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_flags_encoder.lo -MD -MP -MF .deps/liblzma_la-stream_flags_encoder.Tpo -c common/stream_flags_encoder.c -fno-common -DPIC -o .libs/liblzma_la-stream_flags_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,635 /lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/lilibtool: compile: gcc -Dck -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/la/simple -I../../src/common -DTUKLIB_SYMBOL_PREFbility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmual -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -We-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls stream_flags_encoder.Tpo -c common/stream_flags_encoder.c -o liblzma_la-stream_flags_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,635 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,635 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:05,721 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che../src/liblzma/rangecoderiblzma/delta -I../../src/liblzmIX=lzma_ -D_THREAD_SAFE -pthread -fvisiissing-include-dirs -Wstrict-aliasing -Wfloat-eqlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl-g -O2 -MT liblzma_la-stream_flags_encoder.lo -MD -MP -MF .deps/liblzma_la-mv -f .deps/liblzma_la-stream_flags_encoder.Tpo .deps/liblzma_la-stream_flags_encoder.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:05,724 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-vli_encoder.lo -MD -MP -MF c' || echo './'`common/vli_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,736 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che../src/liblzma/rangecoderiblzma/delta -I../../src/liblzmIX=lzma_ -D_THREAD_SAFE -pthread -fvisiissing-include-dirs -Wstrict-aliasing -Wfloat-eqlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl-g -O2 -MT liblzma_la-stream_flags_encoder.lo -MD -MP -MF .deps/liblzma_la-mv -f .deps/liblzma_la-stream_flags_encoder.Tpo .deps/liblzma_la-stream_flags_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,736 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-vli_encoder.lo -MD -MP -MF c' || echo './'`common/vli_encoder.c install_environment.STDOUT DEBUG 2017-11-18 17:00:05,833 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-plibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-vli_encoder.lo -MD -MP -MF .deps/liblzma_la-vli_encoder.Tpo -c common/vli_encoder.c -o liblzma_la-vli_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,840 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-n.deps/liblzma_la-vli_encoder.Tpo -c -o liblzma_la-vli_encoder.lo `test -f 'common/vli_encoder.libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-vli_encoder.lo -MD -MP -MF .deps/liblzma_la-vli_encoder.Tpo -c common/vli_encoder.c -fno-common -DPIC -o .libs/liblzma_la-vli_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,840 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-plibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-vli_encoder.lo -MD -MP -MF .deps/liblzma_la-vli_encoder.Tpo -c common/vli_encoder.c -o liblzma_la-vli_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,840 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,840 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:05,908 i_encoder.Tpo .deps/liblzma_la-vli_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,944 i_encoder.Tpo .deps/liblzma_la-vli_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:05,944 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../srcmv -f .deps/liblzma_la-vl/bin/sh ../../libtool --tag=CCn -I../../src/liblzma/check -I../../srciblzma/rangecoder -I../../src/liblzma/lzma -I../c/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lity=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-alone_decoder.lo -MD -MP -MF .deps/libl/alone_decoder.c' || echo './'`common/alone_decoder.c install_environment.STDOUT DEBUG 2017-11-18 17:00:05,946 --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commo/liblzma/lz -I../../src/l../src/liblzma/delta -I../../srzma_ -D_THREAD_SAFE -pthread -fvisibils -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadt-prototypes -Wold-style-definition -Wmissing-prototypes -Wmzma_la-alone_decoder.Tpo -c -o liblzma_la-alone_decoder.lo `test -f 'commonlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmaliblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_Tibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -ngs -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-ala_la-alone_decoder.Tpo -c common/alone_decoder.c -fno-common -DPIC -o .libs/liblzma_la-alone_decoder.o install_environment.STDOUT DEBUG 2017-11-18 17:00:06,046 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/I../../src/liblzma/delta -D_THREAD_SAFE -pthread -fvisibng -Wfloat-equal -Wundef -Wshadow -Wpoiion -Wmissing-prototypes -Wmissing-declarations c -o liblzma_la-alone_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,046 --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commo/liblzma/lz -I../../src/l../src/liblzma/delta -I../../srzma_ -D_THREAD_SAFE -pthread -fvisibils -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadt-prototypes -Wold-style-definition -Wmissing-prototypes -Wmzma_la-alone_decoder.Tpo -c -o liblzma_la-alone_decoder.lo `test -f 'commonlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmaliblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_Tibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -ngs -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-ala_la-alone_decoder.Tpo -c common/alone_decoder.c -fno-common -DPIC -o .libs/liblzma_la-alone_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,047 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/I../../src/liblzma/delta -D_THREAD_SAFE -pthread -fvisibng -Wfloat-equal -Wundef -Wshadow -Wpoiion -Wmissing-prototypes -Wmissing-declarations c -o liblzma_la-alone_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,047 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,047 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:06,198 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-n .deps/liblzma_la-auto_decoder.Tpo -c -o liblzma_la-auto_decoder.lo `test -f 'common/auto_decolibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-auto_decoder.lo -MD -MP -MF .deps/liblzma_la-auto_decoder.Tpo -c common/auto_decoder.c -fno-common -DPIC -o .libs/liblzma_la-auto_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,251 /common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/HREAD_SAFE -pthread -fvisWbad-function-cast -Wwrite-strione_decoder.lo -MD -MP -MF .deps/liblzmlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-alone_decoder.lo -MD -MP -MF .deps/liblzma_la-alone_decoder.Tpo -c common/alone_decoder.mv -f .deps/liblzma_la-alone_decoder.Tpo .deps/liblzma_la-alone_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,251 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-auto_decoder.lo -MD -MP -MFder.c' || echo './'`common/auto_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,251 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-n .deps/liblzma_la-auto_decoder.Tpo -c -o liblzma_la-auto_decoder.lo `test -f 'common/auto_decolibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-auto_decoder.lo -MD -MP -MF .deps/liblzma_la-auto_decoder.Tpo -c common/auto_decoder.c -fno-common -DPIC -o .libs/liblzma_la-auto_decoder.o 127.0.0.1 - - [18/Nov/2017:17:00:06 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,253 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,357 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../srclibtool: compile: gcc -Dck -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/la/simple -I../../src/common -DTUKLIB_SYMBOL_PREFbility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmual -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -We-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls oder.Tpo -c common/auto_decoder.c -o liblzma_la-auto_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,357 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:06,377 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che../src/liblzma/rangecoderiblzma/delta -I../../src/liblzmIX=lzma_ -D_THREAD_SAFE -pthread -fvisiissing-include-dirs -Wstrict-aliasing -Wfloat-eqlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl-g -O2 -MT liblzma_la-auto_decoder.lo -MD -MP -MF .deps/liblzma_la-auto_decmv -f .deps/liblzma_la-auto_decoder.Tpo .deps/liblzma_la-auto_decoder.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:06,379 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_buffer_decoder.lo -MDest -f 'common/block_buffer_decoder.c' || echo './'`common/block_buffer_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,459 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che../src/liblzma/rangecoderiblzma/delta -I../../src/liblzmIX=lzma_ -D_THREAD_SAFE -pthread -fvisiissing-include-dirs -Wstrict-aliasing -Wfloat-eqlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl-g -O2 -MT liblzma_la-auto_decoder.lo -MD -MP -MF .deps/liblzma_la-auto_decmv -f .deps/liblzma_la-auto_decoder.Tpo .deps/liblzma_la-auto_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,459 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_buffer_decoder.lo -MDest -f 'common/block_buffer_decoder.c' || echo './'`common/block_buffer_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,459 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-n -MP -MF .deps/liblzma_la-block_buffer_decoder.Tpo -c -o liblzma_la-block_buffer_decoder.lo `tlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_buffer_decoder.lo -MD -MP -MF .deps/liblzma_la-block_buffer_decoder.Tpo -c common/block_buffer_decoder.c -fno-common -DPIC -o .libs/liblzma_la-block_buffer_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,459 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,560 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commo/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_buffer_decoder.lo -MD -MP -MF .deps/liblzma_la-block_buffer_decoder.Tpo -c common/block_buffer_decoder.c -o liblzma_la-block_buffer_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,560 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:06,570 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-pn -I../../src/liblzma/check -I../../src/bin/sh ../../libtool --tag=CC --mode=compilelzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangeclzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/commo -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissoat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_decoder.lo -MD -MP -MF .deps/liblzma_la-block_decolock_decoder.c' || echo './'`common/block_decoder.c install_environment.STDOUT DEBUG 2017-11-18 17:00:06,607 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangrc/common -DTUKLIB_SYMBOL-dirs -Wstrict-aliasing -Wfloation -Wmissing-prototypes -Wmissing-decls/liblzma_la-block_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,662 mv -f .deps/liblzma_la-block_buffer_decoder.Tpo .deps/liblzma_la-block_buffer_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,662 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-pn -I../../src/liblzma/check -I../../src/bin/sh ../../libtool --tag=CC --mode=compilelzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangeclzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/commo -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissoat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_decoder.lo -MD -MP -MF .deps/liblzma_la-block_decolock_decoder.c' || echo './'`common/block_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,662 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangrc/common -DTUKLIB_SYMBOL-dirs -Wstrict-aliasing -Wfloation -Wmissing-prototypes -Wmissing-decls/liblzma_la-block_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,662 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:06,693 ta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_decoder.lo -MD -MP -MF .deps/liblzma_la-block_decoder.Tpo -c common/block_decoder.c -o liblzma_la-block_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,768 ta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_decoder.lo -MD -MP -MF .deps/liblzma_la-block_decoder.Tpo -c common/block_decoder.c -o liblzma_la-block_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,768 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:06,782 mv -f .deps/liblzma_la-block_decoder.Tpo .deps/liblzma_la-block_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,870 mv -f .deps/liblzma_la-block_decoder.Tpo .deps/liblzma_la-block_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,871 gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liboder -I../../src/liblzma/n -DTUKLIB_SYMBOL_PREFIX=lzma_ ing-include-dirs -Wstrict-aliasing -Wflt-prototypes -Wold-style-definition -Wmissing-prder.Tpo -c -o liblzma_la-block_decoder.lo `test -f 'common/blibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../s_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definitarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_decoder.lo -MD -MP -MF .deps/liblzma_la-block_decoder.Tpo -c common/block_decoder.c -fno-common -DPIC -o .liblibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/del/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simll -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_header_decoliblzma_la-block_header_decoder.Tpo -c -o liblzma_la-block_header_decoder.lo `test -f 'common/block_header_decoder.c' || echo './'`common/block_header_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,871 ONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I./rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_header_decoder.lo -MD -MP -MF .deps/liblzma_la-block_header_decoder.Tpo -c common/block_header_decoder.c -fno-common -DPIC -o .libs/liblzma_la-block_header_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,871 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:06,924 ple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wader.lo -MD -MP -MF .deps/libtool: compile: gcc -DHAVE_C./../src/liblzma/lz -I../../src/liblzman -I../../src/liblzma/check -I../../src/liblzma/ngecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta /../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -WpoiWlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_header_decoder.lo -MD -MP -MF .deps/liblzma_la-block_header_decoder.Tpo -c common/block_header_decoder.c -o liblzma_la-block_header_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,975 ple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wader.lo -MD -MP -MF .deps/libtool: compile: gcc -DHAVE_C./../src/liblzma/lz -I../../src/liblzman -I../../src/liblzma/check -I../../src/liblzma/ngecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta /../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -WpoiWlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-block_header_decoder.lo -MD -MP -MF .deps/liblzma_la-block_header_decoder.Tpo -c common/block_header_decoder.c -o liblzma_la-block_header_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:06,975 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:07,021 a_la-block_header_decoder.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:07,066 ../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/libl../src/liblzma/simple -I.=2 -Winit-self -Wmissing-includt-prototypes -Wold-style-definition -Wmo liblzma_la-easy_decoder_memusage.lo `test -f 'libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I-I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast e-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT libps/liblzma_la-easy_decoder_memusage.Tpo -c common/easy_decoder_memusage.c -fno-common -DPIC -o .libs/liblzma_la-easy_decoder_memusage.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,075 a_la-block_header_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,076 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commolz -I../../src/liblzma/ra-I../../src/liblzma/simple -I..ility=hidden -Wall -Wextra -Wvla -Wformnter-arith -Wbad-function-cast -Wwrite-strings -mv -f .deps/liblzma_la-block_header_decoder.Tpo .deps/liblzm/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -Izma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I.././../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformate-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_decoder_memusage.lo -MD -MP -MF .deps/liblzma_la-easy_decoder_memusage.Tpo -c -common/easy_decoder_memusage.c' || echo './'`common/easy_decoder_memusage.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,078 ../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/libl../src/liblzma/simple -I.=2 -Winit-self -Wmissing-includt-prototypes -Wold-style-definition -Wmo liblzma_la-easy_decoder_memusage.lo `test -f 'libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I-I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast e-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT libps/liblzma_la-easy_decoder_memusage.Tpo -c common/easy_decoder_memusage.c -fno-common -DPIC -o .libs/liblzma_la-easy_decoder_memusage.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,178 rc/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../s../../src/liblzma/simple all -Wextra -Wvla -Wformat=2 -W-Wwrite-strings -Wlogical-op -Waggregatlzma_la-easy_decoder_memusage.lo -MD -MP -MF .delibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-easy_decoder_memusage.lo -MD -MP -MF .deps/liblzma_la-easy_decoder_memusage.Tpo -c common/easy_decoder_memusage.c -o liblzma_la-easy_decoder_memusage.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,178 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,178 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:07,252 rc/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../s/bin/sh ../../libtool --/common -I../../src/liblzma/che -I../../src/liblzma/rangecoder -I../..iblzma/delta -I../../src/liblzma/simple -I../../ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra irs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-n -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmis.lo -MD -MP -MF .deps/liblzma_la-filter_buffer_decoder.Tpo -c -o liblzma_la-filter_buffer_decoder.lo `test -f 'common/libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliaf -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT r.lo -MD -MP -MF .deps/liblzma_la-filter_buffer_decoder.Tpo -c common/filter_buffer_decoder.c -fno-common -DPIC -o .libs/liblzma_la-filter_buffer_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,279 mv -f .deps/liblzma_la-easy_decoder_memusage.Tpo .deps/liblzma_la-easy_decoder_memusage.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,280 tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmack -I../../src/liblzma/lz/src/liblzma/lzma -I../../src/lsrc/common -DTUKLIB_SYMBOL_PREFIX=lzma_-Wvla -Wformat=2 -Winit-self -Wmissing-include-dfunction-cast -Wwrite-strings -Wlogical-op -Waggregate-retursing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_buffer_decoderfilter_buffer_decoder.c' || echo './'`common/filter_buffer_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,280 rc/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../s/bin/sh ../../libtool --/common -I../../src/liblzma/che -I../../src/liblzma/rangecoder -I../..iblzma/delta -I../../src/liblzma/simple -I../../ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra irs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-n -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmis.lo -MD -MP -MF .deps/liblzma_la-filter_buffer_decoder.Tpo -c -o liblzma_la-filter_buffer_decoder.lo `test -f 'common/libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliaf -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT r.lo -MD -MP -MF .deps/liblzma_la-filter_buffer_decoder.Tpo -c common/filter_buffer_decoder.c -fno-common -DPIC -o .libs/liblzma_la-filter_buffer_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,280 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,381 /lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/lising -Wfloat-equal -Wundeliblzma_la-filter_buffer_decodelibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/zma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wform -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite--prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -gps/liblzma_la-filter_buffer_decoder.Tpo -c common/filter_buffer_decoder.c -o liblzma_la-filter_buffer_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,381 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:07,423 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src../src/liblzma/lzma -I../common -DTUKLIB_SYMBOL_PREFIX=lat=2 -Winit-self -Wmissing-include-dirsstrings -Wlogical-op -Waggregate-return -Wstrict -O2 -MT liblzma_la-filter_buffer_decoder.lo -MD -MP -MF .demv -f .deps/liblzma_la-filter_buffer_decoder.Tpo .deps/liblzma_la-filter_bu/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -D_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -W-Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundancoder.lo -MD -MP -MF .deps/liblzma_la-filter_decoder.Tpo -c -o liblzma_la-filter_decoder.lo `test -f 'common/filter_decoder.c' || echo './'`common/filter_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,482 ffer_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,482 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src../src/liblzma/lzma -I../common -DTUKLIB_SYMBOL_PREFIX=lat=2 -Winit-self -Wmissing-include-dirsstrings -Wlogical-op -Waggregate-return -Wstrict -O2 -MT liblzma_la-filter_buffer_decoder.lo -MD -MP -MF .demv -f .deps/liblzma_la-filter_buffer_decoder.Tpo .deps/liblzma_la-filter_bu/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -D_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -W-Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundancoder.lo -MD -MP -MF .deps/liblzma_la-filter_decoder.Tpo -c -o liblzma_la-filter_decoder.lo `test -f 'common/filter_decoder.c' || echo './'`common/filter_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,482 liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/TUKLIB_SYMBOL_PREFIX=lzmaundef -Wshadow -Wpointer-arith t-decls -g -O2 -MT liblzma_la-filter_delibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_decoder.lo -MD -MP -MF .deps/liblzma_la-filter_decoder.Tpo -c common/filter_decod install_environment.STDOUT DEBUG 2017-11-18 17:00:07,549 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/I../../src/liblzma/delta -D_THREAD_SAFE -pthread -fvisibng -Wfloat-equal -Wundef -Wshadow -Wpoiion -Wmissing-prototypes -Wmissing-declarations er.c -fno-common -DPIC -o .libs/liblzma_la-filter_decoder.olibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_decoder.lo -MD -MP -MF .deps/liblzma_la-filter_decoder.Tpo -c common/filter_decoder.c -o liblzma_la-filter_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,587 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/I../../src/liblzma/delta -D_THREAD_SAFE -pthread -fvisibng -Wfloat-equal -Wundef -Wshadow -Wpoiion -Wmissing-prototypes -Wmissing-declarations er.c -fno-common -DPIC -o .libs/liblzma_la-filter_decoder.olibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_decoder.lo -MD -MP -MF .deps/liblzma_la-filter_decoder.Tpo -c common/filter_decoder.c -o liblzma_la-filter_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,587 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,587 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:07,642 lter_decoder.Tpo .deps/liblzma_la-filter_decoder.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:07,645 --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commo/liblzma/lz -I../../src/l../src/liblzma/delta -I../../srzma_ -D_THREAD_SAFE -pthread -fvisibils -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadt-prototypes -Wold-style-definition -Wmissing-prototypes -Wmps/liblzma_la-filter_flags_decoder.Tpo -c -o liblzma_la-filter_flags_decoder.lo `test -f 'common/filter_flags_decoder.c' || echo './'`common/filter_flags_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,688 lter_decoder.Tpo .deps/liblzma_la-filter_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,689 --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commo/liblzma/lz -I../../src/l../src/liblzma/delta -I../../srzma_ -D_THREAD_SAFE -pthread -fvisibils -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadt-prototypes -Wold-style-definition -Wmissing-prototypes -Wmps/liblzma_la-filter_flags_decoder.Tpo -c -o liblzma_la-filter_flags_decoder.lo `test -f 'common/filter_flags_decoder.c' || echo './'`common/filter_flags_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,689 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangmv -f .deps/liblzma_la-fi/bin/sh ../../libtool --tag=CCn -I../../src/liblzma/check -I../../srciblzma/rangecoder -I../../src/liblzma/lzma -I../c/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lity=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-filter_flags_decoder.lo -MD -MP -MF .delibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliaf -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT .lo -MD -MP -MF .deps/liblzma_la-filter_flags_decoder.Tpo -c common/filter_flags_decoder.c -fno-common -DPIC -o .libs/liblzma_la-filter_flags_decoder.o install_environment.STDOUT DEBUG 2017-11-18 17:00:07,747 /lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/lising -Wfloat-equal -Wundeliblzma_la-filter_flags_decoderlibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/zma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wform -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite--prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -gs/liblzma_la-filter_flags_decoder.Tpo -c common/filter_flags_decoder.c -o liblzma_la-filter_flags_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,791 /lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/lising -Wfloat-equal -Wundeliblzma_la-filter_flags_decoderlibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/zma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wform -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite--prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -gs/liblzma_la-filter_flags_decoder.Tpo -c common/filter_flags_decoder.c -o liblzma_la-filter_flags_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,791 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,791 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:07,825 gs_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,895 gs_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,895 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src../src/liblzma/lzma -I../common -DTUKLIB_SYMBOL_PREFIX=lat=2 -Winit-self -Wmissing-include-dirsstrings -Wlogical-op -Waggregate-return -Wstrict -O2 -MT liblzma_la-filter_flags_decoder.lo -MD -MP -MF .depmv -f .deps/liblzma_la-filter_flags_decoder.Tpo .deps/liblzma_la-filter_fla/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -D_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -W-Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundanoder.lo -MD -MP -MF .deps/liblzma_la-index_decoder.Tpo -c -o liblzma_la-index_decoder.lo `test -f 'common/index_decoder.c' || echo './'`common/index_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,895 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/I../../src/liblzma/delta -D_THREAD_SAFE -pthread -fvisibng -Wfloat-equal -Wundef -Wshadow -Wpoiion -Wmissing-prototypes -Wmissing-declarations c -fno-common -DPIC -o .libs/liblzma_la-index_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:07,895 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:07,963 liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/TUKLIB_SYMBOL_PREFIX=lzmaundef -Wshadow -Wpointer-arith t-decls -g -O2 -MT liblzma_la-index_declibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index_decoder.lo -MD -MP -MF .deps/liblzma_la-index_decoder.Tpo -c common/index_decoder.libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index_decoder.lo -MD -MP -MF .deps/liblzma_la-index_decoder.Tpo -c common/index_decoder.c -o liblzma_la-index_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,000 liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/TUKLIB_SYMBOL_PREFIX=lzmaundef -Wshadow -Wpointer-arith t-decls -g -O2 -MT liblzma_la-index_declibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index_decoder.lo -MD -MP -MF .deps/liblzma_la-index_decoder.Tpo -c common/index_decoder.libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index_decoder.lo -MD -MP -MF .deps/liblzma_la-index_decoder.Tpo -c common/index_decoder.c -o liblzma_la-index_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,001 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:08,068 coder.Tpo .deps/liblzma_la-index_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,103 coder.Tpo .deps/liblzma_la-index_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,103 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggremv -f .deps/liblzma_la-index_de/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arl-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissish.lo -MD -MP -MF .deps/liblzma_la-index_hash.Tpo -c -o liblzma_la-index_hash.lo `test -f 'common/index_hash.c' || echo './'`common/index_hash.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,207 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangrc/common -DTUKLIB_SYMBOL-dirs -Wstrict-aliasing -Wfloation -Wmissing-prototypes -Wmissing-decl_la-index_hash.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,208 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:08,229 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index_halibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../s_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definitarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index_hash.lo -MD -MP -MF .deps/liblzma_la-index_hash.Tpo -c common/index_hash.c -fno-common -DPIC -o .libs/liblzmalibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/deld -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wssing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index_hash.lo -MD -MP -MF .deps/liblzma_la-index_hash.Tpo -c common/index_hash.c -o liblzma_la-index_hash.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,312 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index_halibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../s_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definitarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index_hash.lo -MD -MP -MF .deps/liblzma_la-index_hash.Tpo -c common/index_hash.c -fno-common -DPIC -o .libs/liblzmalibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/deld -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wssing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-index_hash.lo -MD -MP -MF .deps/liblzma_la-index_hash.Tpo -c common/index_hash.c -o liblzma_la-index_hash.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,312 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:08,333 sh.Tpo .deps/liblzma_la-index_hash.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:08,336 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_bcoder.c' || echo './'`common/stream_buffer_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,413 sh.Tpo .deps/liblzma_la-index_hash.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,413 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_bcoder.c' || echo './'`common/stream_buffer_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,413 ta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthreamissing-declarations -Wmimv -f .deps/liblzma_la-index_ha/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arl-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissiuffer_decoder.lo -MD -MP -MF .deps/liblzma_la-stream_buffer_decoder.Tpo -c -o liblzma_la-stream_buffer_decoder.lo `test -f 'common/stream_buffer_delibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_buffer_decoder.lo -MD -MP -MF .deps/liblzma_la-stream_buffer_decoder.Tpo -c common/stream_buffer_decoder.c -fno-common -DPIC -o .libs/liblzma_la-stream_buffer_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,414 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:08,454 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKn -I../../src/liblzma/che -I../../src/liblzma/rangecoder../src/liblzma/delta -I../../src/liblzmMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-eqrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl -Wredundant-decls -g -O2 -MT liblzma_la-stream_buffer_decoder.lo -MD -MP -MF .deps/liblzma_laer.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,514 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKn -I../../src/liblzma/che -I../../src/liblzma/rangecoder../src/liblzma/delta -I../../src/liblzmMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-eqrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl -Wredundant-decls -g -O2 -MT liblzma_la-stream_buffer_decoder.lo -MD -MP -MF .deps/liblzma_laer.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,515 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:08,585 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nMF .deps/liblzma_la-stream_decoder.Tpo -c -o liblzma_la-stream_decoder.lo `test -f 'common/strlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_decoder.lo -MD -MP -MF .deps/liblzma_la-stream_decoder.Tpo -c common/stream_decoder.c -fno-common -DPIC -o .libs/liblzma_la-stream_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,620 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commock -I../../src/liblzma/lz -I../../src/liblzma/lzma -I../a/simple -I../../src/common -DTUKLIB_SYbility=hidden -Wall -Wextra -Wvla -Wformat=2 -Wiual -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwe-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn-stream_buffer_decoder.Tpo -c common/stream_buffer_decoder.c -o liblzma_la-stream_buffer_decodmv -f .deps/liblzma_la-stream_buffer_decoder.Tpo .deps/liblzma_la-stream_buffer_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,620 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_decoder.lo -MD -MP -eam_decoder.c' || echo './'`common/stream_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,620 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nMF .deps/liblzma_la-stream_decoder.Tpo -c -o liblzma_la-stream_decoder.lo `test -f 'common/strlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_decoder.lo -MD -MP -MF .deps/liblzma_la-stream_decoder.Tpo -c common/stream_decoder.c -fno-common -DPIC -o .libs/liblzma_la-stream_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,622 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,727 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../srclibtool: compile: gcc -Dck -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_decoder.lo -MD -MP -MF .deps/liblzma_la-stream_decoder.Tpo -c common/stream_decoder.c -o liblzma_la-stream_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,727 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:08,800 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che/bin/sh ../../libtool --/common -I../../src/liblzma/che -I../../src/liblzma/rangecoder -I../..iblzma/delta -I../../src/liblzma/simple -I../../ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra irs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-n -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmislo -MD -MP -MF .deps/liblzma_la-stream_flags_decoder.Tpo -c -o liblzma_la-stream_flags_decoder.lo `test -f 'common/stream_flags_decoder.c' || echo './'`common/stream_flags_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,831 mv -f .deps/liblzma_la-stream_decoder.Tpo .deps/liblzma_la-stream_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,831 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che/bin/sh ../../libtool --/common -I../../src/liblzma/che -I../../src/liblzma/rangecoder -I../..iblzma/delta -I../../src/liblzma/simple -I../../ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra irs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-n -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmislo -MD -MP -MF .deps/liblzma_la-stream_flags_decoder.Tpo -c -o liblzma_la-stream_flags_decoder.lo `test -f 'common/stream_flags_decoder.c' || echo './'`common/stream_flags_decoder.c install_environment.STDOUT DEBUG 2017-11-18 17:00:08,909 /common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/HREAD_SAFE -pthread -fvisWbad-function-cast -Wwrite-striream_flags_decoder.lo -MD -MP -MF .depslibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_flags_decoder.lo -MD -MP -MF .deps/liblzma_la-stream_flags_decoder.Tpo -c common/>/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,934 tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmack -I../../src/liblzma/lz/src/liblzma/lzma -I../../src/lsrc/common -DTUKLIB_SYMBOL_PREFIX=lzma_-Wvla -Wformat=2 -Winit-self -Wmissing-include-dfunction-cast -Wwrite-strings -Wlogical-op -Waggregate-retursing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_flags_decoder.libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmaliblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_Tibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -ngs -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-st/liblzma_la-stream_flags_decoder.Tpo -c common/stream_flags_decoder.c -fno-common -DPIC -o .libs/liblzma_la-stream_flags_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,934 /common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/HREAD_SAFE -pthread -fvisWbad-function-cast -Wwrite-striream_flags_decoder.lo -MD -MP -MF .depslibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-stream_flags_decoder.lo -MD -MP -MF .deps/liblzma_la-stream_flags_decoder.Tpo -c common/>/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,934 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:08,934 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:08,982 gs_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,037 gs_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,038 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/I../../src/liblzma/delta -D_THREAD_SAFE -pthread -fvisibng -Wfloat-equal -Wundef -Wshadow -Wpoiion -Wmissing-prototypes -Wmissing-declarations stream_flags_decoder.c -o liblzma_la-stream_flags_decoder.o mv -f .deps/liblzma_la-stream_flags_decoder.Tpo .deps/liblzma_la-stream_fla/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -D_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -W-Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundaner.lo -MD -MP -MF .deps/liblzma_la-vli_decoder.Tpo -c -o liblzma_la-vli_decoder.lo `test -f 'common/vli_decoder.c' || echo './'`common/vli_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,038 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/I../../src/liblzma/delta -D_THREAD_SAFE -pthread -fvisibng -Wfloat-equal -Wundef -Wshadow -Wpoiion -Wmissing-prototypes -Wmissing-declarations o-common -DPIC -o .libs/liblzma_la-vli_decoder.o install_environment.STDOUT DEBUG 2017-11-18 17:00:09,100 liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/TUKLIB_SYMBOL_PREFIX=lzmaundef -Wshadow -Wpointer-arith t-decls -g -O2 -MT liblzma_la-vli_decodlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-vli_decoder.lo -MD -MP -MF .deps/liblzma_la-vli_decoder.Tpo -c common/vli_decoder.c -fnlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-vli_decoder.lo -MD -MP -MF .deps/liblzma_la-vli_decoder.Tpo -c common/vli_decoder.c -o liblzma_la-vli_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,140 liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/TUKLIB_SYMBOL_PREFIX=lzmaundef -Wshadow -Wpointer-arith t-decls -g -O2 -MT liblzma_la-vli_decodlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-vli_decoder.lo -MD -MP -MF .deps/liblzma_la-vli_decoder.Tpo -c common/vli_decoder.c -fnlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-vli_decoder.lo -MD -MP -MF .deps/liblzma_la-vli_decoder.Tpo -c common/vli_decoder.c -o liblzma_la-vli_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,140 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,141 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:09,193 der.Tpo .deps/liblzma_la-vli_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,241 der.Tpo .deps/liblzma_la-vli_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,241 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggremv -f .deps/liblzma_la-vli_deco/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arl-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissi -MD -MP -MF .deps/liblzma_la-check.Tpo -c -o liblzma_la-check.lo `test -f 'check/check.c' || echo './'`check/check.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,242 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rang.deps/liblzma_la-check.Tpo -c check/check.c -fno-common -DPIC -o .libs/liblzma_la-check.o 127.0.0.1 - - [18/Nov/2017:17:00:09 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,342 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commod -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-check.lo -MD -MP -MF .deps/liblzma_la-check.Tpo -c check/check.c -o liblzma_la-check.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,342 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,342 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:09,399 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-check.lolibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-check.lo -MD -MP -MF n -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthrea/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simll -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-crc32_table.lo -Ma-crc32_table.Tpo -c -o liblzma_la-crc32_table.lo `test -f 'check/crc32_table.c' || echo './'`check/crc32_table.c install_environment.STDOUT DEBUG 2017-11-18 17:00:09,438 ONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I./rangecoder -I../../src/lc/liblzma/simple -I../../src/covisibility=hidden -Wall -Wextra -Wvla -l -Wundef -Wshadow -Wpointer-arith -Wbad-functioion -Wmissing-prototypes -Wmissing-declarations -Wmissing-noc32_table.c -fno-common -DPIC -o .libs/liblzma_la-crc32_table.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,448 mv -f .deps/liblzma_la-check.Tpo .deps/liblzma_la-check.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,448 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-check.lolibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-check.lo -MD -MP -MF n -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthrea/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simll -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-crc32_table.lo -Ma-crc32_table.Tpo -c -o liblzma_la-crc32_table.lo `test -f 'check/crc32_table.c' || echo './'`check/crc32_table.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,448 ONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I./rangecoder -I../../src/lc/liblzma/simple -I../../src/covisibility=hidden -Wall -Wextra -Wvla -l -Wundef -Wshadow -Wpointer-arith -Wbad-functioion -Wmissing-prototypes -Wmissing-declarations -Wmissing-noc32_table.c -fno-common -DPIC -o .libs/liblzma_la-crc32_table.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,553 ple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -WaD -MP -MF .deps/liblzma_llibtool: compile: gcc -DHAVE_C./../src/liblzma/lz -I../../src/liblzmaiblzma/lzma -I../../src/liblzma/delta -I../../srmmon -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fWformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equan-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definitreturn -Wredundant-decls -g -O2 -MT liblzma_la-crc32_table.lo -MD -MP -MF .deps/liblzma_la-crc32_table.Tpo -c check/crlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliaf -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT MP -MF .deps/liblzma_la-crc32_table.Tpo -c check/crc32_table.c -o liblzma_la-crc32_table.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,553 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,553 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:09,579 /lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/lising -Wfloat-equal -Wundeliblzma_la-crc32_table.lo -MD -mv -f .deps/liblzma_la-crc32_table.Tpo /bin/sh ../../libtool --tag=CC --mode=compilelzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangeclzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/commo -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissoat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-crc32_fast.lo -MD -MP -MF .deps/liblzma_la-crc32_fast.Tpc' || echo './'`check/crc32_fast.c install_environment.STDOUT DEBUG 2017-11-18 17:00:09,623 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rang -MF .deps/liblzma_la-crc32_fast.Tpo -c check/crc32_fast.c -fno-common -DPIC -o .libs/liblzma_la-crc32_fast.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,657 .deps/liblzma_la-crc32_table.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,657 /lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/lising -Wfloat-equal -Wundeliblzma_la-crc32_table.lo -MD -mv -f .deps/liblzma_la-crc32_table.Tpo /bin/sh ../../libtool --tag=CC --mode=compilelzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangeclzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/commo -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissoat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-crc32_fast.lo -MD -MP -MF .deps/liblzma_la-crc32_fast.Tpc' || echo './'`check/crc32_fast.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,657 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rang -MF .deps/liblzma_la-crc32_fast.Tpo -c check/crc32_fast.c -fno-common -DPIC -o .libs/liblzma_la-crc32_fast.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,658 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,761 gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liboder -I../../src/liblzma/n -DTUKLIB_SYMBOL_PREFIX=lzma_ ing-include-dirs -Wstrict-aliasing -Wflt-prototypes -Wold-style-definition -Wmissing-pro -c -o liblzma_la-crc32_fast.lo `test -f 'check/crc32_fast.libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-crc32_fast.lo -MD -MPlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/deld -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wssing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-crc32_fast.lo -MD -MP -MF .deps/liblzma_la-crc32_fast.Tpo -c check/crc32_fast.c -o liblzma_la-crc32_fast.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,762 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,866 st.Tpo .deps/liblzma_la-crc32_fast.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,866 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.oreturn -Wredundant-decls -g -O2 -MT liblzma_la-crc64_table.lo -MD -MP -MF .deps/liblzma_la-crc64_table.Tpo -c -o liblzma_la-crc64_table.lo `test -f 'check/crc64_table.c' || echo './'`check/crc64_table.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,866 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commoLIB_SYMBOL_PREFIX=lzma_ -gate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-crc64_table.lo -MD -MP -MF .deps/liblzma_la-crc64_table.Tpo -c check/crc64_table.c -fno-common -DPIC -o .libs/liblzma_la-crc64_table.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,866 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:09,881 ta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthreamissing-declarations -Wmimv -f .deps/liblzma_la-crc32_fa/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nn -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKD_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggrelibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIBit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-crc64_table.lo -MD -MP -MF .deps/liblzma_la-crc64_table.Tpo -c check/crc64_table.c -o liblzma_la-crc64_table.o >/dev/null 2>&1 install_environment.STDOUT DEBUG 2017-11-18 17:00:09,943 c64_table.Tpo .deps/liblzma_la-crc64_table.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:09,946 --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commoWaggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-crc64_fast.lo -MD -MP -MF .deps/liblzma_la-crc64_fast.Tpo -c -o liblzma_la-crc64_fast.lo `test -f 'check/crc64_fast.c' || echo './'`check/crc64_fast.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,967 ta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthreamissing-declarations -Wmimv -f .deps/liblzma_la-crc32_fa/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nn -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKD_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggrelibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIBit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-crc64_table.lo -MD -MP -MF .deps/liblzma_la-crc64_table.Tpo -c check/crc64_table.c -o liblzma_la-crc64_table.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,967 c64_table.Tpo .deps/liblzma_la-crc64_table.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,968 --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commoWaggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-crc64_fast.lo -MD -MP -MF .deps/liblzma_la-crc64_fast.Tpo -c -o liblzma_la-crc64_fast.lo `test -f 'check/crc64_fast.c' || echo './'`check/crc64_fast.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:09,968 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:10,057 /lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/lising -Wfloat-equal -Wundeliblzma_la-crc64_fast.lo -MD -Mlibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/zma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wform -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite--prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -gla-crc64_fast.Tpo -c check/crc64_fast.c -o liblzma_la-crc64_fast.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:10,068 _SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winmv -f .deps/liblzma_la-cr/bin/sh ../../libtool --tag=CCn -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliaf -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT P -MF .deps/liblzma_la-crc64_fast.Tpo -c check/crc64_fast.c -fno-common -DPIC -o .libs/liblzma_la-crc64_fast.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:10,068 /lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/lising -Wfloat-equal -Wundeliblzma_la-crc64_fast.lo -MD -Mlibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/zma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wform -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite--prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -gla-crc64_fast.Tpo -c check/crc64_fast.c -o liblzma_la-crc64_fast.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:10,068 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:10,068 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:10,173 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src../src/liblzma/lzma -I../common -DTUKLIB_SYMBOL_PREFIX=lat=2 -Winit-self -Wmissing-include-dirsstrings -Wlogical-op -Waggregate-return -Wstrict -O2 -MT liblzma_la-crc64_fast.lo -MD -MP -MF .deps/liblzma_mv -f .deps/liblzma_la-crc64_fast.Tpo .deps/liblzma_la-crc64_fast.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:10,173 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-sha256.lo -MD -MP -MF .deps/sha256.c install_environment.STDOUT DEBUG 2017-11-18 17:00:10,181 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-n/liblzma_la-sha256.Tpo -c -o liblzma_la-sha256.lo `test -f 'check/sha256.c' || echo './'`checklibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-sha256.lo -MD -MP -MF .deps/liblzma_la-sha256.Tpo -c check/sha256.c -fno-common -DPIC -o .libs/liblzma_la-sha256.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:10,279 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-n/liblzma_la-sha256.Tpo -c -o liblzma_la-sha256.lo `test -f 'check/sha256.c' || echo './'`checklibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-sha256.lo -MD -MP -MF .deps/liblzma_la-sha256.Tpo -c check/sha256.c -fno-common -DPIC -o .libs/liblzma_la-sha256.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:10,279 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:10,470 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/chenter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-sha256.lo -MD -MP -MF .deps/liblzma_la-sha256.Tpo -c check/sha256.c -o liblzma_la-sha256.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:10,488 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/chenter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-sha256.lo -MD -MP -MF .deps/liblzma_la-sha256.Tpo -c check/sha256.c -o liblzma_la-sha256.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:10,488 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:10,751 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lz_encoder.lo -MD -MP -MF .deps/liblzma_la-lz_encoder.Tpo -c -o liblzma_la-lz_encoder.lo `test -f 'lz/lz_encoder.c' || echo './'`lz/lz_encoder.c install_environment.STDOUT DEBUG 2017-11-18 17:00:10,790 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/I../../src/liblzma/delta -D_THREAD_SAFE -pthread -fvisibng -Wfloat-equal -Wundef -Wshadow -Wpoiion -Wmissing-prototypes -Wmissing-declarations n -DPIC -o .libs/liblzma_la-lz_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:10,801 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../srclibtool: compile: gcc -Dck -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpoimv -f .deps/liblzma_la-sha256.Tpo .deps/liblzma_la-sha256.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:10,801 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lz_encoder.lo -MD -MP -MF .deps/liblzma_la-lz_encoder.Tpo -c -o liblzma_la-lz_encoder.lo `test -f 'lz/lz_encoder.c' || echo './'`lz/lz_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:10,801 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/I../../src/liblzma/delta -D_THREAD_SAFE -pthread -fvisibng -Wfloat-equal -Wundef -Wshadow -Wpoiion -Wmissing-prototypes -Wmissing-declarations n -DPIC -o .libs/liblzma_la-lz_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:10,905 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:11,011 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lz_encoder.lo -MD -MP -MF .deps/liblzma_la-lz_encoder.Tpo -c lz/lz_encoder.c -fno-commolibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lz_encoder.lo -MD -MP -MF .deps/liblzma_la-lz_encoder.Tpo -c lz/lz_encoder.c -o liblzma_la-lz_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:11,011 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:11,116 er.Tpo .deps/liblzma_la-lz_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:11,116 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lz_encodmf.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:11,116 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggrencoder_mf.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:11,116 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:11,511 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggremv -f .deps/liblzma_la-lz_encod/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arl-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissier_mf.lo -MD -MP -MF .deps/liblzma_la-lz_encoder_mf.Tpo -c -o liblzma_la-lz_encoder_mf.lo `test -f 'lz/lz_encoder_mf.c' || echo './'`lz/lz_encoder_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lz_encoder_mf.lo -MD -MP -MF .deps/liblzma_la-lz_encoder_mf.Tpo -c lz/lz_encoder_mf.c -fno-common -DPIC -o .libs/liblzma_la-lz_elibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lz_encoder_mf.lo -MD -MP -MF .deps/liblzma_la-lz_encoder_mf.Tpo -c lz/lz_encoder_mf.c -o liblzma_la-lz_encoder_mf.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:11,528 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggremv -f .deps/liblzma_la-lz_encod/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arl-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissier_mf.lo -MD -MP -MF .deps/liblzma_la-lz_encoder_mf.Tpo -c -o liblzma_la-lz_encoder_mf.lo `test -f 'lz/lz_encoder_mf.c' || echo './'`lz/lz_encoder_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lz_encoder_mf.lo -MD -MP -MF .deps/liblzma_la-lz_encoder_mf.Tpo -c lz/lz_encoder_mf.c -fno-common -DPIC -o .libs/liblzma_la-lz_elibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lz_encoder_mf.lo -MD -MP -MF .deps/liblzma_la-lz_encoder_mf.Tpo -c lz/lz_encoder_mf.c -o liblzma_la-lz_encoder_mf.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:11,528 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:11,927 _encoder_mf.Tpo .deps/liblzma_la-lz_encoder_mf.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:11,940 _encoder_mf.Tpo .deps/liblzma_la-lz_encoder_mf.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:11,941 Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -mv -f .deps/liblzma_la-lz/bin/sh ../../libtool --tag=CCn -I../../src/liblzma/check -I../../srciblzma/rangecoder -I../../src/liblzma/lzma -I../c/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lity=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lz_decoder.lo -MD -MP -MF .deps/liblzma' || echo './'`lz/lz_decoder.c install_environment.STDOUT DEBUG 2017-11-18 17:00:11,968 --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commo/liblzma/lz -I../../src/l../src/liblzma/delta -I../../srzma_ -D_THREAD_SAFE -pthread -fvisibils -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadt-prototypes -Wold-style-definition -Wmissing-prototypes -Wm_la-lz_decoder.Tpo -c -o liblzma_la-lz_decoder.lo `test -f 'lz/lz_decoder.clibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmaliblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_Tibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -ngs -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lza-lz_decoder.Tpo -c lz/lz_decoder.c -fno-common -DPIC -o .libs/liblzma_la-lz_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,042 --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commo/liblzma/lz -I../../src/l../src/liblzma/delta -I../../srzma_ -D_THREAD_SAFE -pthread -fvisibils -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadt-prototypes -Wold-style-definition -Wmissing-prototypes -Wm_la-lz_decoder.Tpo -c -o liblzma_la-lz_decoder.lo `test -f 'lz/lz_decoder.clibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmaliblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_Tibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -ngs -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lza-lz_decoder.Tpo -c lz/lz_decoder.c -fno-common -DPIC -o .libs/liblzma_la-lz_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,042 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:12,058 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/I../../src/liblzma/delta -D_THREAD_SAFE -pthread -fvisibng -Wfloat-equal -Wundef -Wshadow -Wpoiion -Wmissing-prototypes -Wmissing-declarations la-lz_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,144 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/I../../src/liblzma/delta -D_THREAD_SAFE -pthread -fvisibng -Wfloat-equal -Wundef -Wshadow -Wpoiion -Wmissing-prototypes -Wmissing-declarations la-lz_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,144 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:12,202 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-n .deps/liblzma_la-lzma_encoder.Tpo -c -o liblzma_la-lzma_encoder.lo `test -f 'lzma/lzma_encodelibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_encoder.lo -MD -MP -MF .deps/liblzma_la-lzma_encoder.Tpo -c lzma/lzma_encoder.c -fno-common -DPIC -o .libs/liblzma_la-lzma_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,246 /common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/HREAD_SAFE -pthread -fvisWbad-function-cast -Wwrite-stri_decoder.lo -MD -MP -MF .deps/liblzma_llibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lz_decoder.lo -MD -MP -MF .deps/liblzma_la-lz_decoder.Tpo -c lz/lz_decoder.c -o liblzma_mv -f .deps/liblzma_la-lz_decoder.Tpo .deps/liblzma_la-lz_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,246 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_encoder.lo -MD -MP -MFr.c' || echo './'`lzma/lzma_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,246 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-n .deps/liblzma_la-lzma_encoder.Tpo -c -o liblzma_la-lzma_encoder.lo `test -f 'lzma/lzma_encodelibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_encoder.lo -MD -MP -MF .deps/liblzma_la-lzma_encoder.Tpo -c lzma/lzma_encoder.c -fno-common -DPIC -o .libs/liblzma_la-lzma_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,246 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] 127.0.0.1 - - [18/Nov/2017:17:00:12 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,558 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../srclibtool: compile: gcc -Dck -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_encoder.lo -MD -MP -MF .deps/liblzma_la-lzma_encoder.Tpo -c lzma/lzma_encoder.c -o liblzma_la-lzma_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,559 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:12,818 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che/bin/sh ../../libtool --/common -I../../src/liblzma/che -I../../src/liblzma/rangecoder -I../..iblzma/delta -I../../src/liblzma/simple -I../../ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra irs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-n -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmislo -MD -MP -MF .deps/liblzma_la-lzma_encoder_presets.Tpo -c -o liblzma_la-lzma_encoder_presets.lo `test -f 'lzma/lzma_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliaf -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT .lo -MD -MP -MF .deps/liblzma_la-lzma_encoder_presets.Tpo -c lzma/lzma_encoder_presets.c -fno-common -DPIC -o .libs/liblzma_la-lzma_encoder_presets.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,867 mv -f .deps/liblzma_la-lzma_encoder.Tpo .deps/liblzma_la-lzma_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,867 tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmack -I../../src/liblzma/lz/src/liblzma/lzma -I../../src/lsrc/common -DTUKLIB_SYMBOL_PREFIX=lzma_-Wvla -Wformat=2 -Winit-self -Wmissing-include-dfunction-cast -Wwrite-strings -Wlogical-op -Waggregate-retursing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_encoder_presets.encoder_presets.c' || echo './'`lzma/lzma_encoder_presets.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,867 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che/bin/sh ../../libtool --/common -I../../src/liblzma/che -I../../src/liblzma/rangecoder -I../..iblzma/delta -I../../src/liblzma/simple -I../../ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra irs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-n -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmislo -MD -MP -MF .deps/liblzma_la-lzma_encoder_presets.Tpo -c -o liblzma_la-lzma_encoder_presets.lo `test -f 'lzma/lzma_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliaf -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT .lo -MD -MP -MF .deps/liblzma_la-lzma_encoder_presets.Tpo -c lzma/lzma_encoder_presets.c -fno-common -DPIC -o .libs/liblzma_la-lzma_encoder_presets.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,870 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:12,965 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src../src/liblzma/lzma -I../common -DTUKLIB_SYMBOL_PREFIX=lat=2 -Winit-self -Wmissing-include-dirsstrings -Wlogical-op -Waggregate-return -Wstrict -O2 -MT liblzma_la-lzma_encoder_presets.lo -MD -MP -MF .depmv -f .deps/liblzma_la-lzma_encoder_presets.Tpo .deps/liblzma_la-lzma_encod/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -D_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_encoder_optimum_fast.lo -MD -MP -MF .deps/liblzma_la-lzma_encoder_optimum_fast.Tpo -c -o liblzma_la-lzma_encoder_optimum_fast.lo `test -f 'lzma/lzma_encoder_optimum_fast.c' || echo './'`lzma/lzma_encoder_optimum_fast.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,974 /lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/lising -Wfloat-equal -Wundeliblzma_la-lzma_encoder_presetslibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/zma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wform -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite--prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -gs/liblzma_la-lzma_encoder_presets.Tpo -c lzma/lzma_encoder_presets.c -o liblzma_la-lzma_encoder_presets.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,975 er_presets.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,975 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src../src/liblzma/lzma -I../common -DTUKLIB_SYMBOL_PREFIX=lat=2 -Winit-self -Wmissing-include-dirsstrings -Wlogical-op -Waggregate-return -Wstrict -O2 -MT liblzma_la-lzma_encoder_presets.lo -MD -MP -MF .depmv -f .deps/liblzma_la-lzma_encoder_presets.Tpo .deps/liblzma_la-lzma_encod/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -D_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_encoder_optimum_fast.lo -MD -MP -MF .deps/liblzma_la-lzma_encoder_optimum_fast.Tpo -c -o liblzma_la-lzma_encoder_optimum_fast.lo `test -f 'lzma/lzma_encoder_optimum_fast.c' || echo './'`lzma/lzma_encoder_optimum_fast.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:12,975 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:13,076 liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/TUKLIB_SYMBOL_PREFIX=lzmalibtool: compile: gcc -DHAVE_C./../src/liblzma/lz -I../../src/liblzmaiblzma/lzma -I../../src/liblzma/delta -I../../srmmon -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fWformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equan-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definitreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_encoder_optimum_fast.lo -MD -MP -MF .deps/liblzma_la-lzma_encoder_.libs/liblzma_la-lzma_encoder_optimum_fast.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:13,076 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:13,123 ONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I./rangecoder -I../../src/lc/liblzma/simple -I../../src/covisibility=hidden -Wall -Wextra -Wvla -l -Wundef -Wshadow -Wpointer-arith -Wbad-functioion -Wmissing-prototypes -Wmissing-declarations -Wmissing-nooptimum_fast.Tpo -c lzma/lzma_encoder_optimum_fast.c -fno-common -DPIC -o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmaliblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_Tibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -ngs -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lz.deps/liblzma_la-lzma_encoder_optimum_fast.Tpo -c lzma/lzma_encoder_optimum_fast.c -o liblzma_la-lzma_encoder_optimum_fast.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:13,178 ONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I./rangecoder -I../../src/lc/liblzma/simple -I../../src/covisibility=hidden -Wall -Wextra -Wvla -l -Wundef -Wshadow -Wpointer-arith -Wbad-functioion -Wmissing-prototypes -Wmissing-declarations -Wmissing-nooptimum_fast.Tpo -c lzma/lzma_encoder_optimum_fast.c -fno-common -DPIC -o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmaliblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_Tibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -ngs -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lz.deps/liblzma_la-lzma_encoder_optimum_fast.Tpo -c lzma/lzma_encoder_optimum_fast.c -o liblzma_la-lzma_encoder_optimum_fast.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:13,181 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:13,264 .Tpo .deps/liblzma_la-lzma_encoder_optimum_fast.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:13,267 CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -ma -I../../src/liblzma/de -pthread -fvisibility=hidden -inter-arith -Wbad-function-cast -Wwrite-Wredundant-decls -g -O2 -MT liblzma_la-lzma_enco './'`lzma/lzma_encoder_optimum_normal.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:13,282 .Tpo .deps/liblzma_la-lzma_encoder_optimum_fast.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:13,282 CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -ma -I../../src/liblzma/de -pthread -fvisibility=hidden -inter-arith -Wbad-function-cast -Wwrite-Wredundant-decls -g -O2 -MT liblzma_la-lzma_enco './'`lzma/lzma_encoder_optimum_normal.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:13,385 /common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/HREAD_SAFE -pthread -fvisWbad-function-cast -Wwrite-strima_encoder_optimum_fast.lo -MD -MP -MF mv -f .deps/liblzma_la-lzma_encoder_optimum_fast/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzlta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFEWall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpo-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn oder_optimum_normal.lo -MD -MP -MF .deps/liblzma_la-lzma_encoder_optimum_normal.Tpo -c -o liblzma_la-lzma_encoder_optimum_normal.lo `test -f 'lzma/lzma_encoder_optimum_normal.c' || echlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/deld -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wssing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_encoder_optimum_normal.lo -MD -MP -MF .deps/liblzma_la-lzma_encoder_optimum_normal.Tpo -c lzma/lzma_encoder_optimum_normal.c -fno-common -DPIC -o .libs/liblzma_la-lzma_encoder_optimum_normal.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:13,385 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:13,796 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:13,799 ta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthreamissing-declarations -Wmilibtool: compile: gcc -DHAVE_C./../src/liblzma/lz -I../../src/liblzmaiblzma/lzma -I../../src/liblzma/delta -I../../srmmon -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fWformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equan-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definitreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_encoder_optimum_normal.lo -MD -MP -MF .deps/liblzma_la-lzma_encodema_encoder_optimum_normal.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:13,900 ta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthreamissing-declarations -Wmilibtool: compile: gcc -DHAVE_C./../src/liblzma/lz -I../../src/liblzmaiblzma/lzma -I../../src/liblzma/delta -I../../srmmon -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fWformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equan-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definitreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_encoder_optimum_normal.lo -MD -MP -MF .deps/liblzma_la-lzma_encodema_encoder_optimum_normal.o >/dev/null 2>&1 install_environment.STDOUT DEBUG 2017-11-18 17:00:14,271 ormal.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:14,308 ormal.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:14,308 ONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I./rangecoder -I../../src/lc/liblzma/simple -I../../src/covisibility=hidden -Wall -Wextra -Wvla -l -Wundef -Wshadow -Wpointer-arith -Wbad-functioion -Wmissing-prototypes -Wmissing-declarations -Wmissing-nor_optimum_normal.Tpo -c lzma/lzma_encoder_optimum_normal.c -o liblzma_la-lzmv -f .deps/liblzma_la-lzma_encoder_optimum_normal.Tpo .deps/liblzma_la-lzma_encoder_optimum_n/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread --Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregatold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-fastpos_table.lo -MD -MP -MF .deps/liblzma_la-fastpos_table.Tpo -c -o liblzma_la-fastpos_table.lo `test -fma/fastpos_table.c install_environment.STDOUT DEBUG 2017-11-18 17:00:14,387 liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../fvisibility=hidden -Wall e-return -Wstrict-prototypes -W 'lzma/fastpos_table.c' || echo './'`lzlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-fastpos_table.lo -MD -MP -MF .deps/liblzma_la-fastpos_table.Tpo -c lzma/fastpos_table.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-fastpos_table.lo -MD -MP -MF .deps/liblzma_la-fastpos_table.Tpo -c lzma/fastpos_table.c -o liblzma_la-fastpos_table.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:14,410 .. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/I../../src/liblzma/delta -D_THREAD_SAFE -pthread -fvisibng -Wfloat-equal -Wundef -Wshadow -Wpoiion -Wmissing-prototypes -Wmissing-declarations -fno-common -DPIC -o .libs/liblzma_la-fastpos_table.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:14,411 liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../fvisibility=hidden -Wall e-return -Wstrict-prototypes -W 'lzma/fastpos_table.c' || echo './'`lzlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma --I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ ility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasinter-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definit-Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-fastpos_table.lo -MD -MP -MF .deps/liblzma_la-fastpos_table.Tpo -c lzma/fastpos_table.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-fastpos_table.lo -MD -MP -MF .deps/liblzma_la-fastpos_table.Tpo -c lzma/fastpos_table.c -o liblzma_la-fastpos_table.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:14,411 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:14,411 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:14,460 table.Tpo .deps/liblzma_la-fastpos_table.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:14,462 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_decr.c install_environment.STDOUT DEBUG 2017-11-18 17:00:14,498 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggredecoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:14,515 table.Tpo .deps/liblzma_la-fastpos_table.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:14,516 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_decr.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:14,516 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggredecoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:14,617 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:15,344 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggremv -f .deps/liblzma_la-fastpos_/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arl-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissioder.lo -MD -MP -MF .deps/liblzma_la-lzma_decoder.Tpo -c -o liblzma_la-lzma_decoder.lo `test -f 'lzma/lzma_decoder.c' || echo './'`lzma/lzma_decodelibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_decoder.lo -MD -MP -MF .deps/liblzma_la-lzma_decoder.Tpo -c lzma/lzma_decoder.c -fno-common -DPIC -o .libs/liblzma_la-lzma_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma_decoder.lo -MD -MP -MF .deps/liblzma_la-lzma_decoder.Tpo -c lzma/lzma_decoder.c -o liblzma_la-lzma_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:15,345 1 warning generated. 127.0.0.1 - - [18/Nov/2017:17:00:15 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:00:16,150 Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -mv -f .deps/liblzma_la-lz/bin/sh ../../libtool --tag=CCn -I../../src/liblzma/check -I../../srciblzma/rangecoder -I../../src/liblzma/lzma -I../c/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lity=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma2_encoder.lo -MD -MP -MF .deps/liblzma2_encoder.c' || echo './'`lzma/lzma2_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,174 ma_decoder.Tpo .deps/liblzma_la-lzma_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,174 Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -mv -f .deps/liblzma_la-lz/bin/sh ../../libtool --tag=CCn -I../../src/liblzma/check -I../../srciblzma/rangecoder -I../../src/liblzma/lzma -I../c/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lity=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma2_encoder.lo -MD -MP -MF .deps/liblzma2_encoder.c' || echo './'`lzma/lzma2_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,276 --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commo/liblzma/lz -I../../src/l../src/liblzma/delta -I../../srzma_ -D_THREAD_SAFE -pthread -fvisibils -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadt-prototypes -Wold-style-definition -Wmissing-prototypes -Wmzma_la-lzma2_encoder.Tpo -c -o liblzma_la-lzma2_encoder.lo `test -f 'lzma/llibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmaliblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_Tibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma2_encoder.lo -MD -MP -MF .deps/liblzma_la-lzma2_encoder.Tpo -c lzma/lzma2_encoder.c -fno-common -DPIC -o .libs/liblzma_la-lzma2_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,277 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:16,294 /common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/HREAD_SAFE -pthread -fvisn -I../../src/liblzma/check -I.../src/liblzma/rangecoder -I../../src/l/delta -I../../src/liblzma/simple -I../../src/coREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -trict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-functioict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-no .deps/liblzma_la-lzma2_encoder.Tpo -c lzma/lzma2_encoder.c -o liblzma_la-lzma2_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,383 /common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/HREAD_SAFE -pthread -fvisn -I../../src/liblzma/check -I.../src/liblzma/rangecoder -I../../src/l/delta -I../../src/liblzma/simple -I../../src/coREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -trict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-functioict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-no .deps/liblzma_la-lzma2_encoder.Tpo -c lzma/lzma2_encoder.c -o liblzma_la-lzma2_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,383 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:16,451 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nF .deps/liblzma_la-lzma2_decoder.Tpo -c -o liblzma_la-lzma2_decoder.lo `test -f 'lzma/lzma2_delibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma2_decoder.lo -MD -MP -MF .deps/liblzma_la-lzma2_decoder.Tpo -c lzma/lzma2_decoder.c -fno-common -DPIC -o .libs/liblzma_la-lzma2_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,484 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commo./../src/liblzma/lz -I../iblzma/lzma -I../../src/liblzmammon -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THWformat=2 -Winit-self -Wmissing-include-dirs -Wsn-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma2_encoder.lo -MD -MP -MFmv -f .deps/liblzma_la-lzma2_encoder.Tpo .deps/liblzma_la-lzma2_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,484 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma2_decoder.lo -MD -MP -Mcoder.c' || echo './'`lzma/lzma2_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,485 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nF .deps/liblzma_la-lzma2_decoder.Tpo -c -o liblzma_la-lzma2_decoder.lo `test -f 'lzma/lzma2_delibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma2_decoder.lo -MD -MP -MF .deps/liblzma_la-lzma2_decoder.Tpo -c lzma/lzma2_decoder.c -fno-common -DPIC -o .libs/liblzma_la-lzma2_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,485 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,590 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-plibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/zma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wform -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-lzma2_decoder.lo -MD -MP -MF .deps/liblzma_la-lzma2_decoder.Tpo -c lzma/lzma2_decoder.c -o liblzma_la-lzma2_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,590 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:16,632 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src../src/liblzma/lzma -I../common -DTUKLIB_SYMBOL_PREFIX=lat=2 -Winit-self -Wmissing-include-dirs/bin/sh ../../libtool --tag=CC --mode=compilelzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangeclzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/commo -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissoat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-price_table.lo -MD -MP -MF .deps/liblzma_la-price_table.ce_table.c' || echo './'`rangecoder/price_table.c install_environment.STDOUT DEBUG 2017-11-18 17:00:16,672 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangaggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-price_table.lo -MD -MP -MF .deps/liblzma_la-price_table.Tpo -c rangecoder/price_table.c -fno-common -DPIC -o .libs/liblzma_la-price_table.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,693 mv -f .deps/liblzma_la-lzma2_decoder.Tpo .deps/liblzma_la-lzma2_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,693 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src../src/liblzma/lzma -I../common -DTUKLIB_SYMBOL_PREFIX=lat=2 -Winit-self -Wmissing-include-dirs/bin/sh ../../libtool --tag=CC --mode=compilelzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangeclzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/commo -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissoat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-price_table.lo -MD -MP -MF .deps/liblzma_la-price_table.ce_table.c' || echo './'`rangecoder/price_table.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,693 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangaggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-price_table.lo -MD -MP -MF .deps/liblzma_la-price_table.Tpo -c rangecoder/price_table.c -fno-common -DPIC -o .libs/liblzma_la-price_table.o install_environment.STDOUT DEBUG 2017-11-18 17:00:16,732 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggre&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,796 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggre&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,796 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,796 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,901 gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liboder -I../../src/liblzma/n -DTUKLIB_SYMBOL_PREFIX=lzma_ ing-include-dirs -Wstrict-aliasing -Wflt-prototypes -Wold-style-definition -Wmissing-prTpo -c -o liblzma_la-price_table.lo `test -f 'rangecoder/prilibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Wlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-price_table.lo -MD -MP -MF .deps/liblzma_la-price_table.Tpo -c rangecoder/price_table.c -o liblzma_la-price_table.o >/dev/null 2>mv -f .deps/liblzma_la-price_table.Tpo .deps/liblzma_la-price_table.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,901 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-delta_common.lo -MD -MP -MFon.c' || echo './'`delta/delta_common.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,902 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:16,902 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:16,998 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-n .deps/liblzma_la-delta_common.Tpo -c -o liblzma_la-delta_common.lo `test -f 'delta/delta_commlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-delta_common.lo -MD -MP -MF .deps/liblzma_la-delta_common.Tpo -c delta/delta_common.c -fno-common -DPIC -o .libs/liblzma_la-delta_common.libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIBit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-delta_common.lo -MD -MP -MF .deps/liblzma_la-delt/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirss -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-delta_encoder.lo -MD -MP -MF .deps/liblzma_la-delta_encoder.Tpo -c -o liblzma_la-delta_encoder.lo `test -f 'delta/delta_encoder.c' || echo './'`delta/delta_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,007 _SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Wina_common.Tpo -c delta/delta_common.c -o liblzma_la-delta_common.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,007 mv -f .deps/liblzma_la-delta_common.Tpo .deps/liblzma_la-delta_common.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,007 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-n .deps/liblzma_la-delta_common.Tpo -c -o liblzma_la-delta_common.lo `test -f 'delta/delta_commlibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-delta_common.lo -MD -MP -MF .deps/liblzma_la-delta_common.Tpo -c delta/delta_common.c -fno-common -DPIC -o .libs/liblzma_la-delta_common.libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIBit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-delta_common.lo -MD -MP -MF .deps/liblzma_la-delt/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirss -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-delta_encoder.lo -MD -MP -MF .deps/liblzma_la-delta_encoder.Tpo -c -o liblzma_la-delta_encoder.lo `test -f 'delta/delta_encoder.c' || echo './'`delta/delta_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,007 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,112 -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-stringlibtool: compile: gcc -Dck -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/la/simple -I../../src/common -DTUKLIB_SYMBOL_PREFbility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmual -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -We-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls ncoder.Tpo -c delta/delta_encoder.c -fno-common -DPIC -o .libs/liblzma_la-delta_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,112 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:17,127 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che../src/liblzma/rangecoderiblzma/delta -I../../src/liblzmIX=lzma_ -D_THREAD_SAFE -pthread -fvisiissing-include-dirs -Wstrict-aliasing -Wfloat-eqlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl-g -O2 -MT liblzma_la-delta_encoder.lo -MD -MP -MF .deps/liblzma_la-delta_elibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmaliblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_Tibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -ngs -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-dea_la-delta_encoder.Tpo -c delta/delta_encoder.c -o liblzma_la-delta_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,214 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che../src/liblzma/rangecoderiblzma/delta -I../../src/liblzmIX=lzma_ -D_THREAD_SAFE -pthread -fvisiissing-include-dirs -Wstrict-aliasing -Wfloat-eqlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl-g -O2 -MT liblzma_la-delta_encoder.lo -MD -MP -MF .deps/liblzma_la-delta_elibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzmaliblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_Tibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -ngs -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-dea_la-delta_encoder.Tpo -c delta/delta_encoder.c -o liblzma_la-delta_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,215 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:17,226 iblzma_la-delta_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,319 iblzma_la-delta_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,319 /common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/HREAD_SAFE -pthread -fvisWbad-function-cast -Wwrite-strilta_encoder.lo -MD -MP -MF .deps/liblzmmv -f .deps/liblzma_la-delta_encoder.Tpo .deps/l/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzlta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFEWall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpo-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn coder.lo -MD -MP -MF .deps/liblzma_la-delta_decoder.Tpo -c -o liblzma_la-delta_decoder.lo `test -f 'delta/delta_decoder.c' || echo './'`delta/delta_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,319 rc/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../s../../src/liblzma/simple all -Wextra -Wvla -Wformat=2 -W-Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-delta_decoder.lo -MD -MP -MF .deps/liblzma_la-delta_decoder.Tpo -c delta/delta_decoder.c -fno-common -DPIC -o .libs/liblzma_la-delta_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,319 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,420 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commoblzma/simple -I../../src/f -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-delta_decoder.lo -MD -MP -MF .deps/liblzma_la-delta_decoder.Tpo -c delta/delta_decoder.c -o liblzma_la-delta_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,421 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:17,428 CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -ma -I../../src/liblzma/de -pthread -fvisibility=hidden -inter-arith -Wbad-function-cast -Wwrite-Wredundant-decls -g -O2 -MT liblzma_la-delta_delibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I-I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast n -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/licommon -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wunde/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-deypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-simple_coder.lo -MD -MP -MF .deps/liblzma_la-simple_coder.Tpo -c -o liblzma_la-simple_coder.lo `test -f 'simple/simple_coder.c' || echo './'`simple/simple_coder.c install_environment.STDOUT DEBUG 2017-11-18 17:00:17,467 ONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I./rangecoder -I../../src/lc/liblzma/simple -I../../src/covisibility=hidden -Wall -Wextra -Wvla -l -Wundef -Wshadow -Wpointer-arith -Wbad-functioion -Wmissing-prototypes -Wmissing-declarations -Wmissing-no/simple_coder.c -fno-common -DPIC -o .libs/liblzma_la-simple_coder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,524 mv -f .deps/liblzma_la-delta_decoder.Tpo .deps/liblzma_la-delta_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,524 CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -ma -I../../src/liblzma/de -pthread -fvisibility=hidden -inter-arith -Wbad-function-cast -Wwrite-Wredundant-decls -g -O2 -MT liblzma_la-delta_delibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I-I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast n -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/licommon -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wunde/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-deypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-simple_coder.lo -MD -MP -MF .deps/liblzma_la-simple_coder.Tpo -c -o liblzma_la-simple_coder.lo `test -f 'simple/simple_coder.c' || echo './'`simple/simple_coder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,524 ONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I./rangecoder -I../../src/lc/liblzma/simple -I../../src/covisibility=hidden -Wall -Wextra -Wvla -l -Wundef -Wshadow -Wpointer-arith -Wbad-functioion -Wmissing-prototypes -Wmissing-declarations -Wmissing-no/simple_coder.c -fno-common -DPIC -o .libs/liblzma_la-simple_coder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,524 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,626 ma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFfinition -Wmissing-prototlibtool: compile: gcc -DHAVE_C./../src/liblzma/lz -I../../src/liblzmaiblzma/lzma -I../../src/liblzma/delta -I../../srmmon -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fWformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equan-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definitreturn -Wredundant-decls -g -O2 -MT liblzma_la-simple_coder.lo -MD -MP -MF .deps/liblzma_la-simple_coder.Tpo -c simplelibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzmablzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliaf -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT -MP -MF .deps/liblzma_la-simple_coder.Tpo -c simple/simple_coder.c -o liblzma_la-simple_coder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,626 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:17,686 /lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/lising -Wfloat-equal -Wundeliblzma_la-simple_coder.lo -MD mv -f .deps/liblzma_la-simple_coder.Tpo/bin/sh ../../libtool --tag=CC --mode=compilelzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangeclzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/commo -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissoat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-simple_encoder.lo -MD -MP -MF .deps/liblzma_la-simple_ene/simple_encoder.c' || echo './'`simple/simple_encoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,729 .deps/liblzma_la-simple_coder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,730 /lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/lising -Wfloat-equal -Wundeliblzma_la-simple_coder.lo -MD mv -f .deps/liblzma_la-simple_coder.Tpo/bin/sh ../../libtool --tag=CC --mode=compilelzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangeclzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/commo -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissoat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstricototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-simple_encoder.lo -MD -MP -MF .deps/liblzma_la-simple_ene/simple_encoder.c' || echo './'`simple/simple_encoder.c install_environment.STDOUT DEBUG 2017-11-18 17:00:17,741 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangrc/common -DTUKLIB_SYMBOL-dirs -Wstrict-aliasing -Wfloation -Wmissing-prototypes -Wmissing-decllibs/liblzma_la-simple_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,830 -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangrc/common -DTUKLIB_SYMBOL-dirs -Wstrict-aliasing -Wfloation -Wmissing-prototypes -Wmissing-decllibs/liblzma_la-simple_encoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,831 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,831 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,932 gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liboder -I../../src/liblzma/n -DTUKLIB_SYMBOL_PREFIX=lzma_ ing-include-dirs -Wstrict-aliasing -Wflt-prototypes -Wold-style-definition -Wmissing-prcoder.Tpo -c -o liblzma_la-simple_encoder.lo `test -f 'simpllibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api ecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../s_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definitarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-simple_encoder.lo -MD -MP -MF .deps/liblzma_la-simple_encoder.Tpo -c simple/simple_encoder.c -fno-common -DPIC -o .libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/deld -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wssing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-simple_encoder.lo -MD -MP -MF .deps/liblzma_la-simple_encoder.Tpo -c simple/simple_encoder.c -o liblzma_la-simple_encoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:17,932 ncoder.Tpo .deps/liblzma_la-simple_encoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,039 e=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../.../src/liblzma/rangecodersrc/liblzma/simple -I../../src/idden -Wall -Wextra -Wvla -Wformat=2 -With -Wbad-function-cast -Wwrite-strings -Wlogicang-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-simple_d/simple_decoder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,039 ../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKings -Wlogical-op -Waggrela-simple_decoder.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,040 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:18,082 ta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthreamissing-declarations -Wmimv -f .deps/liblzma_la-simple_e/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arl-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissiecoder.lo -MD -MP -MF .deps/liblzma_la-simple_decoder.Tpo -c -o liblzma_la-simple_decoder.lo `test -f 'simple/simple_decoder.c' || echo './'`simplelibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-simple_decoder.lo -MD -MP -MF .deps/liblzma_la-simple_decoder.Tpo -c simple/simple_decoder.c -fno-common -DPIC -o .libs/liblzma_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-simple_decoder.lo -MD -MP -MF .deps/liblzma_la-simple_decoder.Tpo -c simple/simple_decoder.c -o liblzma_la-simple_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,141 ta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthreamissing-declarations -Wmimv -f .deps/liblzma_la-simple_e/bin/sh ../../libtool --tag=CC --mod./src/liblzma/check -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arl-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissiecoder.lo -MD -MP -MF .deps/liblzma_la-simple_decoder.Tpo -c -o liblzma_la-simple_decoder.lo `test -f 'simple/simple_decoder.c' || echo './'`simplelibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -ILIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strgate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-simple_decoder.lo -MD -MP -MF .deps/liblzma_la-simple_decoder.Tpo -c simple/simple_decoder.c -fno-common -DPIC -o .libs/liblzma_libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-simple_decoder.lo -MD -MP -MF .deps/liblzma_la-simple_decoder.Tpo -c simple/simple_decoder.c -o liblzma_la-simple_decoder.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,141 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:18,172 mple_decoder.Tpo .deps/liblzma_la-simple_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,242 mple_decoder.Tpo .deps/liblzma_la-simple_decoder.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,242 Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -mv -f .deps/liblzma_la-si/bin/sh ../../libtool --tag=CCn -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -t-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-x86.lo -.Tpo -c -o liblzma_la-x86.lo `test -f 'simple/x86.c' || echo './'`simple/x86.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,242 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commo/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-x86.lo -MD -MP -MF .deps/liblzma_la-x86.Tpo -c simple/x86.c -fno-common -DPIC -o .libs/liblzma_la-x86.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,242 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:18,298 --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commoWaggregate-return -WstricMD -MP -MF .deps/liblzma_la-x86n -I../../src/liblzma/check -I../../srcn -I../../src/liblzma/check -I../../src/liblzma/ngecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta /../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -WpoiWlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations 86.lo -MD -MP -MF .deps/liblzma_la-x86.Tpo -c simple/x86.c -o liblzma_la-x86.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,345 --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commoWaggregate-return -WstricMD -MP -MF .deps/liblzma_la-x86n -I../../src/liblzma/check -I../../srcn -I../../src/liblzma/check -I../../src/liblzma/ngecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta /../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -WpoiWlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations 86.lo -MD -MP -MF .deps/liblzma_la-x86.Tpo -c simple/x86.c -o liblzma_la-x86.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,345 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,449 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/commolz -I../../src/liblzma/ra-I../../src/liblzma/simple -I..ility=hidden -Wall -Wextra -Wvla -Wformnter-arith -Wbad-function-cast -Wwrite-strings --Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-xmv -f .deps/liblzma_la-x86.Tpo .deps/liblzma_la-x86.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,449 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-powerpc.lo -MD -MP -MF .depsimple/powerpc.c install_environment.STDOUT DEBUG 2017-11-18 17:00:18,452 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-ns/liblzma_la-powerpc.Tpo -c -o liblzma_la-powerpc.lo `test -f 'simple/powerpc.c' || echo './'`libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-powerpc.lo -MD -MP -MF .deps/liblzma_la-powerpc.Tpo -c simple/powerpc.c -fno-common -DPIC -o .libs/liblzma_la-powerpc.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,551 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-ns/liblzma_la-powerpc.Tpo -c -o liblzma_la-powerpc.lo `test -f 'simple/powerpc.c' || echo './'`libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-powerpc.lo -MD -MP -MF .deps/liblzma_la-powerpc.Tpo -c simple/powerpc.c -fno-common -DPIC -o .libs/liblzma_la-powerpc.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,551 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../srclibtool: compile: gcc -Dck -I../../src/liblzma/lz -I../ -I../../src/liblzma/lzma -I../../src/la/simple -I../../src/common -DTUKLIB_SYMBOL_PREFbility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmual -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -We-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls c simple/powerpc.c -o liblzma_la-powerpc.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,551 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,554 1 warning generated. 127.0.0.1 - - [18/Nov/2017:17:00:18 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:00:18,635 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che../src/liblzma/rangecoderiblzma/delta -I../../src/liblzmIX=lzma_ -D_THREAD_SAFE -pthread -fvisiissing-include-dirs -Wstrict-aliasing -Wfloat-eqlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl-g -O2 -MT liblzma_la-powerpc.lo -MD -MP -MF .deps/liblzma_la-powerpc.Tpo -mv -f .deps/liblzma_la-powerpc.Tpo .deps/liblzma_la-powerpc.Plo install_environment.STDOUT DEBUG 2017-11-18 17:00:18,639 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-ia64.lo -MD -MP -MF .deps/lc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,657 HAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/che../src/liblzma/rangecoderiblzma/delta -I../../src/liblzmIX=lzma_ -D_THREAD_SAFE -pthread -fvisiissing-include-dirs -Wstrict-aliasing -Wfloat-eqlogical-op -Waggregate-return -Wstrict-prototypes -Wold-styl-g -O2 -MT liblzma_la-powerpc.lo -MD -MP -MF .deps/liblzma_la-powerpc.Tpo -mv -f .deps/liblzma_la-powerpc.Tpo .deps/liblzma_la-powerpc.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,658 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-ia64.lo -MD -MP -MF .deps/lc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,763 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-niblzma_la-ia64.Tpo -c -o liblzma_la-ia64.lo `test -f 'simple/ia64.c' || echo './'`simple/ia64.libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-ia64.lo -MD -MP -MF .deps/liblzma_la-ia64.Tpo -c simple/ia64.c -fno-common -DPIC -o .libs/liblzma_la-ia64.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,763 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,867 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../srcaggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-ia64.lo -MD -MP -MF .deps/liblzma_la-ia64.Tpo -c simple/ia64.c -o liblzma_la-ia64.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,867 mv -f .deps/liblzma_la-ia64.Tpo .deps/liblzma_la-ia64.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,868 blzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../sssing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-arm.lo -MD -MP -MF .deps/liblzma_la-arm.Tpo -c -o liblzma_la-arm.lo `test -f 'simple/arm.c' || echo './'`simple/arm.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,868 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:18,906 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-plibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -W/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/lirc/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmilibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/deld -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wssing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-arm.lo -MD -MP -MF .deps/liblzma_la-arm.Tpo -c simple/arm.c -fno-common -DPIC -o .libs/liblzma_la-arm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,970 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-plibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -W/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/lirc/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmilibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/deld -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wssing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-arm.lo -MD -MP -MF .deps/liblzma_la-arm.Tpo -c simple/arm.c -fno-common -DPIC -o .libs/liblzma_la-arm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:18,971 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,076 ta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthreamissing-declarations -Wmilibtool: compile: gcc -DHAVE_C./../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -lzma_la-arm.Tpo -c simple/arm.c -o liblzma_la-arm.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,076 mv -f .deps/liblzma_la-arm.Tpo .deps/liblzma_la-arm.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,077 liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../fvisibility=hidden -Wall e-return -Wstrict-prototypes -Wmb.c' || echo './'`simple/armthumb.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,077 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:19,103 ONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I.Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-arm.lo -MD -MP -MF .deps/lib/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread --Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregatold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-armthumb.lo -MD -MP -MF .deps/liblzma_la-armthumb.Tpo -c -o liblzma_la-armthumb.lo `test -f 'simple/armthulibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIBit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-armthumb.lo -MD -MP -MF .deps/liblzma_la-armthumb -fno-common -DPIC -o .libs/liblzma_la-armthumb.o install_environment.STDOUT DEBUG 2017-11-18 17:00:19,171 ONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I. -MP -MF .deps/liblzma_la-armthumb.Tpo -c simple/armthumb.c -o liblzma_la-armthumb.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,178 ONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I.Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-arm.lo -MD -MP -MF .deps/lib/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread --Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregatold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-armthumb.lo -MD -MP -MF .deps/liblzma_la-armthumb.Tpo -c -o liblzma_la-armthumb.lo `test -f 'simple/armthulibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIBit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-armthumb.lo -MD -MP -MF .deps/liblzma_la-armthumb -fno-common -DPIC -o .libs/liblzma_la-armthumb.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,178 ONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I. -MP -MF .deps/liblzma_la-armthumb.Tpo -c simple/armthumb.c -o liblzma_la-armthumb.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,178 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,178 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,279 _SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Win.Tpo -c simple/armthumb.clibtool: compile: gcc -DHAVE_C./../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-armthumb.lo -MDmv -f .deps/liblzma_la-armthumb.Tpo .deps/liblzma_la-armthumb.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,279 a/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../src/liblzma/lz -I../../src/liblzmliblzma/lzma -I../../src/ma/simple -I../../src/common -DAFE -pthread -fvisibility=hidden -Wall nclude-dirs -Wstrict-aliasing -Wfloat-equal -Wunings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wooreturn -Wredundant-decls -g -O2 -MT liblzma_la-sparc.lo -MD -MP -MF .deps/parc.c install_environment.STDOUT DEBUG 2017-11-18 17:00:19,287 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nliblzma_la-sparc.Tpo -c -o liblzma_la-sparc.lo `test -f 'simple/sparc.c' || echo './'`simple/slibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-sparc.lo -MD -MP -MF .deps/liblzma_la-sparc.Tpo -c simple/sparc.c -fno-common -DPIC -o .libs/liblzma_la-sparc.o install_environment.STDOUT DEBUG 2017-11-18 17:00:19,367 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../srcaggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-sparc.lo -MD -MP -MF .deps/liblzma_la-sparc.Tpo -c simple/sparc.c -o liblzma_la-sparc.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,384 /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/rangecoder -I../../src/liblzma/delta -I../../src/liblzTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_S-Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-idef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strld-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-nliblzma_la-sparc.Tpo -c -o liblzma_la-sparc.lo `test -f 'simple/sparc.c' || echo './'`simple/slibtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/libl/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextraself -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Worototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-sparc.lo -MD -MP -MF .deps/liblzma_la-sparc.Tpo -c simple/sparc.c -fno-common -DPIC -o .libs/liblzma_la-sparc.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,384 -I. -I../.. -I../../src/liblzma/api -I../../src/liblzma/common -I../../src/liblzma/check -I../../srcaggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT liblzma_la-sparc.lo -MD -MP -MF .deps/liblzma_la-sparc.Tpo -c simple/sparc.c -o liblzma_la-sparc.o >/dev/null 2>&1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,384 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,384 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:19,456 /bin/sh ../../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wshadow -Wpointer-arith te-strings -Wlogical-op -Waggre -Wold-style-definition -Wmissing-protonoreturn -Wredundant-decls -g -O2 -no-undefined xydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5a-common.lo liblzma_la-block_util.lo liblzma_la-easy_preset.lo liblzma_la-fla-stream_flags_common.lo liblzma_la-vli_size.lo liblzma_la-alone_encoder.lo liblzma_la-block_sy_buffer_encoder.lo liblzma_la-easy_encoder.lo liblzma_la-easy_encoder_memusage.lo liblzma_la-filter_buffer_encoder.l_encoder.lo liblzma_la-stream_encoder.lo liblzma_la-stream_flags_encoder.lo liblzma_la-vli_encoder.lo liblzma_la-alone_decoder.lo liblzma_la-auto_dlzma_la-filter_buffer_decoder.lo liblzma_la-filter_decoder.lo liblzma_la-filter_flags_decoder.lo liblzma_la-index_decoder.lo liblzma_la-index_hash.lo liblzma_la-stream_buffer_decoder.lable.lo liblzma_la-crc64_fast.lo liblzma_la-sha256.lo liblzma_la-lz_encoder.lo liblzma_la-lz_encoder_mf.lo liblzma_la-lz_decoder.lo liblzma_la-lzma_encoder.lo liblzma_la-lzma_encoder_presets.lo liblzma_la-lzma_encoder_optimum_fa_encoder.lo liblzma_la-delta_decoder.lo liblzma_la-simple_coder.lo liblzma_la-simple_encoder.lo liblzma_la-simple_decoder.lo liblzma_la-x86.lo liblzma_la-powerpc.lo liblzma_la-ia64.lo liblzma_la-arm.lo liblzma_la-armthumb.lo liblzma_la-sparc.lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,490 zma/check -I../../src/liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src -Wvla -Wformat=2 -Winit-ld-style-definition -Wmissing-plibtool: compile: gcc -DHAVE_CONFIG_H /liblzma/lz -I../../src/liblzma/rangecoder -I../../src/liblzma/lzma -I../../src/liblzma/delta -I../../src/liblzma/simple -I../../src/common -DTUKLIB_SYMBOL_PREFIX=lzma_ -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Wmv -f .deps/liblzma_la-sparc.Tpo .deps/liblzma_la-sparc.Plo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,490 /bin/sh ../../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wshadow -Wpointer-arith te-strings -Wlogical-op -Waggre -Wold-style-definition -Wmissing-protonoreturn -Wredundant-decls -g -O2 -no-undefined xydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5a-common.lo liblzma_la-block_util.lo liblzma_la-easy_preset.lo liblzma_la-fla-stream_flags_common.lo liblzma_la-vli_size.lo liblzma_la-alone_encoder.lo liblzma_la-block_sy_buffer_encoder.lo liblzma_la-easy_encoder.lo liblzma_la-easy_encoder_memusage.lo liblzma_la-filter_buffer_encoder.l_encoder.lo liblzma_la-stream_encoder.lo liblzma_la-stream_flags_encoder.lo liblzma_la-vli_encoder.lo liblzma_la-alone_decoder.lo liblzma_la-auto_dlzma_la-filter_buffer_decoder.lo liblzma_la-filter_decoder.lo liblzma_la-filter_flags_decoder.lo liblzma_la-index_decoder.lo liblzma_la-index_hash.lo liblzma_la-stream_buffer_decoder.lable.lo liblzma_la-crc64_fast.lo liblzma_la-sha256.lo liblzma_la-lz_encoder.lo liblzma_la-lz_encoder_mf.lo liblzma_la-lz_decoder.lo liblzma_la-lzma_encoder.lo liblzma_la-lzma_encoder_presets.lo liblzma_la-lzma_encoder_optimum_fa_encoder.lo liblzma_la-delta_decoder.lo liblzma_la-simple_coder.lo liblzma_la-simple_encoder.lo liblzma_la-simple_decoder.lo liblzma_la-x86.lo liblzma_la-powerpc.lo liblzma_la-ia64.lo liblzma_la-arm.lo liblzma_la-armthumb.lo liblzma_la-sparc.lo install_environment.STDOUT DEBUG 2017-11-18 17:00:19,627 la-stream_flags_common.o .libs/liblzma_la-vli_size.o .libs/liblzma_la-alone_encoder.o .libs/liblzma_.libs/liblzma_la-stream_bder.o .libs/liblzma_la-index_deast.o .libs/liblzma_la-lzma_encoder_optt_version 6.5 -Wl,-single_module install_environment.STDOUT DEBUG 2017-11-18 17:00:19,685 libtool: link: ar cru .libs/liblzma.a liblzma_la-tuklib_physmem.o liblzma_la-common.o liblzma_la-bl_la-index.o liblzma_la-stma_la-vli_size.o liblzma_la-alouffer_encoder.o liblzma_la-block_encodeiblzma_la-easy_buffer_encoder.o liblzma_la-easy_lzma_la-filter_buffer_encoder.o liblzma_la-filter_encoder.o liblzma_la-stream_buffer_encoder.o liblzma_la-stream_encoder.o liblzma_la-liblzma_la-auto_decoder.o liblzma_la-block_buffer_decoder.o liblzma_la-block_decoder.o liblzma.o liblzma_la-filter_decoder.o liblzma_la-filter_flags_decoder.o liblzma_la-index_decoder.o liblzma_la-index_hash.o lio liblzma_la-check.o liblzma_la-crc32_table.o liblzma_la-crc32_fast.o liblzma_la-crc64_table.o liblzma_la-crc64_fast.o liblzma_la-sha256.o liblzma_der_optimum_fast.o liblzma_la-lzma_encoder_optimum_normal.o liblzma_la-fastpos_table.o liblzma_la-lzma_decoder.o liblzma_la-lzma2_encoder.o liblzma_la-lzma2_decoder.o liblzma_la-price_table.o liblzma_la-delta_common.o liblzma_la-delta_encoder.o liblzma_la-delta_decoder.o liblzma_la-simple_coder.o liblzma_la-simple_encoder.o liblzma_la-simple_decoder.o liblzma_la-x86.o liblzma_la-powerpc.o liblzma_la-ia64.o liblzma_la-arm.o liblzma_la-armthumb.o liblzma_la-sparc.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,695 la-stream_flags_common.o .libs/liblzma_la-vli_size.o .libs/liblzma_la-alone_encoder.o .libs/liblzma_.libs/liblzma_la-stream_bder.o .libs/liblzma_la-index_deast.o .libs/liblzma_la-lzma_encoder_optt_version 6.5 -Wl,-single_module tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,696 -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wbad-function-cast -Wwrigate-return -Wstrict-prototypestypes -Wmissing-declarations -Wmissing--version-info 5:5:0 -o liblzma.la -rpath /gala_0_5/944f93d45594/lib liblzma_la-tuklib_physmem.lo liblzma_lilter_common.lo liblzma_la-hardware_physmem.lo liblzma_la-index.lo liblzma_buffer_encoder.lo liblzma_la-block_encoder.lo liblzma_la-block_header_encoder.lo liblzma_la-eao liblzma_la-filter_encoder.lo liblzma_la-filter_flags_encoder.lo liblzma_la-index_encoder.lo liblzma_la-stream_bufferecoder.lo liblzma_la-block_buffer_decoder.lo liblzma_la-block_decoder.lo liblzma_la-block_header_decoder.lo liblzma_la-easy_decoder_memusage.lo libo liblzma_la-stream_decoder.lo liblzma_la-stream_flags_decoder.lo liblzma_la-vli_decoder.lo liblzma_la-check.lo liblzma_la-crc32_table.lo liblzma_la-crc32_fast.lo liblzma_la-crc64_tst.lo liblzma_la-lzma_encoder_optimum_normal.lo liblzma_la-fastpos_table.lo liblzma_la-lzma_decoder.lo liblzma_la-lzma2_encoder.lo liblzma_la-lzma2_decoder.lo liblzma_la-price_table.lo liblzma_la-delta_common.lo liblzma_la-deltalibtool: link: gcc -dynamiclib -o .libs/liblzma.5.dylib .libs/liblzma_la-tuklib_physmem.o .libs/liblzma_la-common.o .libs/liblzma_la-block_util.o .libs/liblzma_la-easy_preset.o .libs/liblzma_la-filter_common.o .libs/liblzma_la-hardware_physmem.o .libs/liblzma_la-index.o .libs/liblzma_la-block_buffer_encoder.o .libs/liblzma_la-block_encoder.o .libs/liblzma_la-block_header_encoder.o .libs/liblzma_la-easy_buffer_encoder.o .libs/liblzma_la-easy_encoder.o .libs/liblzma_la-easy_encoder_memusage.o .libs/liblzma_la-filter_buffer_encoder.o .libs/liblzma_la-filter_encoder.o .libs/liblzma_la-filter_flags_encoder.o .libs/liblzma_la-index_encoder.o uffer_encoder.o .libs/liblzma_la-stream_encoder.o .libs/liblzma_la-stream_flags_encoder.o .libs/liblzma_la-vli_encoder.o .libs/liblzma_la-alone_decoder.o .libs/liblzma_la-auto_decoder.o .libs/liblzma_la-block_buffer_decoder.o .libs/liblzma_la-block_decoder.o .libs/liblzma_la-block_header_decoder.o .libs/liblzma_la-easy_decoder_memusage.o .libs/liblzma_la-filter_buffer_decoder.o .libs/liblzma_la-filter_decoder.o .libs/liblzma_la-filter_flags_decocoder.o .libs/liblzma_la-index_hash.o .libs/liblzma_la-stream_buffer_decoder.o .libs/liblzma_la-stream_decoder.o .libs/liblzma_la-stream_flags_decoder.o .libs/liblzma_la-vli_decoder.o .libs/liblzma_la-check.o .libs/liblzma_la-crc32_table.o .libs/liblzma_la-crc32_fast.o .libs/liblzma_la-crc64_table.o .libs/liblzma_la-crc64_fast.o .libs/liblzma_la-sha256.o .libs/liblzma_la-lz_encoder.o .libs/liblzma_la-lz_encoder_mf.o .libs/liblzma_la-lz_decoder.o .libs/liblzma_la-lzma_encoder.o .libs/liblzma_la-lzma_encoder_presets.o .libs/liblzma_la-lzma_encoder_optimum_fimum_normal.o .libs/liblzma_la-fastpos_table.o .libs/liblzma_la-lzma_decoder.o .libs/liblzma_la-lzma2_encoder.o .libs/liblzma_la-lzma2_decoder.o .libs/liblzma_la-price_table.o .libs/liblzma_la-delta_common.o .libs/liblzma_la-delta_encoder.o .libs/liblzma_la-delta_decoder.o .libs/liblzma_la-simple_coder.o .libs/liblzma_la-simple_encoder.o .libs/liblzma_la-simple_decoder.o .libs/liblzma_la-x86.o .libs/liblzma_la-powerpc.o .libs/liblzma_la-ia64.o .libs/liblzma_la-arm.o .libs/liblzma_la-armthumb.o .libs/liblzma_la-sparc.o -pthread -O2 -pthread -install_name /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib/liblzma.5.dylib -compatibility_version 6 -currenlibtool: link: (cd ".libs" && rm -f "liblzma.dylib" && ln -s "liblzma.5.dylib" "liblzma.dylib") tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,697 libtool: link: ar cru .libs/liblzma.a liblzma_la-tuklib_physmem.o liblzma_la-common.o liblzma_la-bl_la-index.o liblzma_la-stma_la-vli_size.o liblzma_la-alouffer_encoder.o liblzma_la-block_encodeiblzma_la-easy_buffer_encoder.o liblzma_la-easy_lzma_la-filter_buffer_encoder.o liblzma_la-filter_encoder.o liblzma_la-stream_buffer_encoder.o liblzma_la-stream_encoder.o liblzma_la-liblzma_la-auto_decoder.o liblzma_la-block_buffer_decoder.o liblzma_la-block_decoder.o liblzma.o liblzma_la-filter_decoder.o liblzma_la-filter_flags_decoder.o liblzma_la-index_decoder.o liblzma_la-index_hash.o lio liblzma_la-check.o liblzma_la-crc32_table.o liblzma_la-crc32_fast.o liblzma_la-crc64_table.o liblzma_la-crc64_fast.o liblzma_la-sha256.o liblzma_der_optimum_fast.o liblzma_la-lzma_encoder_optimum_normal.o liblzma_la-fastpos_table.o liblzma_la-lzma_decoder.o liblzma_la-lzma2_encoder.o liblzma_la-lzma2_decoder.o liblzma_la-price_table.o liblzma_la-delta_common.o liblzma_la-delta_encoder.o liblzma_la-delta_decoder.o liblzma_la-simple_coder.o liblzma_la-simple_encoder.o liblzma_la-simple_decoder.o liblzma_la-x86.o liblzma_la-powerpc.o liblzma_la-ia64.o liblzma_la-arm.o liblzma_la-armthumb.o liblzma_la-sparc.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,697 clang: warning: argument unused during compilation: '-pthread' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,697 clang: warning: argument unused during compilation: '-pthread' install_environment.STDOUT DEBUG 2017-11-18 17:00:19,785 libtool: link: ( cd ".libs" && rm -f "liblzma.la" && ln -s "../liblzma.la" "liblzma.la" ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,801 ock_util.o liblzma_la-easy_preset.o liblzma_la-filter_common.o liblzma_la-hardware_physmem.o liblzmaream_flags_common.o liblzne_encoder.o liblzma_la-block_br.o liblzma_la-block_header_encoder.o lencoder.o liblzma_la-easy_encoder_memusage.o libliblzma_la-filter_flags_encoder.o liblzma_la-index_encoder.ostream_flags_encoder.o liblzma_la-vli_encoder.o liblzma_la-alone_decoder.o _la-block_header_decoder.o liblzma_la-easy_decoder_memusage.o liblzma_la-filter_buffer_decoderblzma_la-stream_buffer_decoder.o liblzma_la-stream_decoder.o liblzma_la-stream_flags_decoder.o liblzma_la-vli_decoder.la-lz_encoder.o liblzma_la-lz_encoder_mf.o liblzma_la-lz_decoder.o liblzma_la-lzma_encoder.o liblzma_la-lzma_encoder_presets.o liblzma_la-lzma_encolibtool: link: ranlib .libs/liblzma.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,801 libtool: link: ( cd ".libs" && rm -f "liblzma.la" && ln -s "../liblzma.la" "liblzma.la" ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,802 Making all in xzdec tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,802 ../lib -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmist-aliasing -Wfloat-equal h -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmisxzdec.o `test -f 'xzdec.c' || echo './'`xzdec.c install_environment.STDOUT DEBUG 2017-11-18 17:00:19,893 gcc -DHAVE_CONFIG_H -I. -I../.. -DTUKLIB_GETTEXT=0 -I../../src/common -I../../src/liblzma/api -I../sing-include-dirs -Wstric-Wundef -Wshadow -Wpointer-aritsing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT xzdec-xzdec.o -MD -MP -MF .deps/xzdec-xzdec.Tpo -c -o xzdec-gcc -DHAVE_CONFIG_H -I. -I../.. -DTUKLIB_GETTEXT=0 -I../../src/common -I..ormat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wion-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypsing-noreturn -Wredundant-decls -g -O2 -MT xzdec-tuklib_progname.o -MD -MP -MF .deps/xzdec-tuklib_progname.Tpo -c -o xzdec-tuklib_progname.o `test || echo './'`../../src/common/tuklib_progname.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,902 mv -f .deps/xzdec-xzdec.Tpo .deps/xzdec-xzdec.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,902 gcc -DHAVE_CONFIG_H -I. -I../.. -DTUKLIB_GETTEXT=0 -I../../src/common -I../../src/liblzma/api -I../sing-include-dirs -Wstric-Wundef -Wshadow -Wpointer-aritsing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT xzdec-xzdec.o -MD -MP -MF .deps/xzdec-xzdec.Tpo -c -o xzdec-gcc -DHAVE_CONFIG_H -I. -I../.. -DTUKLIB_GETTEXT=0 -I../../src/common -I..ormat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wion-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypsing-noreturn -Wredundant-decls -g -O2 -MT xzdec-tuklib_progname.o -MD -MP -MF .deps/xzdec-tuklib_progname.Tpo -c -o xzdec-tuklib_progname.o `test || echo './'`../../src/common/tuklib_progname.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,902 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:19,902 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:19,944 c-tuklib_progname.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,004 c-tuklib_progname.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,004 /../src/liblzma/api -I../../lib -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wfpointer-arith -Wbad-functes -Wmissing-declarations -Wmis-f '../../src/common/tuklib_progname.c'mv -f .deps/xzdec-tuklib_progname.Tpo .deps/xzdegcc -DHAVE_CONFIG_H -I. -I../.. -DTUKLIB_GETTEXT=0 -I../../extra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasingshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT xzdec-tuklib_exit.o -MD -MP -MF .deps/xzdec-tuklib_exit.Tpo -c -o xzdec-tuklib_exit.o `test -f '../../src/common/tuklib_exit.c' || echo './'`../../src/common/tuklib_exit.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,004 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,005 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,005 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,108 po .deps/xzdec-tuklib_exit.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,108 e=link gcc -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wqual -Wundef -Wshadow -Wpp -Waggregate-return -Wstrict-ps -Wmissing-noreturn -Wredundant-decls /liblzma.la tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,108 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,209 clude-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrrn -Wredundant-decls -g -O2 -o .libs/xzdec xzdec-xzdec.o xzdec-tuklib_progname.o xzdec-tuklib_exit.o ../../src/liblzma/.libs/liblzma.dylib -pthread tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,209 gcc -DHAVE_CONFIG_H -I. -I../.. -DTUKLIB_GETTEXT=0 -I../../src/common -I../../src/liblzma/api -I../er-arith -Wbad-function-czdec.Tpo -c -o lzmadec-xzdec.o `test -f 'xzdec.c' || echo './'`xzdec.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,209 clang: warning: argument unused during compilation: '-pthread' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,209 clang: warning: argument unused during compilation: '-pthread' install_environment.STDOUT DEBUG 2017-11-18 17:00:20,289 src/common -I../../src/liblzma/api -I../../lib -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -W -Wfloat-equal -Wundef -Wmv -f .deps/xzdec-tuklib_exit.T/bin/sh ../../libtool --tag=CC --modmissing-include-dirs -Wstrict-aliasing -Wfloat-eointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-orototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declaration-g -O2 -o xzdec xzdec-xzdec.o xzdec-tuklib_progname.o xzdec-tuklib_exit.o ../../src/liblzmalibtool: link: gcc -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-inite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noretu../lib -DLZMADEC -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT lzmadec-xzdec.o -MD -MP -MF .deps/lzmadec-xgcc -DHAVE_CONFIG_H -I. -I../.. -DTUKLIB_GETTEXT=0 -I../../src/common -I../../src/liblzma/api -I../../lib -DLZMADEC -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT lzmadec-tuklib_progname.o -MD -MP -MF .deps/lzmadec-tuklib_progname.Tpo -c -o lzmadec-tuklib_progname.o `test -f '../../src/common/tuklib_progname.c' || echo './'`../../src/common/tuklib_progname.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,311 mv -f .deps/lzmadec-xzdec.Tpo .deps/lzmadec-xzdec.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,311 src/common -I../../src/liblzma/api -I../../lib -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -W -Wfloat-equal -Wundef -Wmv -f .deps/xzdec-tuklib_exit.T/bin/sh ../../libtool --tag=CC --modmissing-include-dirs -Wstrict-aliasing -Wfloat-eointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-orototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declaration-g -O2 -o xzdec xzdec-xzdec.o xzdec-tuklib_progname.o xzdec-tuklib_exit.o ../../src/liblzmalibtool: link: gcc -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-inite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noretu../lib -DLZMADEC -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT lzmadec-xzdec.o -MD -MP -MF .deps/lzmadec-xgcc -DHAVE_CONFIG_H -I. -I../.. -DTUKLIB_GETTEXT=0 -I../../src/common -I../../src/liblzma/api -I../../lib -DLZMADEC -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT lzmadec-tuklib_progname.o -MD -MP -MF .deps/lzmadec-tuklib_progname.Tpo -c -o lzmadec-tuklib_progname.o `test -f '../../src/common/tuklib_progname.c' || echo './'`../../src/common/tuklib_progname.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,312 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,313 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:20,343 b_progname.Tpo .deps/lzmadec-tuklib_progname.Po install_environment.STDOUT DEBUG 2017-11-18 17:00:20,349 gcc -DHAVE_CONFIG_H -I. -I../.. -DTUKLIB_GETTEXT=0 -I../../src/common -I../../src/liblzma/api -I../E -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT lzmadec-tuklib_exit.o -MD -MP -MF .deps/lzmadec-tuklib_exit.Tpo -c -o lzmadec-tuklib_exit.o `test -f '../../src/common/tuklib_exit.c' || echo './'`../../src/common/tuklib_exit.c install_environment.STDOUT DEBUG 2017-11-18 17:00:20,409 c-tuklib_exit.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,413 b_progname.Tpo .deps/lzmadec-tuklib_progname.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,413 gcc -DHAVE_CONFIG_H -I. -I../.. -DTUKLIB_GETTEXT=0 -I../../src/common -I../../src/liblzma/api -I../E -pthread -fvisibility=hinit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT lzmadec-tuklib_exit.o -MD -MP -MF .deps/lzmadec-tuklib_exit.Tpo -c -o lzmadec-tuklib_exit.o `test -f '../../src/common/tuklib_exit.c' || echo './'`../../src/common/tuklib_exit.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,414 c-tuklib_exit.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,414 arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-mv -f .deps/lzmadec-tukli../lib -DLZMADEC -D_THREAD_SAFidden -Wall -Wextra -Wvla -Wformat=2 -Wmv -f .deps/lzmadec-tuklib_exit.Tpo .deps/lzmade/bin/sh ../../libtool --tag=CC --mode=link gcc -D_THREAD_-Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -o lzmadec lzmadec-xzdec.o lzmadec-tuklib_progname.o lzmadec-tuklib_exit.o ../../src/liblzma/liblzma.la tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,414 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,414 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,414 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,414 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:20,588 SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs libtool: link: gcc -D_THRirs -Wstrict-aliasing -Wfloat-eointer-arith -Wbad-function-cast -Wwritate-return -Wstrict-prototypes -Wold-style-definclarations -Wmissing-noreturn -Wredundant-decls -g -O2 -o .lame.o lzmadec-tuklib_exit.o ../../src/liblzma/.libs/liblzma.dylib -pthreadMaking all in xz tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,621 EAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dqual -Wundef -Wshadow -Wpe-strings -Wlogical-op -Waggregition -Wmissing-prototypes -Wmissing-deibs/lzmadec lzmadec-xzdec.o lzmadec-tuklib_progn tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,621 SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs libtool: link: gcc -D_THRirs -Wstrict-aliasing -Wfloat-eointer-arith -Wbad-function-cast -Wwritate-return -Wstrict-prototypes -Wold-style-definclarations -Wmissing-noreturn -Wredundant-decls -g -O2 -o .lame.o lzmadec-tuklib_exit.o ../../src/liblzma/.libs/liblzma.dylib -pthreadMaking all in xz tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,621 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noret/xz-args.Tpo -c -o xz-args.o `test -f 'args.c' || echo './'`args.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,621 clang: warning: argument unused during compilation: '-pthread' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,621 clang: warning: argument unused during compilation: '-pthread' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,621 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:20,720 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-args.o -MD -MP -MF .depsmv -f .deps/xz-args.Tpo .deps/xz-args.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,725 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-args.o -MD -MP -MF .depsmv -f .deps/xz-args.Tpo .deps/xz-args.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,725 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-norets/xz-coder.Tpo -c -o xz-coder.o `test -f 'coder.c' || echo './'`coder.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,725 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,827 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:20,864 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-coder.o -MD -MP -MF .depmv -f .deps/xz-coder.Tpo .deps/xz-coder.Po install_environment.STDOUT DEBUG 2017-11-18 17:00:20,867 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-file_io.o -MD -MP -MF .de_io.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,928 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-coder.o -MD -MP -MF .depmv -f .deps/xz-coder.Tpo .deps/xz-coder.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,929 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-file_io.o -MD -MP -MF .de_io.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,929 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:20,929 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,030 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreteps/xz-file_io.Tpo -c -o xz-file_io.o `test -f 'file_io.c' || echo './'`filmv -f .deps/xz-file_io.Tpo .deps/xz-file_io.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,030 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-hardware.o -MD -MP -MF .`hardware.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,031 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:21,102 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noretdeps/xz-hardware.Tpo -c -o xz-hardware.o `test -f 'hardware.c' || echo './'mv -f .deps/xz-hardware.Tpo .deps/xz-hardware.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,134 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noretdeps/xz-hardware.Tpo -c -o xz-hardware.o `test -f 'hardware.c' || echo './'mv -f .deps/xz-hardware.Tpo .deps/xz-hardware.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,134 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noret/xz-list.Tpo -c -o xz-list.o `test -f 'list.c' || echo './'`list.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,134 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,134 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,134 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:21,364 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-list.o -MD -MP -MF .depsmv -f .deps/xz-list.Tpo .deps/xz-list.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,435 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-list.o -MD -MP -MF .depsmv -f .deps/xz-list.Tpo .deps/xz-list.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,435 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noret/xz-main.Tpo -c -o xz-main.o `test -f 'main.c' || echo './'`main.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,435 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,436 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:21,459 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-main.o -MD -MP -MF .depsmv -f .deps/xz-main.Tpo .deps/xz-main.Po install_environment.STDOUT DEBUG 2017-11-18 17:00:21,461 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-message.o -MD -MP -MF .dsage.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,538 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-main.o -MD -MP -MF .depsmv -f .deps/xz-main.Tpo .deps/xz-main.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,539 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-message.o -MD -MP -MF .dsage.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,539 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,539 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,640 message.c:734:20: warning: format string is not a string literal [-Wformat-nonliteral] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,640 vfprintf(stderr, fmt, ap); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,640 ^~~ 127.0.0.1 - - [18/Nov/2017:17:00:21 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:00:21,678 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT xz-options.o -MD -MP -MF .deps/xz-options.Tpo -c -o xz-options.o `test -f 'options.c' || echo './'`options.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,744 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreteps/xz-message.Tpo -c -o xz-message.o `test -f 'message.c' || echo './'`mesmv -f .deps/xz-message.Tpo .deps/xz-message.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,744 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT xz-options.o -MD -MP -MF .deps/xz-options.Tpo -c -o xz-options.o `test -f 'options.c' || echo './'`options.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,744 2 warnings generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,744 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:21,788 s/xz-options.Po install_environment.STDOUT DEBUG 2017-11-18 17:00:21,790 LEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/loc -I../../lib -D_THREAD_St=2 -Winit-self -Wmissing-inclubad-function-cast -Wwrite-strings -Wlogissing-declarations -Wmissing-noreturn -Wredunda`signals.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,845 s/xz-options.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,845 LEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/loc -I../../lib -D_THREAD_St=2 -Winit-self -Wmissing-inclubad-function-cast -Wwrite-strings -Wlogissing-declarations -Wmissing-noreturn -Wredunda`signals.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,845 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,845 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,948 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallmv -f .deps/xz-options.Tpo .depgcc -DHAVE_CONFIG_H -I. -I../.. -DLOCAale\" -I../../src/common -I../../src/liblzma/apiAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformade-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmnt-decls -g -O2 -MT xz-signals.o -MD -MP -MF .deps/xz-signals.Tpo -c -o xz-signals.o `test -f 'signals.c' || echo './'mv -f .deps/xz-signals.Tpo .deps/xz-signals.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,948 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-suffix.o -MD -MP -MF .dec tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,948 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:21,948 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:22,000 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noretps/xz-suffix.Tpo -c -o xz-suffix.o `test -f 'suffix.c' || echo './'`suffix.mv -f .deps/xz-suffix.Tpo .deps/xz-suffix.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,049 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noretps/xz-suffix.Tpo -c -o xz-suffix.o `test -f 'suffix.c' || echo './'`suffix.mv -f .deps/xz-suffix.Tpo .deps/xz-suffix.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,049 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noret/xz-util.Tpo -c -o xz-util.o `test -f 'util.c' || echo './'`util.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,049 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,049 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:22,124 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-util.o -MD -MP -MF .depsmv -f .deps/xz-util.Tpo .deps/xz-util.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,152 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-util.o -MD -MP -MF .depsmv -f .deps/xz-util.Tpo .deps/xz-util.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,156 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noret -MP -MF .deps/xz-tuklib_open_stdxxx.Tpo -c -o xz-tuklib_open_stdxxx.o `testuklib_open_stdxxx.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,156 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,157 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:22,195 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-tuklib_open_stdxxx.o -MDt -f '../../src/common/tuklib_open_stdxxx.c' || echo './'`../../src/common/mv -f .deps/xz-tuklib_open_stdxxx.Tpo .deps/xz-tuklib_open_stdxxx.Po install_environment.STDOUT DEBUG 2017-11-18 17:00:22,254 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-tuklib_progname.o -MD -M../src/common/tuklib_progname.c' || echo './'`../../src/common/tuklib_prognmv -f .deps/xz-tuklib_progname.Tpo .deps/xz-tuklib_progname.Po install_environment.STDOUT DEBUG 2017-11-18 17:00:22,257 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-tuklib_exit.o -MD -MP -MF .deps/xz-tuklib_exit.Tpo -c -o xz-tuklib_exit.o `test -f '../../src/common/tuklib_exit.c' || echo './'`../../src/common/tuklib_exit.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,261 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-tuklib_open_stdxxx.o -MDt -f '../../src/common/tuklib_open_stdxxx.c' || echo './'`../../src/common/mv -f .deps/xz-tuklib_open_stdxxx.Tpo .deps/xz-tuklib_open_stdxxx.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,262 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noretP -MF .deps/xz-tuklib_progname.Tpo -c -o xz-tuklib_progname.o `test -f '../ame.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,262 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-tuklib_progname.o -MD -M../src/common/tuklib_progname.c' || echo './'`../../src/common/tuklib_prognmv -f .deps/xz-tuklib_progname.Tpo .deps/xz-tuklib_progname.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,262 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-tuklib_exit.o -MD -MP -MF .deps/xz-tuklib_exit.Tpo -c -o xz-tuklib_exit.o `test -f '../../src/common/tuklib_exit.c' || echo './'`../../src/common/tuklib_exit.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,262 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,262 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,262 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:22,315 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noretP -MF .deps/xz-tuklib_cpucores.Tpo -c -o xz-tuklib_cpucores.o `test -f '../res.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,367 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noretmv -f .deps/xz-tuklib_exit.Tpo .deps/xz-tuklib_exit.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,367 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noretP -MF .deps/xz-tuklib_cpucores.Tpo -c -o xz-tuklib_cpucores.o `test -f '../res.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,367 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,368 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,369 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:22,383 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noret -MP -MF .deps/xz-tuklib_mbstr_width.Tpo -c -o xz-tuklib_mbstr_width.o `testuklib_mbstr_width.c install_environment.STDOUT DEBUG 2017-11-18 17:00:22,458 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noretP -MF .deps/xz-tuklib_mbstr_fw.Tpo -c -o xz-tuklib_mbstr_fw.o `test -f '../_fw.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,473 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-tuklib_cpucores.o -MD -M../src/common/tuklib_cpucores.c' || echo './'`../../src/common/tuklib_cpucomv -f .deps/xz-tuklib_cpucores.Tpo .deps/xz-tuklib_cpucores.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,473 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noret -MP -MF .deps/xz-tuklib_mbstr_width.Tpo -c -o xz-tuklib_mbstr_width.o `testuklib_mbstr_width.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,473 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-tuklib_mbstr_width.o -MDt -f '../../src/common/tuklib_mbstr_width.c' || echo './'`../../src/common/mv -f .deps/xz-tuklib_mbstr_width.Tpo .deps/xz-tuklib_mbstr_width.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,473 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noretP -MF .deps/xz-tuklib_mbstr_fw.Tpo -c -o xz-tuklib_mbstr_fw.o `test -f '../_fw.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,473 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,473 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,473 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,579 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT xz-tuklib_mbstr_fw.o -MD -M../src/common/tuklib_mbstr_fw.c' || echo './'`../../src/common/tuklib_mbstrmv -f .deps/xz-tuklib_mbstr_fw.Tpo .deps/xz-tuklib_mbstr_fw.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,579 -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wbad-function-cast -Wwrigate-return -Wstrict-prototypestypes -Wmissing-declarations -Wmissing-s.o xz-coder.o xz-file_io.o xz-hardware.o xz-lisix.o xz-util.o xz-tuklib_open_stdxxx.o xz-tuklib_progname.o tr_fw.o ../../src/liblzma/liblzma.la tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,579 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,579 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:22,661 /bin/sh ../../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wshadow -Wpointer-arith te-strings -Wlogical-op -Waggre -Wold-style-definition -Wmissing-protonoreturn -Wredundant-decls -g -O2 -o xz xz-argt.o xz-main.o xz-message.o xz-options.o xz-signals.o xz-suffxz-tuklib_exit.o xz-tuklib_cpucores.o xz-tuklib_mbstr_width.o xz-tuklib_mbslibtool: link: gcc -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -o .libs/xz xz-args.o xz-coder.o xz-file_io.o xz-hardware.o xz-list.o xz-main.o xz-message.o xz-options.o xz-signals.o xz-suffix.o xz-util.o xz-tuklib_open_stdxxx.o xz-tuklib_progname.o xz-tuklib_exit.o xz-tuklib_cpucores.o xz-tuklib_mbstr_width.o xz-tuklib_mbstr_fw.o ../../src/liblzma/.libs/liblzma.dylib -pthread tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,680 /bin/sh ../../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wshadow -Wpointer-arith te-strings -Wlogical-op -Waggre -Wold-style-definition -Wmissing-protonoreturn -Wredundant-decls -g -O2 -o xz xz-argt.o xz-main.o xz-message.o xz-options.o xz-signals.o xz-suffxz-tuklib_exit.o xz-tuklib_cpucores.o xz-tuklib_mbstr_width.o xz-tuklib_mbslibtool: link: gcc -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wextra -Wvla -Wformat=2 -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -o .libs/xz xz-args.o xz-coder.o xz-file_io.o xz-hardware.o xz-list.o xz-main.o xz-message.o xz-options.o xz-signals.o xz-suffix.o xz-util.o xz-tuklib_open_stdxxx.o xz-tuklib_progname.o xz-tuklib_exit.o xz-tuklib_cpucores.o xz-tuklib_mbstr_width.o xz-tuklib_mbstr_fw.o ../../src/liblzma/.libs/liblzma.dylib -pthread tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,681 clang: warning: argument unused during compilation: '-pthread' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,681 clang: warning: argument unused during compilation: '-pthread' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,785 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith Making all in lzmainfo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,785 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallt-self -Wmissing-include-dirs --Wshadow -Wpointer-arith -Wbad-functioneturn -Wstrict-prototypes -Wold-style-definitionurn -Wredundant-decls -g -O2 -MT lzmainfo-lzmainfo.o -MD -MPfo.c' || echo './'`lzmainfo.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,785 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] install_environment.STDOUT DEBUG 2017-11-18 17:00:22,807 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noret -MF .deps/lzmainfo-lzmainfo.Tpo -c -o lzmainfo-lzmainfo.o `test -f 'lzmainmv -f .deps/lzmainfo-lzmainfo.Tpo .deps/lzmainfo-lzmainfo.Po install_environment.STDOUT DEBUG 2017-11-18 17:00:22,866 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallgcc -DHAVE_CONFIG_H -I. -I../..hare/locale\" -I../../src/common -I.././lib -D_THREAD_SAFE -pthread -fvisibility=hidde2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloth -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wst-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT lzmainfo-tu lzmainfo-tuklib_exit.o `test -f '../../src/common/tuklib_exit.c' || echo './'`../../src/common/tuklib_exit.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,887 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -WiniWstrict-aliasing -Wfloat-equal -Wundef -cast -Wwrite-strings -Wlogical-op -Waggregate-r -Wmissing-prototypes -Wmissing-declarations -Wmissing-noret -MF .deps/lzmainfo-lzmainfo.Tpo -c -o lzmainfo-lzmainfo.o `test -f 'lzmainmv -f .deps/lzmainfo-lzmainfo.Tpo .deps/lzmainfo-lzmainfo.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,887 gcc -DHAVE_CONFIG_H -I. -I../.. -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/ -D_THREAD_SAFE -pthread -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT lzmainfo-tuklib_progname.o -MD -MP -MF .deps/lzmainfo-tuklib_progname.Tpo -c -o lzmainfo-tuklib_progname.o `test -f '../../src/common/tuklib_progname.c' || echo './'`../../src/common/tuklib_progname.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,888 mv -f .deps/lzmainfo-tuklib_progname.Tpo .deps/lzmainfo-tuklib_progname.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,888 package_xz_5_0_5/944f93d45594/share/locale\" -I../../src/common -I../../src/liblzma/api -I../../lib -fvisibility=hidden -Wallgcc -DHAVE_CONFIG_H -I. -I../..hare/locale\" -I../../src/common -I.././lib -D_THREAD_SAFE -pthread -fvisibility=hidde2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloth -Wbad-function-cast -Wwrite-strings -Wlogical-op -Waggregate-return -Wst-prototypes -Wmissing-declarations -Wmissing-noreturn -Wredundant-decls -g -O2 -MT lzmainfo-tu lzmainfo-tuklib_exit.o `test -f '../../src/common/tuklib_exit.c' || echo './'`../../src/common/tuklib_exit.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,888 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,888 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,888 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:22,927 /bin/sh ../../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wshadow -Wpointer-arith te-strings -Wlogical-op -Waggre -Wold-style-definition -Wmissing-protonoreturn -Wredundant-decls -g -O2 -o lzmainfo zmainfo-tuklib_exit.o ../../src/liblzma/liblzma.la tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,989 -DLOCALEDIR=\"/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/s./src/liblzma/api -I../..n -Wall -Wextra -Wvla -Wformat=at-equal -Wundef -Wshadow -Wpointer-aririct-prototypes -Wold-style-definition -Wmissingklib_exit.o -MD -MP -MF .deps/lzmainfo-tuklib_exit.Tpo -c -omv -f .deps/lzmainfo-tuklib_exit.Tpo .deps/lzmainfo-tuklib_exit.Po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,989 /bin/sh ../../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -pthread -fvisibility=hidden -Wall -Wshadow -Wpointer-arith te-strings -Wlogical-op -Waggre -Wold-style-definition -Wmissing-protonoreturn -Wredundant-decls -g -O2 -o lzmainfo zmainfo-tuklib_exit.o ../../src/liblzma/liblzma.la tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,989 warning: unknown warning option '-Wlogical-op'; did you mean '-Wliblto'? [-Wunknown-warning-option] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:22,989 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:23,061 en -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equalical-op -Waggregate-retursing-noreturn -Wredundant-declsbs/liblzma.dylib -pthread tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,092 en -Wall -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equalical-op -Waggregate-retursing-noreturn -Wredundant-declsbs/liblzma.dylib -pthread tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,092 clang: warning: argument unused during compilation: '-pthread' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,093 clang: warning: argument unused during compilation: '-pthread' install_environment.STDOUT DEBUG 2017-11-18 17:00:23,117 make[3]: Nothing to be done for `all'. install_environment.STDOUT DEBUG 2017-11-18 17:00:23,124 Making all in po install_environment.STDOUT DEBUG 2017-11-18 17:00:23,142 make[2]: Nothing to be done for `all'. install_environment.STDOUT DEBUG 2017-11-18 17:00:23,163 Making install in src tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,200 -Wextra -Wvla -Wformat=2 -Winit-self -Wmissing-include-dirs -Wstrict-aliasing -Wfloat-equal -Wundef -Wbad-function-cast -Wwrigate-return -Wstrict-prototypestypes -Wmissing-declarations -Wmissing-lzmainfo-lzmainfo.o lzmainfo-tuklib_progname.o llibtool: link: gcc -D_THREAD_SAFE -pthread -fvisibility=hidd -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wwrite-strings -Wlogn -Wstrict-prototypes -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wmis -g -O2 -o .libs/lzmainfo lzmainfo-lzmainfo.o lzmainfo-tuklib_progname.o lzmainfo-tuklib_exit.o ../../src/liblzma/.liMaking all in scripts tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,201 make[3]: Nothing to be done for `all'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,201 make[3]: Nothing to be done for `all-am'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,201 Making all in po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,201 Making all in tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,201 make[2]: Nothing to be done for `all'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,202 make[2]: Nothing to be done for `all-am'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,202 Making install in src tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,202 Making install in liblzma install_environment.STDOUT DEBUG 2017-11-18 17:00:23,256 Making install in api tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,303 Making install in api tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,303 make[4]: Nothing to be done for `install-exec-am'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,303 z_5_0_5/944f93d45594/include' install_environment.STDOUT DEBUG 2017-11-18 17:00:23,310 ../../../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_x ../../../build-aux/instaude/lzma' install_environment.STDOUT DEBUG 2017-11-18 17:00:23,351 44 lzma/base.h lzma/bcj.h lzma/block.h lzma/check.h lzma/container.h lzma/delta.h lzma/filter.h lzmindex_hash.h lzma/lzma.h /vli.h '/galaxydir/galaxy/datab44f93d45594/include/lzma' install_environment.STDOUT DEBUG 2017-11-18 17:00:23,360 ase/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/include/.' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,405 ../../../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_x ../../../build-aux/instaude/lzma' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,405 44 lzma/base.h lzma/bcj.h lzma/block.h lzma/check.h lzma/container.h lzma/delta.h lzma/filter.h lzmindex_hash.h lzma/lzma.h /vli.h '/galaxydir/galaxy/datab44f93d45594/include/lzma' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,405 ase/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/include/.' install_environment.STDOUT DEBUG 2017-11-18 17:00:23,544 xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib' install_environment.STDOUT DEBUG 2017-11-18 17:00:23,578 tabase/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib' install_environment.STDOUT DEBUG 2017-11-18 17:00:23,603 ge_xz_5_0_5/944f93d45594/lib/liblzma.5.dylib install_environment.STDOUT DEBUG 2017-11-18 17:00:23,608 dylib || { rm -f liblzma.dylib && ln -s liblzma.5.dylib liblzma.dylib; }; }) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,612 xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,613 tabase/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,613 ge_xz_5_0_5/944f93d45594/lib/liblzma.5.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,613 dylib || { rm -f liblzma.dylib && ln -s liblzma.5.dylib liblzma.dylib; }; }) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,613 ll-sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/incl /usr/bin/install -c -m 6a/hardware.h lzma/index.h lzma/lzma/stream_flags.h lzma/version.h lzmaase/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/9 /usr/bin/install -c -m 644 lzma.h '/galaxydir/galaxy/datab ../../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/ /bin/sh ../../libtool --mode=install /usr/bin/install -c liblzma.la '/galaxydir/galaxy/dalibtool: install: /usr/bin/install -c .libs/liblzma.5.dylib /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/packalibtool: install: (cd /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib && { ln -s -f liblzma.5.dylib liblzma.libtool: install: /usr/bin/install -c .libs/liblzma.lai /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib/liblzma.la tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,713 .5/iuc/package_xz_5_0_5/944f93d45594/lib/liblzma.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,713 44 /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib/liblzma.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,714 ydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib/liblzma.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,714 axydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib/pkgconfig' install_environment.STDOUT DEBUG 2017-11-18 17:00:23,727 libtool: install: /usr/bin/install -c .libs/liblzma.a /galaxydir/galaxy/database/dependencies/xz/5.0libtool: install: chmod 6libtool: install: ranlib /galax ../../build-aux/install-sh -c -d '/gal /usr/bin/install -c -m 644 liblzma.pc '/galaxydMaking install in xzdec install_environment.STDOUT DEBUG 2017-11-18 17:00:23,777 _0_5/944f93d45594/bin' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,814 ir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib/pkgconfig' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,815 libtool: install: /usr/bin/install -c .libs/liblzma.a /galaxydir/galaxy/database/dependencies/xz/5.0libtool: install: chmod 6libtool: install: ranlib /galax ../../build-aux/install-sh -c -d '/gal /usr/bin/install -c -m 644 liblzma.pc '/galaxydMaking install in xzdec tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,815 _0_5/944f93d45594/bin' install_environment.STDOUT DEBUG 2017-11-18 17:00:23,816 --mode=install /usr/bin/install -c xzdec lzmadec '/galaxydir/galaxy/database/dependencies/xz/5.0.5/94/bin' install_environment.STDOUT DEBUG 2017-11-18 17:00:23,889 libs/xzdec /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/bin/xzlibtool: install: /usr/bif93d45594/bin/lzmadec tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,917 --mode=install /usr/bin/install -c xzdec lzmadec '/galaxydir/galaxy/database/dependencies/xz/5.0.5/94/bin' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,917 ../../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5 /bin/sh ../../libtool iuc/package_xz_5_0_5/944f93d455libtool: install: /usr/bin/install -c .dec tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,917 libs/xzdec /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/bin/xzlibtool: install: /usr/bif93d45594/bin/lzmadec tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:23,917 n/install -c .libs/lzmadec /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944 ../../build-aux/install-an/man1' install_environment.STDOUT DEBUG 2017-11-18 17:00:23,945 sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/m /usr/bin/install -c -m 6/man/man1' install_environment.STDOUT DEBUG 2017-11-18 17:00:23,949 dLineTools/usr/bin/make install-data-hook install_environment.STDOUT DEBUG 2017-11-18 17:00:23,959 ependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/man/man1 && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,021 sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/m /usr/bin/install -c -m 6/man/man1' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,021 dLineTools/usr/bin/make install-data-hook tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,021 44 xzdec.1 '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/Library/Developer/Commancd /galaxydir/galaxy/database/d target=`echo xzdec | sed 's,x,x,'` && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,021 link=`echo lzmadec | sed 's,x,x,'` && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,021 rm -f $link.1 && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,021 ln -s $target.1 $link.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,021 ependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/man/man1 && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,022 Making install in xz install_environment.STDOUT DEBUG 2017-11-18 17:00:24,078 ../../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5 /bin/sh ../../libtool _xz_5_0_5/944f93d45594/bin' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,123 _0_5/944f93d45594/bin' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,124 ../../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5 /bin/sh ../../libtool _xz_5_0_5/944f93d45594/bin' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,124 --mode=install /usr/bin/install -c xz '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/packagelibtool: install: /usr/bi5594/bin/xz install_environment.STDOUT DEBUG 2017-11-18 17:00:24,148 n/install -c .libs/xz /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d4/Library/Developer/Commancd /galaxydir/galaxy/database/d target=`echo xz | sed 's,x,x,'` && \ install_environment.STDOUT DEBUG 2017-11-18 17:00:24,205 _0_5/944f93d45594/share/man/man1' install_environment.STDOUT DEBUG 2017-11-18 17:00:24,219 44 xz.1 '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/man/man1' install_environment.STDOUT DEBUG 2017-11-18 17:00:24,225 ools/usr/bin/make install-data-hook tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,225 dLineTools/usr/bin/make install-exec-hook tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,226 ependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/bin && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,226 for name in unxz xzcat lzma unlzma lzcat; do \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,226 link=`echo $name | sed 's,x,x,'` && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,226 rm -f $link && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,226 ln -s $target $link; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,226 done tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,226 n/install -c .libs/xz /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d4/Library/Developer/Commancd /galaxydir/galaxy/database/d target=`echo xz | sed 's,x,x,'` && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,226 _0_5/944f93d45594/share/man/man1' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,226 44 xz.1 '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/man/man1' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,226 ools/usr/bin/make install-data-hook install_environment.STDOUT DEBUG 2017-11-18 17:00:24,247 ies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/man/man1 && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,327 ../../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5 /usr/bin/install -c -m 6/Library/Developer/CommandLineTcd /galaxydir/galaxy/database/dependenc target=`echo xz | sed 's,x,x,'` && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,327 for name in unxz xzcat lzma unlzma lzcat; do \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,327 link=`echo $name | sed 's,x,x,'` && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,327 rm -f $link.1 && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,327 ln -s $target.1 $link.1; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,327 done tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,327 ies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/man/man1 && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,327 Making install in lzmainfo install_environment.STDOUT DEBUG 2017-11-18 17:00:24,410 ../../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5 /bin/sh ../../libtool ackage_xz_5_0_5/944f93d45594/bilibtool: install: /usr/bin/install -c ./lzmainfo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,429 _0_5/944f93d45594/bin' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,429 --mode=install /usr/bin/install -c lzmainfo '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/pn' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,429 ../../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5 /bin/sh ../../libtool ackage_xz_5_0_5/944f93d45594/bilibtool: install: /usr/bin/install -c ./lzmainfo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,430 libs/lzmainfo /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/bin ../../build-aux/install-an/man1' install_environment.STDOUT DEBUG 2017-11-18 17:00:24,434 sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/m /usr/bin/install -c -m 6are/man/man1' install_environment.STDOUT DEBUG 2017-11-18 17:00:24,439 install_environment.STDOUT DEBUG 2017-11-18 17:00:24,453 -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/bin' install_environment.STDOUT DEBUG 2017-11-18 17:00:24,464 re xzless '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/bin' install_environment.STDOUT DEBUG 2017-11-18 17:00:24,468 install-exec-hook install_environment.STDOUT DEBUG 2017-11-18 17:00:24,474 age_xz_5_0_5/944f93d45594/bin && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,534 sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/m /usr/bin/install -c -m 6are/man/man1' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,634 -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/bin' install_environment.STDOUT DEBUG 2017-11-18 17:00:24,634 _0_5/944f93d45594/share/man/man1' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,634 re xzless '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/bin' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,635 install-exec-hook tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,635 44 lzmainfo.1 '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/shMaking install in scripts ../../build-aux/install-sh -c /usr/bin/install -c xzdiff xzgrep xzmo/Library/Developer/CommandLineTools/usr/bin/makecd /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/pack for pair in xzdiff-xzcmp xzgrep-xzegrep xzgrep-xzfgrep xzdiff-lzdiff xzdiff-lzcmp xzgrep-lzgrep xzgrep-lzegrep xzgrep-lzfgrep xzmore-lzmore xzless-lzless; do \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,635 target=`echo $pair | sed 's/-.*$//' | sed 's,x,x,'` && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,635 link=`echo $pair | sed 's/^.*-//' | sed 's,x,x,'` && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,635 rm -f $link && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,635 ln -s $target $link; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,635 done tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,635 age_xz_5_0_5/944f93d45594/bin && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,635 _0_5/944f93d45594/share/man/man1' install_environment.STDOUT DEBUG 2017-11-18 17:00:24,655 44 xzdiff.1 xzgrep.1 xzmore.1 xzless.1 '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/packagen/man1' install_environment.STDOUT DEBUG 2017-11-18 17:00:24,662 /bin/make install-data-hook install_environment.STDOUT DEBUG 2017-11-18 17:00:24,671 0.5/iuc/package_xz_5_0_5/944f93d45594/share/man/man1 && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,736 44 xzdiff.1 xzgrep.1 xzmore.1 xzless.1 '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/packagen/man1' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,736 /bin/make install-data-hook tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,737 ../../build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5 /usr/bin/install -c -m 6_xz_5_0_5/944f93d45594/share/ma/Library/Developer/CommandLineTools/usrcd /galaxydir/galaxy/database/dependencies/xz/5. for pair in xzdiff-xzcmp xzgrep-xzegrep xzgrep-xzfgrep xzdiff-lzdiff xzdiff-lzcmp xzgrep-lzgrep xzgrep-lzegrep xzgrep-lzfgrep xzmore-lzmore xzless-lzless; do \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,737 target=`echo $pair | sed 's/-.*$//' | sed 's,x,x,'` && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,737 link=`echo $pair | sed 's/^.*-//' | sed 's,x,x,'` && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,737 rm -f $link.1 && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,738 ln -s $target.1 $link.1; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,738 done tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,738 0.5/iuc/package_xz_5_0_5/944f93d45594/share/man/man1 && \ 127.0.0.1 - - [18/Nov/2017:17:00:24 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:00:24,855 make[3]: Nothing to be done for `install-data-am'. install_environment.STDOUT DEBUG 2017-11-18 17:00:24,863 if test "xz" = "gettext-tools"; then \ install_environment.STDOUT DEBUG 2017-11-18 17:00:24,863 do \ install_environment.STDOUT DEBUG 2017-11-18 17:00:24,863 : ; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:24,878 make[2]: Nothing to be done for `install-exec-am'. install_environment.STDOUT DEBUG 2017-11-18 17:00:24,933 build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/9 /usr/bin/install -c -m 6mat.txt doc/lzma-file-format.txbase/dependencies/xz/5.0.5/iuc/package_/xz' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,941 make[3]: Nothing to be done for `install-exec-am'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,942 make[3]: Nothing to be done for `install-data-am'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,942 Making install in po tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,942 ../build-aux/install-sh -c -d /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/gettext/po; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,942 if test "xz" = "gettext-tools"; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,943 for file in Makefile.in.in remove-potcdate.sin quot.sed boldquot.sed en@quot.header en@boldquot.header insert-header.sin Rules-quot Makevars.template; /usr/bin/install -c -m 644 ./$file \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,943 /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/gettext/po/$file; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,943 done; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,943 for file in Makevars; do \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,943 rm -f /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/gettext/po/$file; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,943 done; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,943 do \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,943 else \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,943 fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,943 : ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,943 Making install in tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,944 make[2]: Nothing to be done for `install-data-am'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,944 make[2]: Nothing to be done for `install-exec-am'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,944 make[2]: Nothing to be done for `install-exec-am'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,944 44f93d45594/share/doc/xz' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:24,944 build-aux/install-sh -c -d '/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/9 /usr/bin/install -c -m 6mat.txt doc/lzma-file-format.txbase/dependencies/xz/5.0.5/iuc/package_/xz' install_environment.STDOUT DEBUG 2017-11-18 17:00:24,947 /galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/doc/xz/examples' install_environment.STDOUT DEBUG 2017-11-18 17:00:25,003 ME.txt doc/examples/01_compress_easy.c doc/examples/02_decompress.c doc/examples/03_compress_custom.cies/xz/5.0.5/iuc/package build-aux/install-sh -c -d '/ges_old' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:25,045 /galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/doc/xz/examples' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:25,045 44 AUTHORS COPYING COPYING.GPLv2 NEWS README THANKS TODO doc/faq.txt doc/history.txt doc/xz-file-fort '/galaxydir/galaxy/dataxz_5_0_5/944f93d45594/share/doc build-aux/install-sh -c -d '/galaxydir /usr/bin/install -c -m 644 doc/examples/00_READc doc/examples/Makefile '/galaxydir/galaxy/database/dependen_xz_5_0_5/944f93d45594/share/doc/xz/examples' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:25,045 ME.txt doc/examples/01_compress_easy.c doc/examples/02_decompress.c doc/examples/03_compress_custom.cies/xz/5.0.5/iuc/package build-aux/install-sh -c -d '/ges_old' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:25,045 alaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/share/doc/xz/exampl /usr/bin/install -c -m 6endencies/xz/5.0.5/iuc/package_re/doc/xz/examples_old' install_environment.STDOUT DEBUG 2017-11-18 17:00:25,067 44 doc/examples_old/xz_pipe_comp.c doc/examples_old/xz_pipe_decomp.c '/galaxydir/galaxy/database/depxz_5_0_5/944f93d45594/sha tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:xz DEBUG 2017-11-18 17:00:25,150 44 doc/examples_old/xz_pipe_comp.c doc/examples_old/xz_pipe_decomp.c '/galaxydir/galaxy/database/depxz_5_0_5/944f93d45594/sha tool_shed.galaxy_install.tool_dependencies.recipe.install_environment WARNING 2017-11-18 17:00:25,257 Length of stdout > 32K, so only a portion will be saved in the database. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 17:00:25,363 Changing status for tool dependency xz from Installing to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:25,364 Updating an existing record for version 5.0.5 of tool dependency xz for revision 944f93d45594 of repository package_xz_5_0_5 by updating the status from Installing to Installed. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 17:00:25,403 Tool dependency xz version 5.0.5 has been installed in /galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594. 127.0.0.1 - - [18/Nov/2017:17:00:27 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:28,302 Creating a new record for version 6.0 of tool dependency ncurses for revision ca1a9400d4e1 of repository package_readline_6_3. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:28,323 Creating a new record for version 6.3 of tool dependency readline for revision ca1a9400d4e1 of repository package_readline_6_3. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:28,787 Updating an existing record for version 6.0 of tool dependency ncurses for revision ca1a9400d4e1 of repository package_readline_6_3 by updating the status from Never installed to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:28,840 Updating an existing record for version 6.3 of tool dependency readline for revision ca1a9400d4e1 of repository package_readline_6_3 by updating the status from Never installed to Installing. tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 17:00:29,210 Attempting to download via url: ftp://ftp.gnu.org/gnu/readline/readline-6.3.tar.gz tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 17:00:30,153 Successfully downloaded from url: ftp://ftp.gnu.org/gnu/readline/readline-6.3.tar.gz tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:30,160 + NCURSES_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include; export NCURSES_INCLUDE_PATH NCURSES_LIB_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/; export NCURSES_LIB_PATH NCURSES_ROOT_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd; export NCURSES_ROOT_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib:$LIBRARY_PATH; export LIBRARY_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH NCURSES_ROOT_DIR=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd; export NCURSES_ROOT_DIR ./configure CPPFLAGS=-I$NCURSES_INCLUDE_PATH LDFLAGS=-L$NCURSES_LIB_PATH --prefix /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1 install_environment.STDOUT DEBUG 2017-11-18 17:00:30,479 checking host system type... x86_64-apple-darwin15.6.0 install_environment.STDOUT DEBUG 2017-11-18 17:00:30,479 Beginning configuration for readline-6.3 for x86_64-apple-darwin15.6.0 install_environment.STDOUT DEBUG 2017-11-18 17:00:30,501 checking whether make sets $(MAKE)... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:30,574 checking build system type... x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:30,574 checking host system type... x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:30,676 Beginning configuration for readline-6.3 for x86_64-apple-darwin15.6.0 install_environment.STDOUT DEBUG 2017-11-18 17:00:30,693 checking whether the C compiler works... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:30,751 checking for suffix of executables... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:30,778 checking whether make sets $(MAKE)... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:30,778 checking for gcc... gcc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:30,779 checking whether the C compiler works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:30,779 checking for C compiler default output file name... a.out tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:30,779 checking for suffix of executables... install_environment.STDOUT DEBUG 2017-11-18 17:00:30,880 checking for suffix of object files... o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:30,881 checking whether we are cross compiling... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:30,881 checking for suffix of object files... o 127.0.0.1 - - [18/Nov/2017:17:00:30 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:00:30,973 checking whether gcc accepts -g... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:30,981 checking whether we are using the GNU C compiler... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:30,981 checking whether gcc accepts -g... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:31,082 checking for gcc option to accept ISO C89... none needed install_environment.STDOUT DEBUG 2017-11-18 17:00:31,111 checking how to run the C preprocessor... gcc -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:31,185 checking how to run the C preprocessor... gcc -E install_environment.STDOUT DEBUG 2017-11-18 17:00:31,367 checking for egrep... /usr/bin/grep -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:31,389 checking for grep that handles long lines and -e... /usr/bin/grep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:31,389 checking for egrep... /usr/bin/grep -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:31,492 rm: conftest.dSYM: is a directory tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:31,596 checking for ANSI C header files... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:31,596 rm: conftest.dSYM: is a directory install_environment.STDOUT DEBUG 2017-11-18 17:00:31,651 checking for sys/types.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:31,700 checking for sys/types.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:31,801 checking for sys/stat.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:31,801 checking for stdlib.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:31,905 checking for stdlib.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:31,905 checking for string.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:31,949 checking for memory.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,008 checking for memory.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,109 checking for strings.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:32,116 checking for inttypes.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,214 checking for inttypes.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,215 checking for stdint.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:32,282 checking for unistd.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,317 checking for unistd.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,418 checking minix/config.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:00:32,420 checking minix/config.h presence... no install_environment.STDOUT DEBUG 2017-11-18 17:00:32,497 checking whether it is safe to define __EXTENSIONS__... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,522 checking minix/config.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,522 checking for minix/config.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,522 checking whether it is safe to define __EXTENSIONS__... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:32,588 checking for a BSD-compatible install... /usr/bin/install -c install_environment.STDOUT DEBUG 2017-11-18 17:00:32,590 checking for ranlib... ranlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,625 checking whether gcc needs -traditional... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,625 checking for a BSD-compatible install... /usr/bin/install -c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,625 checking for ar... ar tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,625 checking for ranlib... ranlib install_environment.STDOUT DEBUG 2017-11-18 17:00:32,637 checking for function prototypes... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,731 checking for an ANSI C-conforming const... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,731 checking for function prototypes... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,731 checking whether char is unsigned... no install_environment.STDOUT DEBUG 2017-11-18 17:00:32,746 checking for working volatile... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,835 checking for working volatile... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:32,835 checking return type of signal handlers... void install_environment.STDOUT DEBUG 2017-11-18 17:00:32,950 checking for size_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:33,042 checking for size_t... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:33,081 checking for ANSI C header files... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:33,147 checking for ssize_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:33,147 checking for ANSI C header files... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:33,147 checking whether stat file-mode macros are broken... no install_environment.STDOUT DEBUG 2017-11-18 17:00:33,195 checking for dirent.h that defines DIR... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:33,248 checking for dirent.h that defines DIR... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:33,349 checking for library containing opendir... none required install_environment.STDOUT DEBUG 2017-11-18 17:00:33,402 checking for fcntl... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:33,454 checking for fcntl... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:33,559 checking for kill... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:33,671 checking for lstat... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:33,766 checking for lstat... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:33,869 checking for memmove... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:33,886 checking for putenv... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:33,974 checking for putenv... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:34,077 checking for select... yes 127.0.0.1 - - [18/Nov/2017:17:00:33 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:00:34,157 checking for setenv... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:34,181 checking for setenv... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:34,281 checking for setlocale... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:34,381 checking for strcasecmp... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:34,383 checking for strcasecmp... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:34,483 checking for strpbrk... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:34,561 checking for tcgetattr... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:34,586 checking for tcgetattr... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:34,687 checking for vsnprintf... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:34,742 checking for isascii... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:34,792 checking for isascii... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:34,894 checking for isxdigit... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:34,920 checking for getpwent... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:34,997 checking for getpwent... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:35,095 checking for getpwuid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,097 checking for getpwnam... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,098 checking for getpwuid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,202 checking for working strcoll... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:35,272 checking fcntl.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,303 checking fcntl.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:35,315 checking for fcntl.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:35,353 checking for stdlib.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,405 checking fcntl.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,405 checking for fcntl.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,405 checking for unistd.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,406 checking for stdlib.h... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 17:00:35,498 checking varargs.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,508 checking varargs.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,509 checking varargs.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,509 checking for varargs.h... no install_environment.STDOUT DEBUG 2017-11-18 17:00:35,567 checking stdarg.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:35,603 checking for stdarg.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,611 checking stdarg.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,611 checking stdarg.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,612 checking for stdarg.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,712 checking stdbool.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:35,717 checking stdbool.h presence... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:35,732 checking for string.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,815 checking stdbool.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,815 checking for stdbool.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,815 checking for string.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,815 checking for strings.h... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 17:00:35,828 checking limits.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:35,866 checking for limits.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,916 checking limits.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,916 checking limits.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:35,916 checking for limits.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:35,981 checking locale.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,020 checking locale.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,021 checking locale.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,021 checking for locale.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:36,063 checking pwd.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:36,095 checking for pwd.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,121 checking pwd.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,121 checking pwd.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,121 checking for pwd.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,122 checking for memory.h... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 17:00:36,196 checking termcap.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,223 checking termcap.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:36,235 checking for termcap.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,327 checking termcap.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,327 checking for termcap.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,328 checking termios.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:36,357 checking termios.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,428 checking termios.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,428 checking for termios.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:36,447 checking termio.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:00:36,495 checking for termio.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,529 checking termio.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,531 checking termio.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,531 checking for termio.h... no install_environment.STDOUT DEBUG 2017-11-18 17:00:36,622 checking sys/pte.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,632 checking sys/pte.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,632 checking sys/pte.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,632 checking for sys/pte.h... no install_environment.STDOUT DEBUG 2017-11-18 17:00:36,701 checking sys/stream.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,735 checking sys/stream.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:00:36,747 checking for sys/stream.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,839 checking sys/stream.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,839 checking for sys/stream.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,839 checking sys/select.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:36,850 checking sys/select.h presence... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:36,934 checking sys/file.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,944 checking sys/select.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,945 checking for sys/select.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:36,945 checking sys/file.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:36,979 checking for sys/file.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:37,039 checking for special C compiler options needed for large files... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,045 checking sys/file.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,046 checking for sys/file.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,046 checking for sys/ptem.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,046 checking for special C compiler options needed for large files... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,147 checking for _FILE_OFFSET_BITS value needed for large files... no install_environment.STDOUT DEBUG 2017-11-18 17:00:37,177 checking for type of signal functions... posix 127.0.0.1 - - [18/Nov/2017:17:00:37 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,247 checking for type of signal functions... posix tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,351 checking if signal handlers must be reinstalled when invoked... no install_environment.STDOUT DEBUG 2017-11-18 17:00:37,374 checking for presence of POSIX-style sigsetjmp/siglongjmp... present tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,452 checking for presence of POSIX-style sigsetjmp/siglongjmp... present install_environment.STDOUT DEBUG 2017-11-18 17:00:37,547 checking whether or not strcoll and strcmp differ... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,555 checking for lstat... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,555 checking whether or not strcoll and strcmp differ... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,661 checking whether the ctype macros accept non-ascii characters... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:37,690 checking whether getpw functions are declared in pwd.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,762 checking whether getpw functions are declared in pwd.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,762 checking whether termios.h defines TIOCGWINSZ... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:37,813 checking for sig_atomic_t in signal.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,866 checking for sig_atomic_t in signal.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:37,929 checking for TIOCSTAT in sys/ioctl.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,967 checking whether signal handlers are of type void... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:37,967 checking for TIOCSTAT in sys/ioctl.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:38,041 checking for speed_t in sys/types.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,068 checking for FIONREAD in sys/ioctl.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,068 checking for speed_t in sys/types.h... no install_environment.STDOUT DEBUG 2017-11-18 17:00:38,155 checking for struct dirent.d_ino... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,170 checking for struct winsize in sys/ioctl.h and termios.h... sys/ioctl.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,170 checking for struct dirent.d_ino... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,271 checking for struct dirent.d_fileno... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:38,271 checking whether AUDIT_USER_TTY is declared... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,372 checking whether AUDIT_USER_TTY is declared... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,372 checking for tgetent... no install_environment.STDOUT DEBUG 2017-11-18 17:00:38,424 checking for tgetent in -ltermcap... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,477 checking for tgetent in -ltermcap... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,477 checking which library has the termcap functions... using libtermcap install_environment.STDOUT DEBUG 2017-11-18 17:00:38,497 checking wctype.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:38,539 checking for wctype.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,577 checking wctype.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,578 checking wctype.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,578 checking for wctype.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:38,661 checking wchar.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,680 checking wchar.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,680 checking wchar.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,680 checking for wchar.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:38,734 checking langinfo.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:38,767 checking for langinfo.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,785 checking langinfo.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,785 checking langinfo.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,785 checking for langinfo.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,888 checking for mbrlen... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:38,926 checking for mbscasecmp... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:38,991 checking for mbscasecmp... no install_environment.STDOUT DEBUG 2017-11-18 17:00:39,076 checking for mbsnrtowcs... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:39,095 checking for mbscmp... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:39,095 checking for mbsnrtowcs... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:39,195 checking for mbsrtowcs... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:39,225 checking for mbschr... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:39,297 checking for mbschr... no install_environment.STDOUT DEBUG 2017-11-18 17:00:39,373 checking for wcscoll... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:39,403 checking for wcrtomb... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:39,403 checking for wcscoll... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:39,505 checking for wcsdup... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:39,514 checking for wcwidth... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:39,608 checking for wcwidth... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:39,608 checking for wctype... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:39,661 checking for wcswidth... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:39,712 checking for wcswidth... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:39,812 checking whether mbrtowc and mbstate_t are properly declared... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:39,834 checking for iswlower... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:39,915 checking for iswlower... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:40,007 checking for towlower... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,015 checking for iswupper... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,016 checking for towlower... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,116 checking for towupper... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:40,182 checking for iswctype... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,217 checking for iswctype... yes 127.0.0.1 - - [18/Nov/2017:17:00:40 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,319 checking for nl_langinfo and CODESET... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:40,343 checking for wchar_t in wchar.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,421 checking for wchar_t in wchar.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,421 checking for wctype_t in wctype.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:40,438 checking for wint_t in wctype.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,523 checking for wint_t in wctype.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:00:40,546 checking configuration for building shared libraries... supported tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,627 checking for wcwidth broken with unicode combining characters... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,627 checking configuration for building shared libraries... supported tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,627 configure: creating ./config.status install_environment.STDOUT DEBUG 2017-11-18 17:00:40,827 config.status: creating Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,832 config.status: creating Makefile install_environment.STDOUT DEBUG 2017-11-18 17:00:40,894 config.status: creating examples/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,936 config.status: creating doc/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,936 config.status: creating examples/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:40,936 config.status: creating shlib/Makefile install_environment.STDOUT DEBUG 2017-11-18 17:00:40,967 config.status: creating config.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:41,038 config.status: creating config.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:41,038 config.status: executing default commands tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:41,250 + NCURSES_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include; export NCURSES_INCLUDE_PATH NCURSES_LIB_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/; export NCURSES_LIB_PATH NCURSES_ROOT_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd; export NCURSES_ROOT_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib:$LIBRARY_PATH; export LIBRARY_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH NCURSES_ROOT_DIR=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd; export NCURSES_ROOT_DIR make SHLIB_LIBS=-lncurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:41,368 rm -f readline.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:41,369 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O readline.c install_environment.STDOUT DEBUG 2017-11-18 17:00:41,449 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f vi_mode.o install_environment.STDOUT DEBUG 2017-11-18 17:00:41,451 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O vi_mode.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:41,469 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f vi_mode.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:41,469 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O vi_mode.c install_environment.STDOUT DEBUG 2017-11-18 17:00:41,971 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f keymaps.o install_environment.STDOUT DEBUG 2017-11-18 17:00:41,973 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O keymaps.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:41,979 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f funmap.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:41,979 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O funmap.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:41,979 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f keymaps.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:41,979 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O keymaps.c install_environment.STDOUT DEBUG 2017-11-18 17:00:42,157 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f search.o install_environment.STDOUT DEBUG 2017-11-18 17:00:42,158 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O search.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,182 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f parens.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,183 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O parens.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,183 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f search.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,183 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O search.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,287 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f rltty.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,288 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O rltty.c install_environment.STDOUT DEBUG 2017-11-18 17:00:42,385 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f complete.o install_environment.STDOUT DEBUG 2017-11-18 17:00:42,387 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O complete.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,389 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f complete.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,389 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O complete.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,389 rltty.c:83:7: warning: implicit declaration of function 'ioctl' is invalid in C99 [-Wimplicit-function-declaration] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,389 if (ioctl (tty, TIOCGWINSZ, &w) == 0) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,390 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,390 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,495 complete.c:1085:23: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,495 while (rl_point = MB_PREVCHAR (rl_line_buffer, rl_point, MB_FIND_ANY)) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,495 ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,496 complete.c:1085:23: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,496 while (rl_point = MB_PREVCHAR (rl_line_buffer, rl_point, MB_FIND_ANY)) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,496 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,496 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,496 complete.c:1085:23: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,496 while (rl_point = MB_PREVCHAR (rl_line_buffer, rl_point, MB_FIND_ANY)) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,497 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,497 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,497 complete.c:2119:17: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,497 while (string = (*entry_function) (text, matches)) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,497 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,497 complete.c:2119:17: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,497 while (string = (*entry_function) (text, matches)) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,498 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,498 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,498 complete.c:2119:17: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,498 while (string = (*entry_function) (text, matches)) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,498 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,498 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,498 complete.c:2193:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,498 while (entry = getpwent ()) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,498 ~~~~~~^~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,499 complete.c:2193:16: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,499 while (entry = getpwent ()) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,499 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,499 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,499 complete.c:2193:16: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,499 while (entry = getpwent ()) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,499 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,499 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,807 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f bind.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,807 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O bind.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,807 3 warnings generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,911 bind.c:455:21: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,911 for (i = l = 0; c = seq[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,911 ~~^~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,911 bind.c:455:21: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,911 for (i = l = 0; c = seq[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,911 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,911 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,911 bind.c:455:21: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,911 for (i = l = 0; c = seq[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,911 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,912 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,912 bind.c:1213:31: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,912 for (i = start,passc = 0; c = string[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,912 ~~^~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,912 bind.c:1213:31: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,912 for (i = start,passc = 0; c = string[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,912 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,912 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,912 bind.c:1213:31: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,912 for (i = start,passc = 0; c = string[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,912 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,912 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,913 bind.c:2201:20: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,913 for (i = 0; name = names[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,913 ~~~~~^~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,913 bind.c:2201:20: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,913 for (i = 0; name = names[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,913 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,913 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,913 bind.c:2201:20: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,913 for (i = 0; name = names[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,913 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:42,913 == install_environment.STDOUT DEBUG 2017-11-18 17:00:43,254 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f isearch.o install_environment.STDOUT DEBUG 2017-11-18 17:00:43,256 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O isearch.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:43,327 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f isearch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:43,327 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O isearch.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:43,329 3 warnings generated. 127.0.0.1 - - [18/Nov/2017:17:00:43 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:43,538 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f display.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:43,538 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O display.c install_environment.STDOUT DEBUG 2017-11-18 17:00:43,972 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f signals.o install_environment.STDOUT DEBUG 2017-11-18 17:00:43,974 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O signals.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,052 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f signals.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,053 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O signals.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,158 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f util.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,158 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O util.c install_environment.STDOUT DEBUG 2017-11-18 17:00:44,211 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f kill.o install_environment.STDOUT DEBUG 2017-11-18 17:00:44,214 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O kill.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,263 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f kill.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,263 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O kill.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,367 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f undo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,367 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O undo.c install_environment.STDOUT DEBUG 2017-11-18 17:00:44,452 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f macro.o install_environment.STDOUT DEBUG 2017-11-18 17:00:44,454 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O macro.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,469 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f macro.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,469 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O macro.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,574 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f input.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,575 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O input.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,675 input.c:434:13: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,675 if (c = _rl_next_macro_key ()) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,675 ~~^~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,675 input.c:434:13: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,675 if (c = _rl_next_macro_key ()) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,675 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,676 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,676 input.c:434:13: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,676 if (c = _rl_next_macro_key ()) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,676 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,676 == install_environment.STDOUT DEBUG 2017-11-18 17:00:44,682 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f callback.o install_environment.STDOUT DEBUG 2017-11-18 17:00:44,684 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O callback.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,777 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f callback.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,778 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O callback.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,778 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f terminal.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,778 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O terminal.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,778 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,882 terminal.c:242:7: warning: implicit declaration of function 'ioctl' is invalid in C99 [-Wimplicit-function-declaration] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,882 if (ioctl (tty, TIOCGWINSZ, &window_size) == 0) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,882 ^ install_environment.STDOUT DEBUG 2017-11-18 17:00:44,887 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f text.o install_environment.STDOUT DEBUG 2017-11-18 17:00:44,889 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O text.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,987 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f text.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,987 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O text.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:44,987 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:45,193 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f misc.o install_environment.STDOUT DEBUG 2017-11-18 17:00:45,196 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O misc.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,197 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f nls.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,197 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O nls.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,198 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f misc.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,198 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O misc.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,302 misc.c:458:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,302 if (ul = (UNDO_LIST *)entry->data) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,303 ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,303 misc.c:458:14: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,303 if (ul = (UNDO_LIST *)entry->data) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,303 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,303 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,303 misc.c:458:14: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,303 if (ul = (UNDO_LIST *)entry->data) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,303 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,303 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,303 misc.c:505:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,303 if (ul = (UNDO_LIST *)hent->data) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,304 ~~~^~~~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,304 misc.c:505:14: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,304 if (ul = (UNDO_LIST *)hent->data) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,304 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,304 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,304 misc.c:505:14: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,304 if (ul = (UNDO_LIST *)hent->data) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,304 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,304 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,407 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f history.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,407 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O history.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,407 2 warnings generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,407 history.c:308:31: warning: passing 'const char *' to parameter of type 'char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,408 temp = alloc_history_entry (string, hist_inittime ()); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,408 ^~~~~~ install_environment.STDOUT DEBUG 2017-11-18 17:00:45,493 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f histexpand.o install_environment.STDOUT DEBUG 2017-11-18 17:00:45,496 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O histexpand.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,510 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f histexpand.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,510 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O histexpand.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,510 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,614 histexpand.c:207:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,614 for (local_index = i; c = string[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,614 ~~^~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,615 histexpand.c:207:27: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,615 for (local_index = i; c = string[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,615 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,615 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,616 histexpand.c:207:27: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,616 for (local_index = i; c = string[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,616 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,616 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,920 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f histfile.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,920 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O histfile.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:45,920 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:45,982 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f histsearch.o install_environment.STDOUT DEBUG 2017-11-18 17:00:45,985 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O histsearch.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,024 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f histsearch.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,024 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O histsearch.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,128 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f shell.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,128 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O shell.c install_environment.STDOUT DEBUG 2017-11-18 17:00:46,130 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f mbutil.o install_environment.STDOUT DEBUG 2017-11-18 17:00:46,132 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O mbutil.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,231 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f mbutil.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,231 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O mbutil.c install_environment.STDOUT DEBUG 2017-11-18 17:00:46,330 gcc -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/rm -f colors.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,332 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f tilde.o install_environment.STDOUT DEBUG 2017-11-18 17:00:46,332 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O colors.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,332 0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O -DREADLINE_LIBRARY -c ./tilde.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,333 gcc -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/rm -f colors.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,333 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O colors.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,333 ./tilde.c:199:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,333 if (result = strchr (string, '~')) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,333 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,333 ./tilde.c:199:14: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,333 if (result = strchr (string, '~')) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,333 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,334 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,334 ./tilde.c:199:14: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,334 if (result = strchr (string, '~')) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,334 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,334 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,334 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,438 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f parse-colors.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,438 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O parse-colors.c 127.0.0.1 - - [18/Nov/2017:17:00:46 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:00:46,537 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f xmalloc.o install_environment.STDOUT DEBUG 2017-11-18 17:00:46,539 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O xmalloc.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,540 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f xmalloc.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,540 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O xmalloc.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,643 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f xfree.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,643 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O xfree.c install_environment.STDOUT DEBUG 2017-11-18 17:00:46,646 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f compat.o install_environment.STDOUT DEBUG 2017-11-18 17:00:46,648 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O compat.c install_environment.STDOUT DEBUG 2017-11-18 17:00:46,695 ar cr libreadline.a readline.o vi_mode.o funmap.o keymaps.o parens.o search.o rltty.o complete.o binnls.o misc.o history.o hitsearch.o shell.o mbutil.o tildlloc.o xfree.o compat.o install_environment.STDOUT DEBUG 2017-11-18 17:00:46,725 a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,746 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f compat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,747 _0/0efde9889efd/include -I. -I. -DRL_LIBRARY_VERSION='"6.3"' -g -O compat.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,747 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f libreadline.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,747 ar cr libreadline.a readline.o vi_mode.o funmap.o keymaps.o parens.o search.o rltty.o complete.o binnls.o misc.o history.o hitsearch.o shell.o mbutil.o tildlloc.o xfree.o compat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,747 a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,747 d.o isearch.o display.o signals.o util.o kill.o undo.o macro.o input.o callback.o terminal.o text.o stexpand.o histfile.o hise.o colors.o parse-colors.o xmatest -n "ranlib" && ranlib libreadline.rm -f libhistory.a install_environment.STDOUT DEBUG 2017-11-18 17:00:46,775 ar cr libhistory.a history.o histexpand.o histfile.o histsearch.o shell.o mbutil.o xmalloc.o xfree.otest -n "ranlib" && ranlitest -d shlib || mkdir shlib install_environment.STDOUT DEBUG 2017-11-18 17:00:46,788 rm -f readline.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,850 b libhistory.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,850 ar cr libhistory.a history.o histexpand.o histfile.o histsearch.o shell.o mbutil.o xmalloc.o xfree.otest -n "ranlib" && ranlitest -d shlib || mkdir shlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,850 ( cd shlib ; /Library/Developer/CommandLineTools/usr/bin/make all ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,850 rm -f readline.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:46,851 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6./readline.c install_environment.STDOUT DEBUG 2017-11-18 17:00:46,964 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o readline.o .rm -f vi_mode.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,056 mv readline.o readline.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,056 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o readline.o .rm -f vi_mode.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,056 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6/vi_mode.c install_environment.STDOUT DEBUG 2017-11-18 17:00:47,396 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o vi_mode.o ..mv vi_mode.o vi_mode.so install_environment.STDOUT DEBUG 2017-11-18 17:00:47,400 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6funmap.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,468 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o vi_mode.o ..mv vi_mode.o vi_mode.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,468 rm -f funmap.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,468 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6funmap.c install_environment.STDOUT DEBUG 2017-11-18 17:00:47,478 rm -f keymaps.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,569 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o funmap.o ../mv funmap.o funmap.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,569 rm -f keymaps.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,569 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6/keymaps.c install_environment.STDOUT DEBUG 2017-11-18 17:00:47,608 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o keymaps.o ..rm -f parens.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,670 mv keymaps.o keymaps.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,670 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o keymaps.o ..rm -f parens.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,670 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6parens.c install_environment.STDOUT DEBUG 2017-11-18 17:00:47,688 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o parens.o ../mv parens.o parens.so install_environment.STDOUT DEBUG 2017-11-18 17:00:47,693 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6search.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,772 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o parens.o ../mv parens.o parens.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,774 rm -f search.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,774 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6search.c install_environment.STDOUT DEBUG 2017-11-18 17:00:47,801 rm -f rltty.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,878 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o search.o ../mv search.o search.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,878 rm -f rltty.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,878 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6ltty.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,878 ../rltty.c:83:7: warning: implicit declaration of function 'ioctl' is invalid in C99 [-Wimplicit-function-declaration] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,878 if (ioctl (tty, TIOCGWINSZ, &w) == 0) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,878 ^ install_environment.STDOUT DEBUG 2017-11-18 17:00:47,926 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o rltty.o ../rmv rltty.o rltty.so install_environment.STDOUT DEBUG 2017-11-18 17:00:47,933 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o complete.o ../complete.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,979 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o rltty.o ../rmv rltty.o rltty.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,979 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o complete.o ../complete.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,979 rm -f complete.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:47,979 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,084 ../complete.c:1085:23: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,084 while (rl_point = MB_PREVCHAR (rl_line_buffer, rl_point, MB_FIND_ANY)) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,085 ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,085 ../complete.c:1085:23: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,085 while (rl_point = MB_PREVCHAR (rl_line_buffer, rl_point, MB_FIND_ANY)) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,085 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,085 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,085 ../complete.c:1085:23: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,085 while (rl_point = MB_PREVCHAR (rl_line_buffer, rl_point, MB_FIND_ANY)) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,085 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,085 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,085 ../complete.c:2119:17: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,085 while (string = (*entry_function) (text, matches)) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,086 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,086 ../complete.c:2119:17: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,086 while (string = (*entry_function) (text, matches)) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,086 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,086 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,086 ../complete.c:2119:17: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,086 while (string = (*entry_function) (text, matches)) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,086 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,086 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,086 ../complete.c:2193:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,086 while (entry = getpwent ()) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,086 ~~~~~~^~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,086 ../complete.c:2193:16: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,086 while (entry = getpwent ()) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,087 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,087 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,087 ../complete.c:2193:16: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,087 while (entry = getpwent ()) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,087 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,087 == install_environment.STDOUT DEBUG 2017-11-18 17:00:48,350 mv complete.o complete.so install_environment.STDOUT DEBUG 2017-11-18 17:00:48,354 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6nd.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,399 mv complete.o complete.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,402 rm -f bind.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,402 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6nd.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,402 3 warnings generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,504 ../bind.c:455:21: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,504 for (i = l = 0; c = seq[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,504 ~~^~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,505 ../bind.c:455:21: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,505 for (i = l = 0; c = seq[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,505 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,505 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,505 ../bind.c:455:21: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,505 for (i = l = 0; c = seq[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,505 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,505 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,505 ../bind.c:1213:31: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,505 for (i = start,passc = 0; c = string[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,505 ~~^~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,506 ../bind.c:1213:31: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,506 for (i = start,passc = 0; c = string[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,506 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,506 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,506 ../bind.c:1213:31: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,506 for (i = start,passc = 0; c = string[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,506 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,506 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,506 ../bind.c:2201:20: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,506 for (i = 0; name = names[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,506 ~~~~~^~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,506 ../bind.c:2201:20: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,507 for (i = 0; name = names[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,507 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,507 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,507 ../bind.c:2201:20: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,507 for (i = 0; name = names[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,507 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,507 == install_environment.STDOUT DEBUG 2017-11-18 17:00:48,803 rm -f isearch.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,821 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o bind.o ../bimv bind.o bind.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,821 rm -f isearch.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,821 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6/isearch.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:48,821 3 warnings generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:48,983 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o isearch.o ..mv isearch.o isearch.so install_environment.STDOUT DEBUG 2017-11-18 17:00:48,987 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6/display.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,030 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o isearch.o ..mv isearch.o isearch.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,030 rm -f display.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,030 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6/display.c install_environment.STDOUT DEBUG 2017-11-18 17:00:49,508 rm -f signals.so install_environment.STDOUT DEBUG 2017-11-18 17:00:49,512 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o signals.o ../signals.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,547 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o display.o ..mv display.o display.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,547 rm -f signals.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,548 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o signals.o ../signals.c 127.0.0.1 - - [18/Nov/2017:17:00:49 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:00:49,634 mv signals.o signals.so install_environment.STDOUT DEBUG 2017-11-18 17:00:49,637 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6il.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,650 mv signals.o signals.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,650 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6rm -f util.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,650 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6il.c install_environment.STDOUT DEBUG 2017-11-18 17:00:49,762 rm -f kill.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,858 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o util.o ../utmv util.o util.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,859 rm -f kill.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,859 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6ll.c install_environment.STDOUT DEBUG 2017-11-18 17:00:49,901 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o kill.o ../kimv kill.o kill.so install_environment.STDOUT DEBUG 2017-11-18 17:00:49,905 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6do.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,960 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o kill.o ../kimv kill.o kill.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,960 rm -f undo.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:49,961 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6do.c install_environment.STDOUT DEBUG 2017-11-18 17:00:50,010 rm -f macro.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,061 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o undo.o ../unmv undo.o undo.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,062 rm -f macro.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,062 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6acro.c install_environment.STDOUT DEBUG 2017-11-18 17:00:50,112 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o macro.o ../mmv macro.o macro.so install_environment.STDOUT DEBUG 2017-11-18 17:00:50,116 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6nput.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,163 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o macro.o ../mmv macro.o macro.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,163 rm -f input.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,163 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6nput.c install_environment.STDOUT DEBUG 2017-11-18 17:00:50,255 rm -f callback.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,264 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o input.o ../imv input.o input.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,264 rm -f callback.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,264 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6./callback.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,264 ../input.c:434:13: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,264 if (c = _rl_next_macro_key ()) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,265 ~~^~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,265 ../input.c:434:13: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,265 if (c = _rl_next_macro_key ()) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,265 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,265 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,265 ../input.c:434:13: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,265 if (c = _rl_next_macro_key ()) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,265 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,265 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,266 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:50,342 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o callback.o .mv callback.o callback.sorm -f terminal.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,472 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o callback.o .mv callback.o callback.sorm -f terminal.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,472 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6./terminal.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,472 ../terminal.c:242:7: warning: implicit declaration of function 'ioctl' is invalid in C99 [-Wimplicit-function-declaration] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,472 if (ioctl (tty, TIOCGWINSZ, &window_size) == 0) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,472 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,472 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:50,476 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o terminal.o .mv terminal.o terminal.sorm -f text.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,676 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o terminal.o .mv terminal.o terminal.sorm -f text.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,677 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6xt.c install_environment.STDOUT DEBUG 2017-11-18 17:00:50,734 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o text.o ../temv text.o text.so install_environment.STDOUT DEBUG 2017-11-18 17:00:50,738 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,781 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o text.o ../temv text.o text.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,781 rm -f nls.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,781 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6.c install_environment.STDOUT DEBUG 2017-11-18 17:00:50,805 rm -f misc.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,885 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o nls.o ../nlsmv nls.o nls.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,885 rm -f misc.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,885 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6sc.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,885 ../misc.c:458:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,885 if (ul = (UNDO_LIST *)entry->data) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,885 ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,885 ../misc.c:458:14: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,885 if (ul = (UNDO_LIST *)entry->data) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,885 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,885 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,886 ../misc.c:458:14: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,886 if (ul = (UNDO_LIST *)entry->data) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,886 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,886 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,886 ../misc.c:505:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,886 if (ul = (UNDO_LIST *)hent->data) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,886 ~~~^~~~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,886 ../misc.c:505:14: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,886 if (ul = (UNDO_LIST *)hent->data) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,886 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,886 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,886 ../misc.c:505:14: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,887 if (ul = (UNDO_LIST *)hent->data) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,887 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,887 == install_environment.STDOUT DEBUG 2017-11-18 17:00:50,937 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o misc.o ../mimv misc.o misc.so install_environment.STDOUT DEBUG 2017-11-18 17:00:50,941 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6/history.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,988 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o misc.o ../mimv misc.o misc.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,988 rm -f history.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,988 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6/history.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:50,988 2 warnings generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,090 ../history.c:308:31: warning: passing 'const char *' to parameter of type 'char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,090 temp = alloc_history_entry (string, hist_inittime ()); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,091 ^~~~~~ install_environment.STDOUT DEBUG 2017-11-18 17:00:51,100 rm -f histexpand.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,194 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o history.o ..mv history.o history.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,195 rm -f histexpand.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,195 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6 ../histexpand.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,195 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,195 ../histexpand.c:207:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,195 for (local_index = i; c = string[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,195 ~~^~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,195 ../histexpand.c:207:27: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,195 for (local_index = i; c = string[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,196 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,196 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,196 ../histexpand.c:207:27: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,196 for (local_index = i; c = string[i]; i++) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,196 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,196 == install_environment.STDOUT DEBUG 2017-11-18 17:00:51,433 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o histexpand.omv histexpand.o histexpangcc -c -DHAVE_CONFIG_H -I/gal. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g e.o ../histfile.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,505 d.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,505 rm -f histfile.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,505 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o histexpand.omv histexpand.o histexpangcc -c -DHAVE_CONFIG_H -I/gal. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g e.o ../histfile.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,505 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:51,559 rm -f histsearch.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,609 axydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include -I. -I.-O -fno-common -o histfilmv histfile.o histfile.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,609 rm -f histsearch.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,609 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6 ../histsearch.c install_environment.STDOUT DEBUG 2017-11-18 17:00:51,642 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o histsearch.omv histsearch.o histsearcrm -f shell.so install_environment.STDOUT DEBUG 2017-11-18 17:00:51,707 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o shell.o ../smv shell.o shell.so install_environment.STDOUT DEBUG 2017-11-18 17:00:51,711 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6mbutil.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,713 h.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,713 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o histsearch.omv histsearch.o histsearcrm -f shell.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,713 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6hell.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,713 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o shell.o ../smv shell.o shell.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,713 rm -f mbutil.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,714 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6mbutil.c install_environment.STDOUT DEBUG 2017-11-18 17:00:51,821 rm -f tilde.so install_environment.STDOUT DEBUG 2017-11-18 17:00:51,918 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -DREADLINE_LIBRrm -f colors.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,920 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o mbutil.o ../mv mbutil.o mbutil.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,920 rm -f tilde.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,921 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6ARY -c -o tilde.o ../tilde.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,921 mv tilde.o tilde.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,921 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -DREADLINE_LIBRrm -f colors.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,921 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6colors.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,921 ../tilde.c:199:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,921 if (result = strchr (string, '~')) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,921 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,921 ../tilde.c:199:14: note: place parentheses around the assignment to silence this warning tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,921 if (result = strchr (string, '~')) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,921 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,921 ( ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,921 ../tilde.c:199:14: note: use '==' to turn this assignment into an equality comparison tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,922 if (result = strchr (string, '~')) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,922 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,922 == tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:51,922 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:00:52,009 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o colors.o ../mv colors.o colors.so install_environment.STDOUT DEBUG 2017-11-18 17:00:52,013 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6.o ../parse-colors.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,024 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o colors.o ../mv colors.o colors.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,024 rm -f parse-colors.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,024 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6.o ../parse-colors.c install_environment.STDOUT DEBUG 2017-11-18 17:00:52,111 olors.so install_environment.STDOUT DEBUG 2017-11-18 17:00:52,115 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6/xmalloc.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,126 olors.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,126 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o parse-colorsmv parse-colors.o parse-crm -f xmalloc.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,126 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6/xmalloc.c install_environment.STDOUT DEBUG 2017-11-18 17:00:52,170 rm -f xfree.so install_environment.STDOUT DEBUG 2017-11-18 17:00:52,215 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o xfree.o ../xmv xfree.o xfree.so install_environment.STDOUT DEBUG 2017-11-18 17:00:52,220 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6compat.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,230 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o xmalloc.o ..mv xmalloc.o xmalloc.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,230 rm -f xfree.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,230 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6free.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,230 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o xfree.o ../xmv xfree.o xfree.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,230 rm -f compat.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,231 gcc -c -DHAVE_CONFIG_H -I/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6compat.c install_environment.STDOUT DEBUG 2017-11-18 17:00:52,276 rm -f libreadline.6.3.dylib install_environment.STDOUT DEBUG 2017-11-18 17:00:52,329 s/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/ -dynamiclib -install_name /galaxydir/galaxy/database3/iuc/package_readline_6_dline.6.3.dylib | sed "s:\..*::ibility_version 6 -v -o libreadline.6.3so parens.so search.so rltty.so complete.so bind macro.so input.so callback.so terminal.so text.so nls.so mi tilde.so colors.so parse-colors.so xmalloc.so xfree.so compat.so -lncursesrm -f libhistory.6.3.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,331 _0/0efde9889efd/include -I. -I.. -I.. -DRL_LIBRARY_VERSION='"6.3"' -g -O -fno-common -o compat.o ../mv compat.o compat.so install_environment.STDOUT DEBUG 2017-11-18 17:00:52,331 s/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/ -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib/`echo libhistory.6.3.dylib | sed "s:\..*::"`.6.dylib -current_version 6.3 -compatibility_version 6 -v -o libhistory.6.3.dylib history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so xmalloc.so xfree.so -lncurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,331 rm -f libreadline.6.3.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,331 gcc -dynamiclib -dynamic -undefined dynamic_lookup -L/galaxydir/galaxy/database/dependencies/ncurse/dependencies/readline/6.3/ca1a9400d4e1/lib/`echo librea"`.6.dylib -current_version 6.3 -compat.dylib readline.so vi_mode.so funmap.so keymaps..so isearch.so display.so signals.so util.so kill.so undo.sosc.so history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,331 s/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/ -dynamiclib -install_name /galaxydir/galaxy/database3/iuc/package_readline_6_dline.6.3.dylib | sed "s:\..*::ibility_version 6 -v -o libreadline.6.3so parens.so search.so rltty.so complete.so bind macro.so input.so callback.so terminal.so text.so nls.so mi tilde.so colors.so parse-colors.so xmalloc.so xfree.so compat.so -lncursesrm -f libhistory.6.3.dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,332 s/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/ -dynamiclib -install_name /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib/`echo libhistory.6.3.dylib | sed "s:\..*::"`.6.dylib -current_version 6.3 -compatibility_version 6 -v -o libhistory.6.3.dylib history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so xmalloc.so xfree.so -lncurses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,332 Apple LLVM version 8.0.0 (clang-800.0.42.1) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,332 Target: x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,332 Thread model: posix tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,332 InstalledDir: /Library/Developer/CommandLineTools/usr/bin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,332 "/Library/Developer/CommandLineTools/usr/bin/ld" -demangle -dynamic -dylib -dylib_compatibility_version 6 -dylib_current_version 6.3 -arch x86_64 -dylib_install_name /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib/libreadline.6.dylib -dynamic -macosx_version_min 10.11.0 -undefined dynamic_lookup -undefined dynamic_lookup -o libreadline.6.3.dylib -L/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/ readline.so vi_mode.so funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so callback.so terminal.so text.so nls.so misc.so history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so tilde.so colors.so parse-colors.so xmalloc.so xfree.so compat.so -lncurses -L/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib -L. -lSystem /Library/Developer/CommandLineTools/usr/bin/../lib/clang/8.0.0/lib/darwin/libclang_rt.osx.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,433 gcc -dynamiclib -dynamic -undefined dynamic_lookup -L/galaxydir/galaxy/database/dependencies/ncurse tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,433 Apple LLVM version 8.0.0 (clang-800.0.42.1) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,433 Target: x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,434 Thread model: posix tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,434 InstalledDir: /Library/Developer/CommandLineTools/usr/bin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,434 "/Library/Developer/CommandLineTools/usr/bin/ld" -demangle -dynamic -dylib -dylib_compatibility_version 6 -dylib_current_version 6.3 -arch x86_64 -dylib_install_name /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib/libhistory.6.dylib -dynamic -macosx_version_min 10.11.0 -undefined dynamic_lookup -undefined dynamic_lookup -o libhistory.6.3.dylib -L/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/ history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so xmalloc.so xfree.so -lncurses -L/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib -L. -lSystem /Library/Developer/CommandLineTools/usr/bin/../lib/clang/8.0.0/lib/darwin/libclang_rt.osx.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,538 + NCURSES_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include; export NCURSES_INCLUDE_PATH NCURSES_LIB_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/; export NCURSES_LIB_PATH NCURSES_ROOT_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd; export NCURSES_ROOT_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib:$LIBRARY_PATH; export LIBRARY_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH NCURSES_ROOT_DIR=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd; export NCURSES_ROOT_DIR make install install_environment.STDOUT DEBUG 2017-11-18 17:00:52,564 dline_6_3/ca1a9400d4e1/include \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,616 e1/include /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e /usr/bin/install -c -m line/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/doc/readline install_environment.STDOUT DEBUG 2017-11-18 17:00:52,617 install_environment.STDOUT DEBUG 2017-11-18 17:00:52,631 6_3/ca1a9400d4e1/share/info /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/man/man3 install_environment.STDOUT DEBUG 2017-11-18 17:00:52,633 if test -n "" ; then \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,633 rs ; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,634 fi install_environment.STDOUT DEBUG 2017-11-18 17:00:52,638 if test -f readline.info; then \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,638 adline.info /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info/readline.info; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,638 else \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,638 /usr/bin/install -c -m 644 ./readline.info /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info/readline.info; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,638 fi install_environment.STDOUT DEBUG 2017-11-18 17:00:52,646 if test -f rluserman.info; then \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,646 info /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/shar else \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,646 uc/package_readline_6_3/ca1a9400d4e1/share/info/rluserman.info; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,656 if test -f history.info; then \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,656 ackage_readline_6_3/ca1a9400d4e1/share/info/history.info; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,657 else \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,657 /usr/bin/install -c -m 644 ./history.info /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info/history.info; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,657 fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,657 /bin/sh ./support/mkinstalldirs /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_rea /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/include/readline /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,657 /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/man/man3 /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/doc/readline tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,657 dline_6_3/ca1a9400d4e1/include \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,657 mkdir -p -- /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d41/include/readline /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/man/man3 /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/doc/readline tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,672 for f in readline.h chardefs.h keymaps.h history.h tilde.h rlstdc.h rlconf.h rltypedefs.h; do \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,672 644 ./$f /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/include/readline ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,672 done tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,672 e1/include /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e /usr/bin/install -c -m line/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/doc/readline tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,672 /usr/bin/install -c -m 644 ./CHANGES ./INSTALL ./README /galaxydir/galaxy/database/dependencies/read( if test -d doc ; then \ cd doc && \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,672 /Library/Developer/CommandLineTools/usr/bin/make infodir=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info DESTDIR= install; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,673 fi ) install_environment.STDOUT DEBUG 2017-11-18 17:00:52,682 if /bin/sh -c 'install-info --version' >/dev/null 2>&1; then \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,706 kage_readline_6_3/ca1a9400d4e1/share/man/man3/readline.3 install_environment.STDOUT DEBUG 2017-11-18 17:00:52,711 4 ./history.3 /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400if test -n "" ; then \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,711 /usr/bin/install -c -m 644 readline.html /readline.html; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,711 else \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,711 /usr/bin/install -c -m 644 ./readline.html /readline.html; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,711 fi ; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,711 if test -f history.html; then \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,712 /usr/bin/install -c -m 644 history.html /history.html; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,712 else \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,712 /usr/bin/install -c -m 644 ./history.html /history.html; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,712 fi ; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,712 if test -f rluserman.html; then \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,712 /usr/bin/install -c -m 644 rluserman.html /rluserman.html; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,712 else \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,712 /usr/bin/install -c -m 644 ./rluserman.html /rluserman.html; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,712 fi ; \ install_environment.STDOUT DEBUG 2017-11-18 17:00:52,713 fi install_environment.STDOUT DEBUG 2017-11-18 17:00:52,718 ( cd examples ; /Library/Developer/CommandLineTools/usr/bin/make DESTDIR= install ) 127.0.0.1 - - [18/Nov/2017:17:00:52 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:00:52,738 6_3/ca1a9400d4e1/share/readline tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,773 6_3/ca1a9400d4e1/share/info /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/man/man3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,773 if test -n "" ; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,773 rs ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,773 fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,773 if test -f readline.info; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,773 adline.info /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info/readline.info; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,773 else \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,774 /usr/bin/install -c -m 644 ./readline.info /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info/readline.info; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,774 fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,774 if test -f rluserman.info; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,774 /bin/sh ../support/mkdirs /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_ /bin/sh ../support/mkdi /usr/bin/install -c -m 644 re /usr/bin/install -c -m 644 rluserman.e/info/rluserman.info; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,774 info /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/shar else \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,774 uc/package_readline_6_3/ca1a9400d4e1/share/info/rluserman.info; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,774 /usr/bin/install -c -m 644 ./rluserman.info /galaxydir/galaxy/database/dependencies/readline/6.3/i fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,774 if test -f history.info; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,774 ackage_readline_6_3/ca1a9400d4e1/share/info/history.info; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,774 else \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,774 /usr/bin/install -c -m 644 ./history.info /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info/history.info; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,775 fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,775 /usr/bin/install -c -m 644 history.info /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/p install-info --dir-file=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info/dir \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,775 /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info/readline.info ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,775 install-info --dir-file=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info/dir \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,775 /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info/history.info ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,775 install-info --dir-file=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info/dir \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,775 /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/info/rluserman.info ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,775 else true; fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,775 if /bin/sh -c 'install-info --version' >/dev/null 2>&1; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,775 kage_readline_6_3/ca1a9400d4e1/share/man/man3/readline.3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,775 /usr/bin/install -c -m 644 ./readline.3 /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/pac/usr/bin/install -c -m 64d4e1/share/man/man3/history.3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,776 4 ./history.3 /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400if test -n "" ; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,776 /usr/bin/install -c -m 644 readline.html /readline.html; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,776 else \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,776 /usr/bin/install -c -m 644 ./readline.html /readline.html; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,776 fi ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,776 if test -f history.html; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,776 /usr/bin/install -c -m 644 history.html /history.html; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,776 else \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,776 /usr/bin/install -c -m 644 ./history.html /history.html; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,777 fi ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,777 if test -f rluserman.html; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,777 /usr/bin/install -c -m 644 rluserman.html /rluserman.html; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,777 else \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,777 /usr/bin/install -c -m 644 ./rluserman.html /rluserman.html; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,777 fi ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,777 fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,777 if test -f readline.html; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,777 ( cd examples ; /Library/Developer/CommandLineTools/usr/bin/make DESTDIR= install ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,777 6_3/ca1a9400d4e1/share/readline install_environment.STDOUT DEBUG 2017-11-18 17:00:52,784 atabase/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/readline tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,879 atabase/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/share/readline install_environment.STDOUT DEBUG 2017-11-18 17:00:52,906 ependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib/libreadline.a /galaxydir/galaxy/dackage_readline_6_3/ca1a9/usr/bin/install -c -m 644 libr/lib/libreadline.a install_environment.STDOUT DEBUG 2017-11-18 17:00:52,930 b /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib/libmv /galaxydir/galaxy/dataaxy/database/dependencies/readline_6_3/ca1a9400d4e1/lib/libhistory.old/usr/bin/install -c -m 644 libhistory.a /galaxyd_6_3/ca1a9400d4e1/lib/libhistory.a install_environment.STDOUT DEBUG 2017-11-18 17:00:52,941 lib install_environment.STDOUT DEBUG 2017-11-18 17:00:52,943 /CommandLineTools/usr/bin/make all ) install_environment.STDOUT DEBUG 2017-11-18 17:00:52,959 ( cd shlib ; /Library/Developer/CommandLineTools/usr/bin/make DESTDIR= install ) install_environment.STDOUT DEBUG 2017-11-18 17:00:52,969 6_3/ca1a9400d4e1/lib install_environment.STDOUT DEBUG 2017-11-18 17:00:52,972 /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/bin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,984 /bin/sh ../support/mkdirs /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_mkdir /galaxydir/galaxy/dmv /galaxydir/galaxy/database/database/dependencies/readline/6.3/iuc/p400d4e1/lib/libreadline.old tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,984 ependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib/libreadline.a /galaxydir/galaxy/dackage_readline_6_3/ca1a9/usr/bin/install -c -m 644 libr/lib/libreadline.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,984 eadline.a /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1test -n "ranlib" && ranlireadline.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,984 base/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib/libhistory.a /galaxydir/galine/6.3/iuc/package_readl tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,985 ir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib/libhistory.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,985 b /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib/libmv /galaxydir/galaxy/dataaxy/database/dependencies/readline_6_3/ca1a9400d4e1/lib/libhistory.old/usr/bin/install -c -m 644 libhistory.a /galaxyd_6_3/ca1a9400d4e1/lib/libhistory.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,985 lib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,985 /CommandLineTools/usr/bin/make all ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,985 test -n "ranlib" && ranlib /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readlinetest -d shlib || mkdir sh( cd shlib ; /Library/Developermake[1]: Nothing to be done for `all'. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,985 ( cd shlib ; /Library/Developer/CommandLineTools/usr/bin/make DESTDIR= install ) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,986 6_3/ca1a9400d4e1/lib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,986 /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/bin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,986 mv: rename /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib/libreadline.a to /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib/libreadline.old: No such file or directory tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,986 make: [install-static] Error 1 (ignored) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,986 mv: rename /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib/libhistory.a to /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib/libhistory.old: No such file or directory tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:52,986 make: [install-static] Error 1 (ignored) install_environment.STDOUT DEBUG 2017-11-18 17:00:53,010 e/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/bin install_environment.STDOUT DEBUG 2017-11-18 17:00:53,057 win15.6.0 -V apple -d /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ependencies/readline/6.3/ll -c -m 644" libhistory.6.3.dy/bin/sh ../support/shlib-install -O darca1a9400d4e1/lib -b /galaxydir/galaxy/database/diuc/package_readline_6_3/ca1a9400d4e1/bin -i "/usr/bin/instaylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:53,087 e/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/bin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:53,090 /bin/sh ../support/mkdirs /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_/bin/sh ../support/mkdirsmkdir /galaxydir/galaxy/databas/bin/sh ../support/shlib-install -O darca1a9400d4e1/lib -b /galaxydir/galaxy/database/diuc/package_readline_6_3/ca1a9400d4e1/bin -i "/usr/bin/instalib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:53,090 win15.6.0 -V apple -d /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ependencies/readline/6.3/ll -c -m 644" libhistory.6.3.dy/bin/sh ../support/shlib-install -O darca1a9400d4e1/lib -b /galaxydir/galaxy/database/diuc/package_readline_6_3/ca1a9400d4e1/bin -i "/usr/bin/instaylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:readline DEBUG 2017-11-18 17:00:53,192 win15.6.0 -V apple -d /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ependencies/readline/6.3/ll -c -m 644" libreadline.6.3.dinstall: you may need to run ldconfig tool_shed.galaxy_install.tool_dependencies.recipe.step_handler INFO 2017-11-18 17:00:53,304 Replacing $ENV[NCURSES_LIB_PATH] with /galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/ in env.sh for this repository. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 17:00:53,335 Changing status for tool dependency readline from Installing to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:53,335 Updating an existing record for version 6.3 of tool dependency readline for revision ca1a9400d4e1 of repository package_readline_6_3 by updating the status from Installing to Installed. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 17:00:53,381 Tool dependency readline version 6.3 has been installed in /galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1. 127.0.0.1 - - [18/Nov/2017:17:00:55 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:56,641 Creating a new record for version 1.2.8 of tool dependency zlib for revision 8b09fe018cac of repository package_python_2_7. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:56,666 Creating a new record for version 6.3 of tool dependency readline for revision 8b09fe018cac of repository package_python_2_7. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:56,692 Creating a new record for version 1.0.6 of tool dependency bzlib for revision 8b09fe018cac of repository package_python_2_7. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:56,715 Creating a new record for version 5.0.5 of tool dependency xz for revision 8b09fe018cac of repository package_python_2_7. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:56,741 Creating a new record for version 3.8.3 of tool dependency sqlite for revision 8b09fe018cac of repository package_python_2_7. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:56,766 Creating a new record for version 1.11 of tool dependency gdbm for revision 8b09fe018cac of repository package_python_2_7. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:56,797 Creating a new record for version 6.0 of tool dependency ncurses for revision 8b09fe018cac of repository package_python_2_7. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:56,820 Creating a new record for version 2.7 of tool dependency python for revision 8b09fe018cac of repository package_python_2_7. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:57,266 Updating an existing record for version 1.2.8 of tool dependency zlib for revision 8b09fe018cac of repository package_python_2_7 by updating the status from Never installed to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:57,395 Updating an existing record for version 6.3 of tool dependency readline for revision 8b09fe018cac of repository package_python_2_7 by updating the status from Never installed to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:57,485 Updating an existing record for version 1.0.6 of tool dependency bzlib for revision 8b09fe018cac of repository package_python_2_7 by updating the status from Never installed to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:57,620 Updating an existing record for version 5.0.5 of tool dependency xz for revision 8b09fe018cac of repository package_python_2_7 by updating the status from Never installed to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:57,739 Updating an existing record for version 3.8.3 of tool dependency sqlite for revision 8b09fe018cac of repository package_python_2_7 by updating the status from Never installed to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:57,838 Updating an existing record for version 1.11 of tool dependency gdbm for revision 8b09fe018cac of repository package_python_2_7 by updating the status from Never installed to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:58,278 Updating an existing record for version 6.0 of tool dependency ncurses for revision 8b09fe018cac of repository package_python_2_7 by updating the status from Never installed to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:00:58,339 Updating an existing record for version 2.7 of tool dependency python for revision 8b09fe018cac of repository package_python_2_7 by updating the status from Never installed to Installing. 127.0.0.1 - - [18/Nov/2017:17:00:58 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 17:00:59,148 Attempting to download via url: https://www.python.org/ftp/python/2.7.10/Python-2.7.10.tgz 127.0.0.1 - - [18/Nov/2017:17:01:01 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:01:05 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 17:01:06,848 Successfully downloaded from url: https://www.python.org/ftp/python/2.7.10/Python-2.7.10.tgz tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:06,862 + ZLIB_ROOT_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8; export ZLIB_ROOT_PATH PKG_CONFIG_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib/pkgconfig:$PKG_CONFIG_PATH; export PKG_CONFIG_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib:$LIBRARY_PATH; export LIBRARY_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH ZLIB_ROOT_DIR=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8; export ZLIB_ROOT_DIR READLINE_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/include; export READLINE_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH READLINE_LIB_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib; export READLINE_LIB_PATH READLINE_BIN_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/bin; export READLINE_BIN_PATH READLINE_ROOT_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1; export READLINE_ROOT_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib:$LIBRARY_PATH; export LIBRARY_PATH PATH=$PATH:/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/bin; export PATH READLINE_ROOT_DIR=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1; export READLINE_ROOT_DIR PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin:$PATH; export PATH BZLIB_LIB_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib; export BZLIB_LIB_DIR BZLIB_INCLUDE_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include; export BZLIB_INCLUDE_DIR BZLIB_SOURCE_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source; export BZLIB_SOURCE_DIR LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib:$LIBRARY_PATH; export LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source:$LIBRARY_PATH; export LIBRARY_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH BZLIB_ROOT_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595; export BZLIB_ROOT_DIR LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH XZ_ROOT_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594; export XZ_ROOT_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH XZ_ROOT_DIR=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594; export XZ_ROOT_DIR PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/bin:$PATH; export PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib:$LIBRARY_PATH; export LIBRARY_PATH SQLITE_ROOT_DIR=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921; export SQLITE_ROOT_DIR C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH PKG_CONFIG_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib/pkgconfig:$PKG_CONFIG_PATH; export PKG_CONFIG_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH GDBM_ROOT_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc; export GDBM_ROOT_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH GDBM_ROOT_DIR=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc; export GDBM_ROOT_DIR NCURSES_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include; export NCURSES_INCLUDE_PATH NCURSES_LIB_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/; export NCURSES_LIB_PATH NCURSES_ROOT_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd; export NCURSES_ROOT_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib:$LIBRARY_PATH; export LIBRARY_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH NCURSES_ROOT_DIR=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd; export NCURSES_ROOT_DIR sed -i.bak -e "s/if host_platform == 'atheos':/if True:/g" setup.py tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:07,115 + ZLIB_ROOT_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8; export ZLIB_ROOT_PATH PKG_CONFIG_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib/pkgconfig:$PKG_CONFIG_PATH; export PKG_CONFIG_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib:$LIBRARY_PATH; export LIBRARY_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH ZLIB_ROOT_DIR=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8; export ZLIB_ROOT_DIR READLINE_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/include; export READLINE_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH READLINE_LIB_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib; export READLINE_LIB_PATH READLINE_BIN_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/bin; export READLINE_BIN_PATH READLINE_ROOT_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1; export READLINE_ROOT_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib:$LIBRARY_PATH; export LIBRARY_PATH PATH=$PATH:/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/bin; export PATH READLINE_ROOT_DIR=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1; export READLINE_ROOT_DIR PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin:$PATH; export PATH BZLIB_LIB_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib; export BZLIB_LIB_DIR BZLIB_INCLUDE_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include; export BZLIB_INCLUDE_DIR BZLIB_SOURCE_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source; export BZLIB_SOURCE_DIR LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib:$LIBRARY_PATH; export LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source:$LIBRARY_PATH; export LIBRARY_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH BZLIB_ROOT_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595; export BZLIB_ROOT_DIR LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH XZ_ROOT_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594; export XZ_ROOT_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH XZ_ROOT_DIR=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594; export XZ_ROOT_DIR PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/bin:$PATH; export PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib:$LIBRARY_PATH; export LIBRARY_PATH SQLITE_ROOT_DIR=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921; export SQLITE_ROOT_DIR C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH PKG_CONFIG_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib/pkgconfig:$PKG_CONFIG_PATH; export PKG_CONFIG_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH GDBM_ROOT_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc; export GDBM_ROOT_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH GDBM_ROOT_DIR=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc; export GDBM_ROOT_DIR NCURSES_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include; export NCURSES_INCLUDE_PATH NCURSES_LIB_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/; export NCURSES_LIB_PATH NCURSES_ROOT_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd; export NCURSES_ROOT_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib:$LIBRARY_PATH; export LIBRARY_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH NCURSES_ROOT_DIR=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd; export NCURSES_ROOT_DIR ./configure --prefix=/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac --enable-shared --enable-unicode=ucs4 && make && make install install_environment.STDOUT DEBUG 2017-11-18 17:01:07,734 checking host system type... x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:07,740 checking build system type... x86_64-apple-darwin15.6.0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:07,740 checking host system type... x86_64-apple-darwin15.6.0 install_environment.STDOUT DEBUG 2017-11-18 17:01:07,766 checking for --with-universal-archs... 32-bit install_environment.STDOUT DEBUG 2017-11-18 17:01:07,801 checking EXTRAPLATDIR... $(PLATMACDIRS) install_environment.STDOUT DEBUG 2017-11-18 17:01:07,803 checking for gcc... gcc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:07,845 checking for --enable-universalsdk... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:07,845 checking for --with-universal-archs... 32-bit tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:07,846 checking MACHDEP... darwin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:07,846 checking EXTRAPLATDIR... $(PLATMACDIRS) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:07,846 checking for --without-gcc... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:07,846 checking for gcc... gcc install_environment.STDOUT DEBUG 2017-11-18 17:01:08,112 checking for C compiler default output file name... a.out tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:08,155 checking whether the C compiler works... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:08,155 checking for C compiler default output file name... a.out tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:08,259 checking for suffix of executables... install_environment.STDOUT DEBUG 2017-11-18 17:01:08,310 checking whether we are cross compiling... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:08,360 checking whether we are cross compiling... no install_environment.STDOUT DEBUG 2017-11-18 17:01:08,445 checking whether we are using the GNU C compiler... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:08,461 checking for suffix of object files... o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:08,461 checking whether we are using the GNU C compiler... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:08,564 checking whether gcc accepts -g... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:08,603 checking for gcc option to accept ISO C89... none needed tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:08,667 checking for --with-cxx-main=<compiler>... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:08,670 checking for gcc option to accept ISO C89... none needed tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:08,670 checking for g++... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:08,671 configure: WARNING: install_environment.STDOUT DEBUG 2017-11-18 17:01:08,761 checking how to run the C preprocessor... gcc -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:08,772 checking how to run the C preprocessor... gcc -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:08,772 By default, distutils will build C++ extension modules with "g++". tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:08,772 If this is not intended, then set CXX on the configure command line. 127.0.0.1 - - [18/Nov/2017:17:01:08 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:01:09,205 checking for egrep... /usr/bin/grep -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:09,280 checking for grep that handles long lines and -e... /usr/bin/grep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:09,280 checking for egrep... /usr/bin/grep -E tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:09,690 checking for ANSI C header files... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:09,698 checking for sys/types.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:09,795 checking for sys/types.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:09,900 checking for sys/stat.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:09,950 checking for stdlib.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:10,003 checking for stdlib.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:10,104 checking for string.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:10,193 checking for memory.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:10,208 checking for memory.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:10,309 checking for strings.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:10,422 checking for inttypes.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:10,516 checking for inttypes.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:10,617 checking for stdint.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:10,679 checking for unistd.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:10,721 checking for unistd.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:10,825 checking minix/config.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:10,878 checking minix/config.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:10,927 checking minix/config.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:10,928 checking for minix/config.h... no install_environment.STDOUT DEBUG 2017-11-18 17:01:10,979 checking whether it is safe to define __EXTENSIONS__... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:10,990 checking for case-insensitive build directory... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:10,996 checking LINKCC... $(PURIFY) $(MAINCC) install_environment.STDOUT DEBUG 2017-11-18 17:01:11,028 checking for --enable-shared... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,028 checking whether it is safe to define __EXTENSIONS__... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,028 checking for --with-suffix... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,028 checking for case-insensitive build directory... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,029 checking LIBRARY... libpython$(VERSION).a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,029 checking LINKCC... $(PURIFY) $(MAINCC) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,029 checking for GNU ld... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,029 checking for --enable-shared... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,029 checking for --enable-profiling... no install_environment.STDOUT DEBUG 2017-11-18 17:01:11,032 checking LDLIBRARY... libpython$(VERSION).dylib install_environment.STDOUT DEBUG 2017-11-18 17:01:11,036 checking for ar... ar install_environment.STDOUT DEBUG 2017-11-18 17:01:11,039 checking for hg... found install_environment.STDOUT DEBUG 2017-11-18 17:01:11,084 checking for a thread-safe mkdir -p... ./install-sh -c -d tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,131 checking LDLIBRARY... libpython$(VERSION).dylib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,131 checking for ranlib... ranlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,131 checking for ar... ar tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,132 checking for svnversion... found tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,132 checking for hg... found tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,132 checking for a BSD-compatible install... /usr/bin/install -c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,132 checking for a thread-safe mkdir -p... ./install-sh -c -d tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,133 checking for --with-pydebug... no install_environment.STDOUT DEBUG 2017-11-18 17:01:11,182 checking whether gcc accepts -fno-strict-aliasing... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,236 checking whether gcc accepts -fno-strict-aliasing... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,236 checking which compiler should be used... gcc install_environment.STDOUT DEBUG 2017-11-18 17:01:11,296 checking whether gcc accepts -OPT:Olimit=0... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,336 checking whether gcc accepts -OPT:Olimit=0... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,437 checking whether gcc supports ParseTuple __format__... no install_environment.STDOUT DEBUG 2017-11-18 17:01:11,508 checking whether pthreads are available without options... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:11,510 checking for ANSI C header files... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,540 checking whether pthreads are available without options... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,540 checking whether g++ also accepts flags for thread support... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,540 checking for ANSI C header files... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,641 checking asm/types.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:11,693 checking asm/types.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,744 checking asm/types.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,746 checking for asm/types.h... no install_environment.STDOUT DEBUG 2017-11-18 17:01:11,828 checking conio.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,850 checking conio.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:11,905 checking for conio.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,951 checking conio.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:11,951 checking for conio.h... no 127.0.0.1 - - [18/Nov/2017:17:01:11 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,054 checking direct.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:12,125 checking direct.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,158 checking direct.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,159 checking for direct.h... no install_environment.STDOUT DEBUG 2017-11-18 17:01:12,240 checking dlfcn.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,259 checking dlfcn.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:12,296 checking for dlfcn.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,364 checking dlfcn.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,364 checking for dlfcn.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:12,465 checking errno.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,465 checking errno.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,465 checking errno.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,465 checking for errno.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:12,566 checking fcntl.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:12,617 checking for fcntl.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,671 checking fcntl.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,671 checking fcntl.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,671 checking for fcntl.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,772 checking grp.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:12,781 checking grp.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,875 checking grp.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,875 checking for grp.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:12,915 checking ieeefp.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:12,976 checking ieeefp.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:12,983 checking for ieeefp.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,076 checking ieeefp.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,076 checking for ieeefp.h... no install_environment.STDOUT DEBUG 2017-11-18 17:01:13,159 checking io.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,179 checking io.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,179 checking for io.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,180 checking io.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,280 checking langinfo.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:13,284 checking langinfo.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,380 checking langinfo.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,380 checking for langinfo.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:13,381 checking libintl.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:13,442 checking for libintl.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,481 checking libintl.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,481 checking libintl.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,482 checking for libintl.h... no install_environment.STDOUT DEBUG 2017-11-18 17:01:13,571 checking poll.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,583 checking poll.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,583 checking poll.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,583 checking for poll.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:13,664 checking process.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,684 checking process.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:13,713 checking for process.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,787 checking process.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,787 checking for process.h... no install_environment.STDOUT DEBUG 2017-11-18 17:01:13,853 checking pthread.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,892 checking pthread.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,892 checking pthread.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,892 checking for pthread.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:13,947 checking shadow.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:13,994 checking shadow.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:13,999 checking for shadow.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,094 checking shadow.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,094 checking for shadow.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,094 checking signal.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:14,121 checking signal.h presence... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:14,159 checking for stdint.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,196 checking signal.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,196 checking for signal.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,196 checking for stdint.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,301 checking stropts.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:14,328 checking stropts.h presence... no install_environment.STDOUT DEBUG 2017-11-18 17:01:14,402 checking termios.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,404 checking stropts.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,404 checking for stropts.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,404 checking termios.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:14,446 checking for termios.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,507 checking termios.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,507 checking for termios.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:14,600 checking thread.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,607 checking thread.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,608 checking thread.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,608 checking for thread.h... no install_environment.STDOUT DEBUG 2017-11-18 17:01:14,609 checking for unistd.h... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,713 checking for unistd.h... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 17:01:14,760 checking utime.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,817 checking utime.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,818 checking utime.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,818 checking for utime.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:14,881 checking sys/audioio.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:14,922 checking sys/audioio.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:14,929 checking for sys/audioio.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,022 checking sys/audioio.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,022 checking for sys/audioio.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,022 checking sys/bsdtty.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:15,081 checking sys/bsdtty.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,128 checking sys/bsdtty.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,128 checking for sys/bsdtty.h... no 127.0.0.1 - - [18/Nov/2017:17:01:14 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:01:15,197 checking sys/epoll.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,229 checking sys/epoll.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:15,250 checking for sys/epoll.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,332 checking sys/epoll.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,332 checking for sys/epoll.h... no install_environment.STDOUT DEBUG 2017-11-18 17:01:15,387 checking sys/event.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,434 checking sys/event.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,435 checking sys/event.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,435 checking for sys/event.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:15,474 checking sys/file.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:15,533 checking for sys/file.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,536 checking sys/file.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,536 checking sys/file.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,536 checking for sys/file.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:15,690 checking sys/loadavg.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,740 checking sys/loadavg.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,740 checking sys/loadavg.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,740 checking for sys/loadavg.h... no install_environment.STDOUT DEBUG 2017-11-18 17:01:15,768 checking sys/lock.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:15,821 checking for sys/lock.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,844 checking sys/lock.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,844 checking for sys/lock.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,844 checking sys/lock.h presence... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:15,921 checking sys/mkdev.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:15,945 checking sys/mkdev.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:15,971 checking for sys/mkdev.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,045 checking sys/mkdev.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,045 checking for sys/mkdev.h... no install_environment.STDOUT DEBUG 2017-11-18 17:01:16,110 checking sys/modem.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,150 checking sys/modem.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,150 checking sys/modem.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,150 checking for sys/modem.h... no install_environment.STDOUT DEBUG 2017-11-18 17:01:16,187 checking sys/param.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:16,237 checking for sys/param.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,255 checking sys/param.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,255 checking sys/param.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,255 checking for sys/param.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:16,352 checking sys/poll.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,356 checking sys/poll.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,356 checking sys/poll.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,356 checking for sys/poll.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:16,429 checking sys/select.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,460 checking sys/select.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:16,461 checking for sys/select.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,561 checking sys/select.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,561 checking for sys/select.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,561 checking sys/socket.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:16,592 checking sys/socket.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,663 checking sys/socket.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,663 checking for sys/socket.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:16,668 checking sys/statvfs.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:16,703 checking for sys/statvfs.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,765 checking sys/statvfs.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,765 checking sys/statvfs.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,766 checking for sys/statvfs.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,766 checking for sys/stat.h... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 17:01:16,810 checking sys/termio.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:16,860 checking for sys/termio.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,870 checking sys/termio.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,870 checking sys/termio.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,871 checking for sys/termio.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:16,972 checking sys/time.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:16,990 checking sys/time.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,073 checking sys/time.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,074 checking for sys/time.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:17,079 checking sys/times.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:17,118 checking for sys/times.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,178 checking sys/times.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,178 checking sys/times.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,178 checking for sys/times.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,178 checking for sys/types.h... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 17:01:17,231 checking sys/un.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:17,268 checking for sys/un.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,282 checking sys/un.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,283 checking sys/un.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,283 checking for sys/un.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,385 checking sys/utsname.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:17,415 checking sys/utsname.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,486 checking sys/utsname.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,486 checking for sys/utsname.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:17,514 checking sys/wait.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:17,573 checking for sys/wait.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,587 checking sys/wait.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,587 checking sys/wait.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,587 checking for sys/wait.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,691 checking pty.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:17,722 checking pty.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,795 checking pty.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,795 checking for pty.h... no install_environment.STDOUT DEBUG 2017-11-18 17:01:17,807 checking libutil.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:17,856 checking for libutil.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,898 checking libutil.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,898 checking libutil.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:17,898 checking for libutil.h... no install_environment.STDOUT DEBUG 2017-11-18 17:01:17,993 checking sys/resource.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,000 checking sys/resource.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,001 checking sys/resource.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,001 checking for sys/resource.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:18,092 checking netpacket/packet.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,105 checking netpacket/packet.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:18,154 checking for netpacket/packet.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,212 checking netpacket/packet.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,212 checking for netpacket/packet.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,313 checking sysexits.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:18,329 checking sysexits.h presence... yes 127.0.0.1 - - [18/Nov/2017:17:01:18 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,419 checking sysexits.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,419 checking for sysexits.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:18,477 checking bluetooth.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,523 checking bluetooth.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:18,547 checking for bluetooth.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,625 checking bluetooth.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,625 checking for bluetooth.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,728 checking bluetooth/bluetooth.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:18,748 checking bluetooth/bluetooth.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,832 checking bluetooth/bluetooth.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,832 checking for bluetooth/bluetooth.h... no install_environment.STDOUT DEBUG 2017-11-18 17:01:18,890 checking linux/tipc.h usability... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:18,938 checking linux/tipc.h usability... no install_environment.STDOUT DEBUG 2017-11-18 17:01:18,971 checking for linux/tipc.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:19,040 checking linux/tipc.h presence... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:19,040 checking for linux/tipc.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:19,141 checking spawn.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:19,162 checking spawn.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:19,248 checking spawn.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:19,248 checking for spawn.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:19,316 checking util.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:19,349 checking util.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:19,403 checking for util.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:19,452 checking util.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:19,452 checking for util.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:19,553 checking alloca.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:19,561 checking alloca.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:19,656 checking alloca.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:19,656 checking for alloca.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:19,680 checking for dirent.h that defines DIR... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:19,760 checking for dirent.h that defines DIR... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:19,863 checking for library containing opendir... none required install_environment.STDOUT DEBUG 2017-11-18 17:01:19,911 checking whether sys/types.h defines makedev... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:19,967 checking whether sys/types.h defines makedev... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:20,043 checking for clock_t in time.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:20,072 checking for linux/netlink.h... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:20,072 checking for clock_t in time.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:20,176 checking for makedev... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:20,176 checking Solaris LFS bug... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:20,280 checking Solaris LFS bug... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:20,380 checking for mode_t... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:20,468 checking for off_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:20,484 checking for off_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:20,684 checking for pid_t... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:20,748 checking for size_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:20,787 checking for size_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:20,888 checking for uid_t in sys/types.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:20,931 checking for uint32_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:20,989 checking for uint32_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:21,091 checking for uint32_t... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:21,135 checking for uint64_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:21,192 checking for uint64_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:21,295 checking for uint64_t... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:21,349 checking for int32_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:21,397 checking for int32_t... yes 127.0.0.1 - - [18/Nov/2017:17:01:21 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:21,605 checking for int32_t... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:21,648 checking for int64_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:21,709 checking for int64_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:21,812 checking for int64_t... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:21,928 checking for ssize_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:22,014 checking for ssize_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:22,115 checking size of int... 4 install_environment.STDOUT DEBUG 2017-11-18 17:01:22,139 checking size of long... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:22,216 checking size of long... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:22,317 checking size of void *... 8 install_environment.STDOUT DEBUG 2017-11-18 17:01:22,353 checking size of short... 2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:22,418 checking size of short... 2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:22,521 checking size of float... 4 install_environment.STDOUT DEBUG 2017-11-18 17:01:22,570 checking size of double... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:22,623 checking size of double... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:22,726 checking size of fpos_t... 8 install_environment.STDOUT DEBUG 2017-11-18 17:01:22,791 checking size of size_t... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:22,830 checking size of size_t... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:22,931 checking size of pid_t... 4 install_environment.STDOUT DEBUG 2017-11-18 17:01:22,949 checking for long long support... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:23,034 checking for long long support... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:23,104 checking for long double support... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:23,139 checking size of long long... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:23,139 checking for long double support... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:23,243 checking size of long double... 16 install_environment.STDOUT DEBUG 2017-11-18 17:01:23,273 checking for _Bool support... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:23,345 checking for _Bool support... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:23,450 checking size of _Bool... 1 install_environment.STDOUT DEBUG 2017-11-18 17:01:23,498 checking for uintptr_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:23,551 checking for uintptr_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:23,654 checking size of uintptr_t... 8 install_environment.STDOUT DEBUG 2017-11-18 17:01:23,724 checking size of off_t... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:23,757 checking size of off_t... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:23,757 checking whether to enable large file support... no install_environment.STDOUT DEBUG 2017-11-18 17:01:23,836 checking size of time_t... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:23,860 checking size of time_t... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:23,964 checking for pthread_t... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:24,009 checking size of pthread_t... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,069 checking size of pthread_t... 8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,069 checking for --enable-toolbox-glue... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:24,132 checking for --enable-framework... no install_environment.STDOUT DEBUG 2017-11-18 17:01:24,133 checking SO... .so install_environment.STDOUT DEBUG 2017-11-18 17:01:24,151 checking CCSHARED... install_environment.STDOUT DEBUG 2017-11-18 17:01:24,152 checking CFLAGSFORSHARED... $(CCSHARED) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,170 checking for --enable-framework... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,170 checking for dyld... always on for Darwin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,170 checking SO... .so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,171 checking LDSHARED... $(CC) -bundle -undefined dynamic_lookup tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,171 checking CCSHARED... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,171 checking LINKFORSHARED... -u _PyMac_Error tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,171 checking CFLAGSFORSHARED... $(CCSHARED) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,171 checking SHLIBS... $(LIBS) install_environment.STDOUT DEBUG 2017-11-18 17:01:24,229 checking for dlopen in -ldl... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,274 checking for dlopen in -ldl... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,376 checking for shl_load in -ldld... no install_environment.STDOUT DEBUG 2017-11-18 17:01:24,399 checking for RAND_egd in -lcrypto... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,478 checking for RAND_egd in -lcrypto... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,479 checking for library containing sem_init... none required install_environment.STDOUT DEBUG 2017-11-18 17:01:24,549 checking for textdomain in -lintl... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,582 checking for textdomain in -lintl... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,684 checking for t_open in -lnsl... no 127.0.0.1 - - [18/Nov/2017:17:01:24 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:01:24,729 checking for socket in -lsocket... no install_environment.STDOUT DEBUG 2017-11-18 17:01:24,732 checking for pkg-config... no install_environment.STDOUT DEBUG 2017-11-18 17:01:24,733 checking for --with-system-ffi... no install_environment.STDOUT DEBUG 2017-11-18 17:01:24,733 checking for --with-tcltk-libs... default install_environment.STDOUT DEBUG 2017-11-18 17:01:24,734 checking for --with-signal-module... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:24,735 checking for --with-threads... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,785 checking for socket in -lsocket... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,785 checking for --with-libs... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,785 checking for pkg-config... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,785 checking for --with-system-expat... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,785 checking for --with-system-ffi... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,785 checking for --with-tcltk-includes... default tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,786 checking for --with-tcltk-libs... default tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,786 checking for --with-dbmliborder... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,786 checking for --with-signal-module... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,786 checking for --with-dec-threads... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,786 checking for --with-threads... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,889 checking if PTHREAD_SCOPE_SYSTEM is supported... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:24,982 checking for pthread_sigmask... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:24,990 checking for pthread_sigmask... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:25,181 checking if --enable-ipv6 is specified... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:25,198 checking for pthread_atfork... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:25,198 checking if --enable-ipv6 is specified... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:25,300 checking if RFC2553 API is available... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:25,430 checking ipv6 stack type... kame tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:25,504 checking ipv6 stack type... kame tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:25,505 using libc install_environment.STDOUT DEBUG 2017-11-18 17:01:26,650 checking for OSX 10.5 SDK or later... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:26,654 checking for --with-tsc... no install_environment.STDOUT DEBUG 2017-11-18 17:01:26,655 checking for --with-valgrind... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:26,732 checking for OSX 10.5 SDK or later... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:26,732 checking for --with-doc-strings... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:26,732 checking for --with-tsc... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:26,732 checking for --with-pymalloc... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:26,732 checking for --with-valgrind... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:26,732 checking for --with-wctype-functions... no install_environment.STDOUT DEBUG 2017-11-18 17:01:26,810 checking for dlopen... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:26,814 checking MACHDEP_OBJS... MACHDEP_OBJS tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:26,835 checking for dlopen... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:26,836 checking DYNLOADFILE... dynload_shlib.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:26,836 checking MACHDEP_OBJS... MACHDEP_OBJS tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:26,936 checking for alarm... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:27,012 checking for setitimer... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:27,040 checking for setitimer... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:27,142 checking for getitimer... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:27,192 checking for bind_textdomain_codeset... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:27,246 checking for bind_textdomain_codeset... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:27,349 checking for chown... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:27,369 checking for clock... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:27,452 checking for clock... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:27,556 checking for confstr... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:27,565 checking for ctermid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:27,657 checking for ctermid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:27,759 checking for execv... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:27,759 checking for fchmod... yes 127.0.0.1 - - [18/Nov/2017:17:01:27 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:27,864 checking for fchmod... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:27,864 checking for fchown... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:27,953 checking for fork... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:27,965 checking for fork... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:28,066 checking for fpathconf... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:28,128 checking for ftime... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:28,168 checking for ftime... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:28,269 checking for ftruncate... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:28,336 checking for gai_strerror... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:28,374 checking for gai_strerror... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:28,476 checking for getgroups... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:28,542 checking for getlogin... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:28,579 checking for getlogin... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:28,680 checking for getloadavg... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:28,724 checking for getpeername... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:28,781 checking for getpeername... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:28,883 checking for getpgid... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:28,916 checking for getpid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:28,984 checking for getpid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:29,085 checking for getentropy... no install_environment.STDOUT DEBUG 2017-11-18 17:01:29,097 checking for getpriority... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:29,188 checking for getpriority... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:29,272 checking for getresgid... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:29,288 checking for getresuid... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:29,289 checking for getresgid... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:29,392 checking for getpwent... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:29,444 checking for getspnam... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:29,493 checking for getspnam... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:29,598 checking for getspent... no install_environment.STDOUT DEBUG 2017-11-18 17:01:29,611 checking for getsid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:29,701 checking for getsid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:29,701 checking for getwd... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:29,791 checking for initgroups... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:29,806 checking for initgroups... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:29,909 checking for kill... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:29,973 checking for killpg... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:30,011 checking for killpg... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:30,112 checking for lchmod... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:30,181 checking for lchown... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:30,215 checking for lchown... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:30,316 checking for lstat... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:30,395 checking for mkfifo... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:30,417 checking for mkfifo... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:30,519 checking for mknod... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:30,596 checking for mktime... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:30,619 checking for mktime... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:30,721 checking for mmap... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:30,785 checking for mremap... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:30,821 checking for mremap... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:30,923 checking for nice... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:30,982 checking for pathconf... yes 127.0.0.1 - - [18/Nov/2017:17:01:30 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:31,026 checking for pathconf... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:31,127 checking for pause... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:31,208 checking for plock... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:31,231 checking for plock... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:31,333 checking for poll... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:31,408 checking for pthread_init... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:31,438 checking for pthread_init... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:31,541 checking for putenv... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:31,588 checking for readlink... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:31,642 checking for readlink... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:31,744 checking for realpath... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:31,787 checking for select... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:31,844 checking for select... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:31,945 checking for sem_open... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:31,992 checking for sem_timedwait... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:32,045 checking for sem_timedwait... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:32,147 checking for sem_getvalue... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:32,179 checking for sem_unlink... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:32,251 checking for sem_unlink... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:32,354 checking for setegid... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:32,370 checking for seteuid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:32,456 checking for seteuid... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:32,548 checking for setlocale... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:32,557 checking for setgid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:32,557 checking for setlocale... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:32,658 checking for setregid... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:32,727 checking for setreuid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:32,758 checking for setreuid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:32,861 checking for setsid... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:32,907 checking for setpgid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:32,965 checking for setpgid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,068 checking for setpgrp... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:33,089 checking for setuid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,170 checking for setuid... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,272 checking for setvbuf... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:33,286 checking for snprintf... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:33,332 checking for setregid... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,375 checking for snprintf... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,376 checking for setlocale... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,376 checking for setregid... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,376 checking for setreuid... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 17:01:33,445 checking for setresuid... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,477 checking for setresuid... no install_environment.STDOUT DEBUG 2017-11-18 17:01:33,555 checking for setsid... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,578 checking for setresgid... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,578 checking for setsid... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,578 checking for setpgid... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 17:01:33,591 checking for setpgrp... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 17:01:33,625 checking for setvbuf... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,679 checking for setpgrp... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,679 checking for setuid... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,679 checking for setvbuf... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,680 checking for snprintf... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 17:01:33,732 checking for sigaction... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,780 checking for sigaction... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,885 checking for siginterrupt... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:33,926 checking for sigrelse... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:33,990 checking for sigrelse... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:34,094 checking for strftime... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:34,122 checking for sysconf... yes 127.0.0.1 - - [18/Nov/2017:17:01:34 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:34,195 checking for sysconf... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:34,299 checking for tcgetpgrp... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:34,317 checking for tcsetpgrp... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:34,401 checking for tcsetpgrp... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:34,501 checking for timegm... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:34,504 checking for tempnam... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:34,505 checking for timegm... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:34,606 checking for times... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:34,685 checking for tmpfile... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:34,711 checking for tmpfile... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:34,814 checking for tmpnam... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:34,870 checking for tmpnam_r... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:34,916 checking for tmpnam_r... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:35,020 checking for truncate... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:35,037 checking for uname... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:35,122 checking for uname... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:35,221 checking for utimes... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:35,224 checking for unsetenv... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:35,225 checking for utimes... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:35,325 checking for waitpid... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:35,404 checking for wait3... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:35,426 checking for wait3... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:35,528 checking for wait4... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:35,589 checking for wcscoll... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:35,630 checking for wcscoll... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:35,733 checking for _getpty... no install_environment.STDOUT DEBUG 2017-11-18 17:01:35,733 checking for chroot... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:35,834 checking for chroot... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:35,835 checking for link... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:35,857 checking for symlink... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:35,940 checking for symlink... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:35,940 checking for fchdir... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:35,963 checking for fsync... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,041 checking for fsync... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,041 checking for fdatasync... no install_environment.STDOUT DEBUG 2017-11-18 17:01:36,070 checking for epoll... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,143 checking for epoll... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,143 checking for kqueue... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:36,174 checking for ctermid_r... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,247 checking for ctermid_r... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,248 checking for flock declaration... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:36,312 checking for flock... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,349 checking for flock... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:36,434 checking for broken unsetenv... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,449 checking for getpagesize... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,449 checking for broken unsetenv... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,450 checking for true... true install_environment.STDOUT DEBUG 2017-11-18 17:01:36,520 checking for inet_aton in -lc... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,553 checking for inet_aton in -lc... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,653 checking for chflags... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:36,692 checking for lchflags... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,754 checking for lchflags... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,856 checking for inflateCopy in -lz... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:36,856 checking for hstrerror... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,956 checking for hstrerror... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:36,957 checking for inet_aton... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:37,005 checking for inet_pton... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:37,058 checking for inet_pton... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:37,137 checking for openpty... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:37,158 checking for setgroups... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:37,159 checking for openpty... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:37,260 checking for forkpty... yes 127.0.0.1 - - [18/Nov/2017:17:01:37 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:01:37,343 checking for memmove... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:37,362 checking for memmove... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:37,462 checking for fseek64... no install_environment.STDOUT DEBUG 2017-11-18 17:01:37,512 checking for fseeko... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:37,564 checking for fseeko... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:37,666 checking for fstatvfs... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:37,705 checking for ftell64... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:37,771 checking for ftell64... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:37,871 checking for ftello... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:37,874 checking for statvfs... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:37,975 checking for statvfs... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:37,975 checking for dup2... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:38,024 checking for getcwd... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:38,076 checking for getcwd... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:38,177 checking for strdup... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:38,185 checking for getpgrp... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:38,281 checking for getpgrp... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:38,281 checking for setpgrp... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 17:01:38,397 checking for gettimeofday... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:38,487 checking for gettimeofday... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:38,592 checking for major... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:38,616 checking for getaddrinfo... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:38,693 checking for getaddrinfo... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:38,796 checking getaddrinfo bug... no install_environment.STDOUT DEBUG 2017-11-18 17:01:38,803 checking for getnameinfo... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:38,901 checking for getnameinfo... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:38,901 checking whether time.h and sys/time.h may both be included... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:38,915 checking whether struct tm is in sys/time.h or time.h... time.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:39,003 checking whether struct tm is in sys/time.h or time.h... time.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:39,004 checking for struct tm.tm_zone... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:39,035 checking for struct stat.st_rdev... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:39,108 checking for struct stat.st_rdev... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:39,183 checking for struct stat.st_flags... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:39,208 checking for struct stat.st_blksize... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:39,208 checking for struct stat.st_flags... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:39,309 checking for struct stat.st_gen... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:39,415 checking for struct stat.st_birthtime... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:39,512 checking for struct stat.st_birthtime... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:39,512 checking for struct stat.st_blocks... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:39,564 checking for time.h that defines altzone... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:39,616 checking for time.h that defines altzone... no install_environment.STDOUT DEBUG 2017-11-18 17:01:39,701 checking for addrinfo... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:39,720 checking whether sys/select.h and sys/time.h may both be included... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:39,720 checking for addrinfo... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:39,824 checking for sockaddr_storage... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:39,830 checking whether char is unsigned... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:39,928 checking whether char is unsigned... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:39,928 checking for an ANSI C-conforming const... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:39,933 checking for working volatile... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,030 checking for working volatile... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,030 checking for working signed char... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:40,035 checking for prototypes... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,135 checking for prototypes... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,135 checking for variable length prototypes and stdarg.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:40,143 checking for socketpair... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,239 checking for socketpair... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,240 checking if sockaddr has sa_len member... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:40,261 checking whether va_list is an array... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,344 checking whether va_list is an array... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:40,445 checking for gethostbyname... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,447 checking for gethostbyname_r... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,448 checking for gethostbyname... yes 127.0.0.1 - - [18/Nov/2017:17:01:40 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:01:40,640 checking for __fpu_control in -lieee... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,655 checking for __fpu_control... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,655 checking for --with-fpectl... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,656 checking for --with-libm=STRING... default LIBM="" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,656 checking for --with-libc=STRING... default LIBC="" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,656 checking for __fpu_control in -lieee... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,758 checking whether C doubles are little-endian IEEE 754 binary64... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:40,854 checking whether C doubles are big-endian IEEE 754 binary64... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:40,860 checking whether C doubles are big-endian IEEE 754 binary64... no install_environment.STDOUT DEBUG 2017-11-18 17:01:41,059 checking whether we can use gcc inline assembler to get and set x87 control word... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:41,063 checking whether C doubles are ARM mixed-endian IEEE 754 binary64... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:41,063 checking whether we can use gcc inline assembler to get and set x87 control word... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:41,271 checking for x87-style double rounding... no install_environment.STDOUT DEBUG 2017-11-18 17:01:41,347 checking whether tanh preserves the sign of zero... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:41,372 checking whether tanh preserves the sign of zero... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:41,577 checking for acosh... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:41,641 checking for asinh... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:41,682 checking for asinh... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:41,890 checking for atanh... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:41,946 checking for copysign... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:41,991 checking for copysign... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:42,193 checking for erf... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:42,261 checking for erfc... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:42,295 checking for erfc... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:42,502 checking for expm1... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:42,571 checking for finite... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:42,609 checking for finite... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:42,812 checking for gamma... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:42,873 checking for hypot... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:42,915 checking for hypot... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:43,018 checking for lgamma... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:43,105 checking for log1p... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:43,119 checking for log1p... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:43,221 checking for round... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:43,310 checking for tgamma... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:43,321 checking for tgamma... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:43,424 checking whether isinf is declared... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:43,453 checking whether isnan is declared... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:43,528 checking whether isnan is declared... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:43,528 checking whether isfinite is declared... yes 127.0.0.1 - - [18/Nov/2017:17:01:43 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:01:43,651 checking whether POSIX semaphores are enabled... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:43,737 checking whether POSIX semaphores are enabled... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:43,753 checking digit size for Python's longs... no value specified tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:43,842 checking for broken sem_getvalue... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:43,842 checking digit size for Python's longs... no value specified tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:43,842 checking wchar.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:43,867 checking wchar.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:43,942 checking wchar.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:43,942 checking for wchar.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:43,971 checking size of wchar_t... 4 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:44,045 checking size of wchar_t... 4 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:44,145 checking for UCS-4 tcl... no install_environment.STDOUT DEBUG 2017-11-18 17:01:44,154 checking whether wchar_t is signed... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:44,247 checking whether wchar_t is signed... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:44,247 checking what type to use for unicode... no type found install_environment.STDOUT DEBUG 2017-11-18 17:01:44,327 checking whether byte ordering is bigendian... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:44,348 checking whether byte ordering is bigendian... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:44,453 checking whether right shift extends the sign bit... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:44,500 checking for getc_unlocked() and friends... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:44,555 checking for getc_unlocked() and friends... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:44,653 checking for rl_callback_handler_install in -lreadline... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:44,658 checking how to link readline libs... -lreadline tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:44,658 checking for rl_callback_handler_install in -lreadline... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:44,864 checking for rl_pre_input_hook in -lreadline... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:44,948 checking for rl_completion_display_matches_hook in -lreadline... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:44,967 checking for rl_completion_display_matches_hook in -lreadline... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,069 checking for rl_completion_matches in -lreadline... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:45,198 checking for broken nice()... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,275 checking for broken nice()... no install_environment.STDOUT DEBUG 2017-11-18 17:01:45,291 checking for struct tm.tm_zone... (cached) yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,377 checking for broken poll()... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,377 checking for struct tm.tm_zone... (cached) yes install_environment.STDOUT DEBUG 2017-11-18 17:01:45,459 checking for tv_nsec in struct stat... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,477 checking for working tzset()... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,478 checking for tv_nsec in struct stat... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,580 checking for tv_nsec2 in struct stat... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:45,601 checking curses.h usability... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:45,651 checking for curses.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,684 checking curses.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,684 checking curses.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,684 checking for curses.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:45,786 checking ncurses.h presence... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,786 checking ncurses.h usability... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,786 checking ncurses.h presence... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:45,859 checking for term.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,890 checking for ncurses.h... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,890 checking for term.h... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:45,978 checking whether WINDOW has _flags... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,990 checking whether mvwdelch is an expression... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:45,991 checking whether WINDOW has _flags... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:46,094 checking for resize_term... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,095 checking for is_term_resized... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,095 checking for resize_term... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:46,158 configure: checking for device files install_environment.STDOUT DEBUG 2017-11-18 17:01:46,159 checking for /dev/ptc... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,200 checking for resizeterm... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,200 configure: checking for device files tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,201 checking for /dev/ptmx... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,201 checking for /dev/ptc... no tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,301 checking for %lld and %llu printf() format support... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:46,352 checking for %zd printf() format support... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,403 checking for %zd printf() format support... yes install_environment.STDOUT DEBUG 2017-11-18 17:01:46,483 checking for build directories... done tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,506 checking for socklen_t... yes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,506 checking for build directories... done tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,507 checking for ensurepip... no install_environment.STDOUT DEBUG 2017-11-18 17:01:46,544 configure: creating ./config.status tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,610 configure: creating ./config.status 127.0.0.1 - - [18/Nov/2017:17:01:46 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:01:46,858 config.status: creating Modules/Setup.config tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,918 config.status: creating Makefile.pre tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,918 config.status: creating Modules/Setup.config tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:46,918 config.status: creating Misc/python.pc install_environment.STDOUT DEBUG 2017-11-18 17:01:46,940 config.status: creating Modules/ld_so_aix install_environment.STDOUT DEBUG 2017-11-18 17:01:47,013 creating Modules/Setup install_environment.STDOUT DEBUG 2017-11-18 17:01:47,019 creating Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:47,022 config.status: creating Modules/ld_so_aix tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:47,023 config.status: creating pyconfig.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:47,023 creating Modules/Setup tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:47,023 creating Modules/Setup.local tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:47,023 creating Makefile install_environment.STDOUT DEBUG 2017-11-18 17:01:47,288 -I./Include -DPy_BUILD_CORE -o Modules/python.o ./Modules/python.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:47,332 -I./Include -DPy_BUILD_CORE -o Modules/python.o ./Modules/python.c install_environment.STDOUT DEBUG 2017-11-18 17:01:47,366 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_/acceler.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:47,432 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_/acceler.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:47,533 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude gcc -c -fno-strict-aliasiCORE -o Parser/acceler.o Parsergcc -c -fno-strict-aliasing -g -O2 -DND/grammar1.o Parser/grammar1.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:47,635 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -o Parser/listnode.o Parser/listnode.c install_environment.STDOUT DEBUG 2017-11-18 17:01:47,694 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Parser-I./Include -DPy_BUILD_-I./Include -DPy_BUILD_CORE -de.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:47,737 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Parser-I./Include -DPy_BUILD_-I./Include -DPy_BUILD_CORE -de.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:47,840 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude o Parser/node.o Parser/nogcc -c -fno-strict-aliasing -g o Parser/parser.o Parser/parser.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:47,940 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_r/parsetok.c install_environment.STDOUT DEBUG 2017-11-18 17:01:48,139 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -gcc -c -fno-strict-aliasiCORE -o Parser/parsetok.o Parsegcc -c -fno-strict-aliasing -g -O2 -DND/bitset.o Parser/bitset.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:48,146 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -gcc -c -fno-strict-aliasiCORE -o Parser/parsetok.o Parsegcc -c -fno-strict-aliasing -g -O2 -DND/bitset.o Parser/bitset.c install_environment.STDOUT DEBUG 2017-11-18 17:01:48,297 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_rser/metagrammar.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:48,349 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_rser/metagrammar.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:48,452 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Parsergcc -c -fno-strict-aliasiCORE -o Parser/metagrammar.o Pagcc -c -fno-strict-aliasing -g -O2 -DND/firstsets.o Parser/firstsets.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:48,656 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_/grammar.c install_environment.STDOUT DEBUG 2017-11-18 17:01:48,767 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Parsergcc -c -fno-strict-aliasiCORE -o Parser/grammar.o Parsergcc -c -fno-strict-aliasing -g -O2 -DND/pgen.o Parser/pgen.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:48,861 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Parsergcc -c -fno-strict-aliasiCORE -o Parser/grammar.o Parsergcc -c -fno-strict-aliasing -g -O2 -DND/pgen.o Parser/pgen.c install_environment.STDOUT DEBUG 2017-11-18 17:01:49,129 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_ser/myreadline.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:49,173 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_ser/myreadline.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:49,277 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Parsergcc -c -fno-strict-aliasiCORE -o Parser/myreadline.o Pargcc -c -fno-strict-aliasing -g -O2 -DND/tokenizer.o Parser/tokenizer.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:49,899 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_cts/abstract.c 127.0.0.1 - - [18/Nov/2017:17:01:49 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:01:51,038 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Parsergcc -c -fno-strict-aliasiCORE -o Objects/abstract.o Objegcc -c -fno-strict-aliasing -g -O2 -DNDs/boolobject.o Objects/boolobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:51,123 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Parsergcc -c -fno-strict-aliasiCORE -o Objects/abstract.o Objegcc -c -fno-strict-aliasing -g -O2 -DNDs/boolobject.o Objects/boolobject.c install_environment.STDOUT DEBUG 2017-11-18 17:01:51,141 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_Objects/bufferobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:51,225 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_Objects/bufferobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:51,432 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objectgcc -c -fno-strict-aliasiCORE -o Objects/bufferobject.o gcc -c -fno-strict-aliasing -g -O2 -DNDs/bytes_methods.o Objects/bytes_methods.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:51,637 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -o Objects/bytearrayobject.o Objects/bytearrayobject.c install_environment.STDOUT DEBUG 2017-11-18 17:01:52,645 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Object-I./Include -DPy_BUILD_-I./Include -DPy_BUILD_CORE -ts/capsule.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:52,661 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Object-I./Include -DPy_BUILD_-I./Include -DPy_BUILD_CORE -ts/capsule.c install_environment.STDOUT DEBUG 2017-11-18 17:01:52,774 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -ct.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:52,867 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -ct.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:52,972 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude o Objects/capsule.o Objecgcc -c -fno-strict-aliasing -g o Objects/cellobject.o Objects/cellobjegcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -ject.o Objects/classobject.c 127.0.0.1 - - [18/Nov/2017:17:01:52 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,e85a3be143d5905b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:53,697 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_ts/cobject.c install_environment.STDOUT DEBUG 2017-11-18 17:01:53,792 fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objects/classobgcc -c -fno-strict-aliasiCORE -o Objects/cobject.o Objecgcc -c -fno-strict-aliasing -g -O2 -DNDs/codeobject.o Objects/codeobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:53,797 fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objects/classobgcc -c -fno-strict-aliasiCORE -o Objects/cobject.o Objecgcc -c -fno-strict-aliasing -g -O2 -DNDs/codeobject.o Objects/codeobject.c install_environment.STDOUT DEBUG 2017-11-18 17:01:54,023 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_ Objects/complexobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:54,101 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_ Objects/complexobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:54,510 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objectgcc -c -fno-strict-aliasiCORE -o Objects/complexobject.ogcc -c -fno-strict-aliasing -g -O2 -DNDs/descrobject.o Objects/descrobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:54,716 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_jects/enumobject.c install_environment.STDOUT DEBUG 2017-11-18 17:01:54,827 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objectgcc -c -fno-strict-aliasiCORE -o Objects/enumobject.o Obgcc -c -fno-strict-aliasing -g -O2 -DNDs/exceptions.o Objects/exceptions.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:54,922 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objectgcc -c -fno-strict-aliasiCORE -o Objects/enumobject.o Obgcc -c -fno-strict-aliasing -g -O2 -DNDs/exceptions.o Objects/exceptions.c 127.0.0.1 - - [18/Nov/2017:17:01:55 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/datasets/error?dataset_id=a799d38679e985db&__identifer=9nms4ovms1v" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:01:55 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:01:55 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:01:55,444 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_ects/genobject.c 127.0.0.1 - - [18/Nov/2017:17:01:55 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:55,545 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_ects/genobject.c 127.0.0.1 - - [18/Nov/2017:17:01:55 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:55,752 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objectgcc -c -fno-strict-aliasiCORE -o Objects/genobject.o Objgcc -c -fno-strict-aliasing -g -O2 -DNDs/fileobject.o Objects/fileobject.c install_environment.STDOUT DEBUG 2017-11-18 17:01:56,086 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Object-I./Include -DPy_BUILD_ct.o Objects/floatobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:56,161 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Object-I./Include -DPy_BUILD_ct.o Objects/floatobject.c install_environment.STDOUT DEBUG 2017-11-18 17:01:56,633 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -ject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:56,677 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -ject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:56,990 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -o Objects/floatobjegcc -c -fno-strict-aliasing -g o Objects/frameobject.o Objects/frameobgcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -ect.o Objects/funcobject.c install_environment.STDOUT DEBUG 2017-11-18 17:01:57,093 fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objects/funcobj-I./Include -DPy_BUILD_.o Objects/intobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:57,193 fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objects/funcobj-I./Include -DPy_BUILD_.o Objects/intobject.c 127.0.0.1 - - [18/Nov/2017:17:01:57 -0400] "GET /admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04 HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:01:57,527 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -ct.c 127.0.0.1 - - [18/Nov/2017:17:01:57 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:57,603 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -ct.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:57,707 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -o Objects/intobjectgcc -c -fno-strict-aliasing -g o Objects/iterobject.o Objects/iterobjegcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -ect.o Objects/listobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:01:58,528 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_jects/longobject.c install_environment.STDOUT DEBUG 2017-11-18 17:02:00,173 fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objects/listobjgcc -c -fno-strict-aliasiCORE -o Objects/longobject.o Obgcc -c -fno-strict-aliasing -g -O2 -DNDs/dictobject.o Objects/dictobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:00,267 fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objects/listobjgcc -c -fno-strict-aliasiCORE -o Objects/longobject.o Obgcc -c -fno-strict-aliasing -g -O2 -DNDs/dictobject.o Objects/dictobject.c 127.0.0.1 - - [18/Nov/2017:17:02:00 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:00,786 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objectgcc -c -fno-strict-aliasiCORE -o Objects/memoryobject.o Objects/memoryobject.c install_environment.STDOUT DEBUG 2017-11-18 17:02:00,933 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_-I./Include -DPy_BUILD_ect.o Objects/methodobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:00,992 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_-I./Include -DPy_BUILD_ect.o Objects/methodobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:01,094 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -o Objects/methodobjgcc -c -fno-strict-aliasing -g o Objects/moduleobject.o Objects/moduleobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:01,197 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -o Objects/object.o Objects/object.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:01,608 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude o Objects/obmalloc.o Objects/obmalloc.c install_environment.STDOUT DEBUG 2017-11-18 17:02:01,647 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE --I./Include -DPy_BUILD_-I./Include -DPy_BUILD_CORE --I./Include -DPy_BUILD_CORE -o Objectangeobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:01,712 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE --I./Include -DPy_BUILD_-I./Include -DPy_BUILD_CORE --I./Include -DPy_BUILD_CORE -o Objectangeobject.c install_environment.STDOUT DEBUG 2017-11-18 17:02:01,757 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:01,815 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:02,325 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude s/rangeobject.o Objects/rgcc -c -fno-strict-aliasing -g o Objects/setobject.o Objects/setobjectgcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -ject.o Objects/sliceobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:02,430 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_Objects/stringobject.c 127.0.0.1 - - [18/Nov/2017:17:02:03 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:02:04,086 fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objects/sliceobgcc -c -fno-strict-aliasiCORE -o Objects/stringobject.o gcc -c -fno-strict-aliasing -g -O2 -DNDs/structseq.o Objects/structseq.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:04,176 fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objects/sliceobgcc -c -fno-strict-aliasiCORE -o Objects/stringobject.o gcc -c -fno-strict-aliasing -g -O2 -DNDs/structseq.o Objects/structseq.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:04,380 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Objectgcc -c -fno-strict-aliasiCORE -o Objects/tupleobject.o Objects/tupleobject.c install_environment.STDOUT DEBUG 2017-11-18 17:02:04,571 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_gcc -c -fno-strict-aliasiCORE -o Objects/typeobject.o Objects/typeobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:04,588 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_gcc -c -fno-strict-aliasiCORE -o Objects/typeobject.o Objects/typeobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:06,334 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_-I./Include -DPy_BUILD_ject.o Objects/weakrefobject.c 127.0.0.1 - - [18/Nov/2017:17:02:06 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:02:06,656 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -o Objects/weakrefobgcc -c -fno-strict-aliasing -g o Objects/unicodeobject.o Objects/unicodeobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:06,747 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -o Objects/weakrefobgcc -c -fno-strict-aliasing -g o Objects/unicodeobject.o Objects/unicodeobject.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:06,852 Objects/unicodeobject.c:3453:31: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:06,852 if (*p > unimax || *p < 0) { tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:06,852 ~~ ^ ~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:08,812 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:02:08,813 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_Objects/unicodectype.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:08,912 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_Objects/unicodectype.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:09,115 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -gcc -c -fno-strict-aliasiCORE -o Objects/unicodectype.o gcc -c -fno-strict-aliasing -g -O2 -DND/_warnings.o Python/_warnings.c install_environment.STDOUT DEBUG 2017-11-18 17:02:09,215 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasiCORE -o Python/Python-ast.o Python/Python-ast.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:09,215 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasiCORE -o Python/Python-ast.o Python/Python-ast.c 127.0.0.1 - - [18/Nov/2017:17:02:09 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:10,957 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_gcc -c -fno-strict-aliasiCORE -o Python/asdl.o Python/asdl.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:11,062 /Library/Developer/CommandLineTools/usr/bin/make Parser/pgen tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:11,063 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_hon/mysnprintf.c install_environment.STDOUT DEBUG 2017-11-18 17:02:11,123 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_gcc -c -fno-strict-aliasiCORE -o Python/mysnprintf.o Pytgcc -c -fno-strict-aliasing -g -O2 -DND/pyctype.o Python/pyctype.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:11,168 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_gcc -c -fno-strict-aliasiCORE -o Python/mysnprintf.o Pytgcc -c -fno-strict-aliasing -g -O2 -DND/pyctype.o Python/pyctype.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:11,271 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasiCORE -o Parser/tokenizer_pgen.o Parser/tokenizer_pgen.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:11,480 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -o Parser/printgrammar.o Parser/printgrammar.c install_environment.STDOUT DEBUG 2017-11-18 17:02:11,570 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_-I./Include -DPy_BUILD_-I./Include -DPy_BUILD_CORE -r/pgenmain.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:11,585 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_-I./Include -DPy_BUILD_-I./Include -DPy_BUILD_CORE -r/pgenmain.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:11,687 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude o Parser/pgenmain.o Parsegcc -DNDEBUG -g -fwrapv -O3 -Warser.o Parser/parsetok.o Parser/bitset.rser/firstsets.o Parser/grammar.o Parser/pgen.o rintf.o Python/pyctype.o Parser/tokenizer_pgen.o Parser/prinmework CoreFoundation -o Parser/pgen tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:11,788 Python/graminit.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:11,788 Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Python/ast.o Python/ast.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:12,613 rototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Python/bltinmodule.o Python/bltinmodule.c 127.0.0.1 - - [18/Nov/2017:17:02:12 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:13,133 clude -I./Include -DPy_BUILD_CORE -o Python/ceval.o Python/ceval.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:14,874 _BUILD_CORE -o Python/compile.o Python/compile.c 127.0.0.1 - - [18/Nov/2017:17:02:15 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:16,208 o Python/codecs.c install_environment.STDOUT DEBUG 2017-11-18 17:02:16,387 ll -Wstrict-prototypes Parser/acceler.o Parser/grammar1.o Parser/listnode.o Parser/node.o Parser/pao Parser/metagrammar.o PaObjects/obmalloc.o Python/mysnptgrammar.o Parser/pgenmain.o -ldl -fraParser/pgen ./Grammar/Grammar Include/graminit.hgcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-pgcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IIngcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPygcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Python/codecs.gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Python/errors.o Python/errors.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:16,410 ll -Wstrict-prototypes Parser/acceler.o Parser/grammar1.o Parser/listnode.o Parser/node.o Parser/pao Parser/metagrammar.o PaObjects/obmalloc.o Python/mysnptgrammar.o Parser/pgenmain.o -ldl -fraParser/pgen ./Grammar/Grammar Include/graminit.hgcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-pgcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IIngcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPygcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Python/codecs.gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Python/errors.o Python/errors.c install_environment.STDOUT DEBUG 2017-11-18 17:02:16,583 -I./Include -DPy_BUILD_CORE -o Python/frozen.o Python/frozen.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:16,616 -I./Include -DPy_BUILD_CORE -o Python/frozen.o Python/frozen.c install_environment.STDOUT DEBUG 2017-11-18 17:02:16,658 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_hon/frozenmain.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:16,720 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_hon/frozenmain.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:16,825 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude gcc -c -fno-strict-aliasiCORE -o Python/frozenmain.o Pytgcc -c -fno-strict-aliasing -g -O2 -DND/future.o Python/future.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:16,929 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_/getargs.c install_environment.STDOUT DEBUG 2017-11-18 17:02:17,445 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasiCORE -o Python/getargs.o Pythongcc -c -fno-strict-aliasing -g -O2 -DND/getcompiler.o Python/getcompiler.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:17,545 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasiCORE -o Python/getargs.o Pythongcc -c -fno-strict-aliasing -g -O2 -DND/getcompiler.o Python/getcompiler.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:17,545 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasiCORE -o Python/getcopyright.o Python/getcopyright.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:17,649 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -DPLATFORM='"darwin"hon/getplatform.c install_environment.STDOUT DEBUG 2017-11-18 17:02:17,678 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_-I./Include -DPy_BUILD_' -o Python/getplatform.o ./Pytgcc -c -fno-strict-aliasing -g -O2 -DND/getversion.o Python/getversion.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:17,753 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_-I./Include -DPy_BUILD_' -o Python/getplatform.o ./Pytgcc -c -fno-strict-aliasing -g -O2 -DND/getversion.o Python/getversion.c install_environment.STDOUT DEBUG 2017-11-18 17:02:17,756 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Python/graminit.o Python/graminit.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:17,857 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Python/graminit.o Python/graminit.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:17,857 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasigcc -c -fno-strict-aliasing -g o Python/import.o Python/import.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:18,381 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_/Python/importdl.c install_environment.STDOUT DEBUG 2017-11-18 17:02:18,424 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -gcc -c -fno-strict-aliasiCORE -I. -o Python/importdl.o .gcc -c -fno-strict-aliasing -g -O2 -DND/marshal.o Python/marshal.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:18,482 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -gcc -c -fno-strict-aliasiCORE -I. -o Python/importdl.o .gcc -c -fno-strict-aliasing -g -O2 -DND/marshal.o Python/marshal.c 127.0.0.1 - - [18/Nov/2017:17:02:18 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:02:18,864 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_hon/modsupport.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:18,892 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_hon/modsupport.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:19,096 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasiCORE -o Python/modsupport.o Pytgcc -c -fno-strict-aliasing -g -O2 -DND/mystrtoul.o Python/mystrtoul.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:19,199 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_n/peephole.c install_environment.STDOUT DEBUG 2017-11-18 17:02:19,382 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasiCORE -o Python/peephole.o Pythogcc -c -fno-strict-aliasing -g -O2 -DND/pyarena.o Python/pyarena.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:19,402 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasiCORE -o Python/peephole.o Pythogcc -c -fno-strict-aliasing -g -O2 -DND/pyarena.o Python/pyarena.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:19,503 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasiCORE -o Python/pyfpe.o Python/pyfpe.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:19,503 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -o Python/pymath.o Python/pymath.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:19,605 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude o Python/pystate.o Python/pystate.c install_environment.STDOUT DEBUG 2017-11-18 17:02:19,718 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_-I./Include -DPy_BUILD_-I./Include -DPy_BUILD_CORE --I./Include -DPy_BUILD_CORE -o Pythonnrun.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:19,808 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_-I./Include -DPy_BUILD_-I./Include -DPy_BUILD_CORE --I./Include -DPy_BUILD_CORE -o Pythonnrun.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:20,119 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude /pythonrun.o Python/pythogcc -c -fno-strict-aliasing -g o Python/random.o Python/random.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:20,220 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_ython/structmember.c install_environment.STDOUT DEBUG 2017-11-18 17:02:20,280 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -gcc -c -fno-strict-aliasiCORE -o Python/structmember.o Pgcc -c -fno-strict-aliasing -g -O2 -DND/symtable.o Python/symtable.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:20,322 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -gcc -c -fno-strict-aliasiCORE -o Python/structmember.o Pgcc -c -fno-strict-aliasing -g -O2 -DND/symtable.o Python/symtable.c install_environment.STDOUT DEBUG 2017-11-18 17:02:20,722 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_on/sysmodule.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:20,729 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_on/sysmodule.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:21,031 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasiCORE -o Python/sysmodule.o Pythgcc -c -fno-strict-aliasing -g -O2 -DND/traceback.o Python/traceback.c install_environment.STDOUT DEBUG 2017-11-18 17:02:21,102 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasiCORE -o Python/getopt.o Python/getopt.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:21,132 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasiCORE -o Python/getopt.o Python/getopt.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:21,236 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_gcc -c -fno-strict-aliasiCORE -o Python/pystrcmp.o Python/pystrcmp.c install_environment.STDOUT DEBUG 2017-11-18 17:02:21,238 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_-I./Include -DPy_BUILD_ Python/pystrtod.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:21,338 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_-I./Include -DPy_BUILD_ Python/pystrtod.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:21,440 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -o Python/pystrtod.ogcc -c -fno-strict-aliasing -g o Python/dtoa.o Python/dtoa.c 127.0.0.1 - - [18/Nov/2017:17:02:21 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:22,265 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -o Python/formatter_ode.c install_environment.STDOUT DEBUG 2017-11-18 17:02:22,371 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE --I./Include -DPy_BUILD_unicode.o Python/formatter_unicgcc -c -fno-strict-aliasing -g -O2 -DND/formatter_string.o Python/formatter_string.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:22,471 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE --I./Include -DPy_BUILD_unicode.o Python/formatter_unicgcc -c -fno-strict-aliasing -g -O2 -DND/formatter_string.o Python/formatter_string.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:22,680 EBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -o Pythongcc -c -fno-strict-aliasiCORE -o Python/dynload_shlib.o Python/dynload_shlib.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:22,782 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -o Python/mactoolboxglue.o Python/mactoolboxglue.c install_environment.STDOUT DEBUG 2017-11-18 17:02:23,269 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_-I./Include -DPy_BUILD_-I./Include -DPy_BUILD_CORE -thread.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:23,295 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_-I./Include -DPy_BUILD_-I./Include -DPy_BUILD_CORE -thread.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:23,496 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude o Python/thread.o Python/gcc -c -fno-strict-aliasing -g o Modules/config.o Modules/config.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:23,496 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude CORE -DPYTHONPATH='":plat-darwin:plat-mac:plat-mac/lib-scriptpackages:lib-tk:lib-old"' \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:23,496 -DPREFIX='"/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac"' \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:23,496 -DEXEC_PREFIX='"/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac"' \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:23,496 -DVERSION='"2.7"' \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:23,496 -DVPATH='""' \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:23,497 -o Modules/getpath.o ./Modules/getpath.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:23,602 ./Modules/getpath.c:353:8: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:23,602 if (n >= 0) { tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:23,602 ~ ^ ~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:23,807 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude o Modules/main.o Modules/main.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:23,808 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:02:23,900 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE --I./Include -DPy_BUILD_-I./Include -DPy_BUILD_CORE --I./Include -DPy_BUILD_CORE -o Moduledule.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:23,916 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE --I./Include -DPy_BUILD_-I./Include -DPy_BUILD_CORE --I./Include -DPy_BUILD_CORE -o Moduledule.c install_environment.STDOUT DEBUG 2017-11-18 17:02:24,152 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -c eadmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,224 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -c eadmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,329 gcc -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude s/gcmodule.o Modules/gcmogcc -fno-strict-aliasing -g -O2./Modules/threadmodule.c -o Modules/thrgcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrodule.c -o Modules/signalmodule.o install_environment.STDOUT DEBUG 2017-11-18 17:02:24,506 apv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -c ./Modules/signalm/Include -DPy_BUILD_CORle.c -o Modules/posixmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,532 apv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -c ./Modules/signalm/Include -DPy_BUILD_CORle.c -o Modules/posixmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,638 ./Modules/posixmodule.c:358:13: warning: comparison of constant 9223372036854775807 with expression of type 'uid_t' (aka 'unsigned int') is always true [-Wtautological-constant-out-of-range-compare] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,638 if (uid <= LONG_MAX) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,638 ~~~ ^ ~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,638 ./Modules/posixmodule.c:366:13: warning: comparison of constant 9223372036854775807 with expression of type 'gid_t' (aka 'unsigned int') is always true [-Wtautological-constant-out-of-range-compare] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,638 if (gid <= LONG_MAX) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,638 ~~~ ^ ~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,638 ./Modules/posixmodule.c:7578:12: warning: 'tempnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tempnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,638 name = tempnam(dir, pfx); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,638 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,639 /usr/include/stdio.h:391:7: note: 'tempnam' has been explicitly marked deprecated here tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,639 char *tempnam(const char *, const char *) __DARWIN_ALIAS(tempnam); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,639 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,639 ./Modules/posixmodule.c:7633:12: warning: 'tmpnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,639 name = tmpnam(buffer); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,639 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,639 /usr/include/stdio.h:276:7: note: 'tmpnam' has been explicitly marked deprecated here tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,639 char *tmpnam(char *); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:24,639 ^ 127.0.0.1 - - [18/Nov/2017:17:02:24 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:02:25,078 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -c omodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:25,159 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -c omodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:25,159 4 warnings generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:25,468 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I.E -c ./Modules/posixmodugcc -fno-strict-aliasing -g -O2./Modules/errnomodule.c -o Modules/errngcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrle.c -o Modules/pwdmodule.o install_environment.STDOUT DEBUG 2017-11-18 17:02:25,548 apv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -c ./Modules/pwdmodugcc -fno-strict-aliasing E -c ./Modules/_sre.c -o Modules/_sre.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:25,569 apv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -c ./Modules/pwdmodugcc -fno-strict-aliasing E -c ./Modules/_sre.c -o Modules/_sre.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:25,569 ./Modules/pwdmodule.c:115:17: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:25,569 if (uid < 0) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:25,569 ~~~ ^ ~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:25,570 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:26,606 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORgcc -fno-strict-aliasing E -c ./Modules/_codecsmodule.c.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:26,811 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -c f.o install_environment.STDOUT DEBUG 2017-11-18 17:02:26,893 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_COR -o Modules/_codecsmodulegcc -fno-strict-aliasing -g -O2./Modules/_weakref.c -o Modules/_weakregcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrrt.c -o Modules/zipimport.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:26,916 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_COR -o Modules/_codecsmodulegcc -fno-strict-aliasing -g -O2./Modules/_weakref.c -o Modules/_weakregcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrrt.c -o Modules/zipimport.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,121 apv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -c ./Modules/zipimpogcc -fno-strict-aliasing E -c ./Modules/symtablemodule.le.o install_environment.STDOUT DEBUG 2017-11-18 17:02:27,208 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORc -o Modules/symtablemodugcc -fno-strict-aliasing -g -O2./Modules/xxsubtype.c -o Modules/xxsubtype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,225 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORc -o Modules/symtablemodugcc -fno-strict-aliasing -g -O2./Modules/xxsubtype.c -o Modules/xxsubtype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,329 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -c gcc -c -fno-strict-aliasiCORE \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,329 -DSVNVERSION="\"`LC_ALL=C svnversion .`\"" \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,329 -DHGVERSION="\"`LC_ALL=C hg id -i .`\"" \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,329 -DHGTAG="\"`LC_ALL=C hg id -t .`\"" \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,329 -DHGBRANCH="\"`LC_ALL=C hg id -b .`\"" \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,329 -o Modules/getbuildinfo.o ./Modules/getbuildinfo.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,534 abort: repository . not found! tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,640 abort: repository . not found! tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,741 rm -f libpython2.7.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,742 les/getbuildinfo.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,742 eler.o Parser/grammar1.o Parser/listnode.o Parser/node.o Parser/parser.o Parser/parsetok.o Parser/bireadline.o Parser/tokenizer.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,742 abort: repository . not found! install_environment.STDOUT DEBUG 2017-11-18 17:02:27,756 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_ar rc libpython2.7.a Moduar rc libpython2.7.a Parser/acctset.o Parser/metagrammar.o Parser/firstsets.o Parser/grammar.o Parser/pgen.o Parser/mythods.o Objects/bytearrayobject.o Objects/capsule.o Objects/sobject.o Objects/cobject.o Objects/codeobject.o Objects/complexobject.o Obmobject.o Objects/exceptions.o Objects/genobject.o Objects/fileobject.o Objects/floatobject.o t.o Objects/intobject.o Objects/iterobject.o Objects/listobject.o Objects/longobject.o Objects/dictobject.o Objects/meleobject.o Objects/object.o Objects/obmalloc.o Objects/rangeobject.o Objects/setobject.o Objects/sliceobject.o Objects/stringobject.o Objects/strucakrefobject.o Objects/unicodeobject.o Objects/unicodectype.o install_environment.STDOUT DEBUG 2017-11-18 17:02:27,814 ython/ast.o Python/bltinmodule.o Python/ceval.o Python/compile.o Python/codecs.o Python/errors.o Pytgetcopyright.o Python/getatter_unicode.o Python/formatter_string.o Python/dynload_shlib.o Python/mactoolboxglue.o Python/thread.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,842 ng -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_ar rc libpython2.7.a Moduar rc libpython2.7.a Parser/acctset.o Parser/metagrammar.o Parser/firstsets.o Parser/grammar.o Parser/pgen.o Parser/mythods.o Objects/bytearrayobject.o Objects/capsule.o Objects/sobject.o Objects/cobject.o Objects/codeobject.o Objects/complexobject.o Obmobject.o Objects/exceptions.o Objects/genobject.o Objects/fileobject.o Objects/floatobject.o t.o Objects/intobject.o Objects/iterobject.o Objects/listobject.o Objects/longobject.o Objects/dictobject.o Objects/meleobject.o Objects/object.o Objects/obmalloc.o Objects/rangeobject.o Objects/setobject.o Objects/sliceobject.o Objects/stringobject.o Objects/strucakrefobject.o Objects/unicodeobject.o Objects/unicodectype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,843 ython/ast.o Python/bltinmodule.o Python/ceval.o Python/compile.o Python/codecs.o Python/errors.o Pytgetcopyright.o Python/getatter_unicode.o Python/formatter_string.o Python/dynload_shlib.o Python/mactoolboxglue.o Python/thread.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,943 ar rc libpython2.7.a Objects/abstract.o Objects/boolobject.o Objects/bufferobject.o Objects/bytes_mecellobject.o Objects/clasjects/descrobject.o Objects/enuObjects/frameobject.o Objects/funcobjecmoryobject.o Objects/methodobject.o Objects/modutseq.o Objects/tupleobject.o Objects/typeobject.o Objects/wear rc libpython2.7.a Python/_warnings.o Python/Python-ast.o Python/asdl.o Phon/frozen.o Python/frozenmain.o Python/future.o Python/getargs.o Python/getcompiler.o Python/platform.o Python/getversion.o Python/graminit.o Python/import.o Python/importdl.o Python/marshal.o Python/modsupport.o Python/mystrtoul.o Python/mysnprintf.o Python/peephole.o Python/pyarena.o Python/pyctype.o Python/pyfpe.o Python/pymath.o Python/pystate.o Python/pythonrun.o Python/random.o Python/structmember.o Python/symtable.o Python/sysmodule.o Python/traceback.o Python/getopt.o Python/pystrcmp.o Python/pystrtod.o Python/dtoa.o Python/formar rc libpython2.7.a Modules/config.o Modules/getpath.o Modules/main.o Modules/gcmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,944 /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libpython2.7.a(pymath.o) has no symbols tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:27,944 /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libpython2.7.a(pymath.o) has no symbols 127.0.0.1 - - [18/Nov/2017:17:02:27 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:02:27,986 ar rc libpython2.7.a Modules/threadmodule.o Modules/signalmodule.o Modules/posixmodule.o Modules/ules/zipimport.o Moduless/xxsubtype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,048 ar rc libpython2.7.a Modules/threadmodule.o Modules/signalmodule.o Modules/posixmodule.o Modules/ules/zipimport.o Moduless/xxsubtype.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,051 /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libpython2.7.a(pymath.o) has no symbols install_environment.STDOUT DEBUG 2017-11-18 17:02:28,123 gcc -dynamiclib -Wl,-single_module -undefined dynamic_lookup -Wl,-install_name,/galaxydir/galaxy/datibility_version,2.7 -Wl,ibpython2.7.dylib Modules/getbuer/grammar1.o Parser/listnode.o Parser/o Parser/bitset.o Parser/metagrammar.o Parser/fimyreadline.o Parser/tokenizer.o Objects/abstract.o Objects/bbjects/bytearrayobject.o Objects/capsule.o Objects/cellobject.o Objects/clabjects/descrobject.o Objects/enumobject.o Objects/exceptions.o Objects/genobject.o Objects/fil Objects/iterobject.o Objects/listobject.o Objects/longobject.o Objects/dictobject.o Objects/memoryobject.o Objects/mects/sliceobject.o Objects/stringobject.o Objects/structseq.o Objects/tupleobject.o Objects/typeobject.o Objects/weakrefobject.o Objects/unicodeobjePython/codecs.o Python/errors.o Python/frozen.o Python/frozenmain.o Python/future.o Python/getargs.o Python/getcompiler.o Python/getcopyright.o Python/getplatform.o Python/getversion.ohon/pyfpe.o Python/pymath.o Python/pystate.o Python/pythonrun.o Python/random.o Python/structmember.o Python/symtable.o Python/sysmodule.o Python/traceback.o Python/getopt.o Python/pystrcmp.o Python/pystrtod.o Python/dtoa.o Pythonodules/posixmodule.o Modules/errnomodule.o Modules/pwdmodule.o Modules/_sre.o Modules/_codecsmodule.o Modules/_weakref.o Modules/zipimport.o Modules/symtablemodule.o Modules/xxsubtype.o -ldl -framework CoreFoundation ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,157 errnomodule.o Modules/pwdmodule.o Modules/_sre.o Modules/_codecsmodule.o Modules/_weakref.o Mod/symtablemodule.o Moduleranlib libpython2.7.a tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,157 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/libpython2.7.dylib -Wl,-compa-current_version,2.7 -o lildinfo.o Parser/acceler.o Parsnode.o Parser/parser.o Parser/parsetok.rstsets.o Parser/grammar.o Parser/pgen.o Parser/oolobject.o Objects/bufferobject.o Objects/bytes_methods.o Ossobject.o Objects/cobject.o Objects/codeobject.o Objects/complexobject.o Oeobject.o Objects/floatobject.o Objects/frameobject.o Objects/funcobject.o Objects/intobject.othodobject.o Objects/moduleobject.o Objects/object.o Objects/obmalloc.o Objects/rangeobject.o Objects/setobject.o Object.o Objects/unicodectype.o Python/_warnings.o Python/Python-ast.o Python/asdl.o Python/ast.o Python/bltinmodule.o Python/ceval.o Python/compile.o Python/graminit.o Python/import.o Python/importdl.o Python/marshal.o Python/modsupport.o Python/mystrtoul.o Python/mysnprintf.o Python/peephole.o Python/pyarena.o Python/pyctype.o Pyt/formatter_unicode.o Python/formatter_string.o Python/dynload_shlib.o Python/mactoolboxglue.o Python/thread.o Modules/config.o Modules/getpath.o Modules/main.o Modules/gcmodule.o Modules/threadmodule.o Modules/signalmodule.o M tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,157 gcc -dynamiclib -Wl,-single_module -undefined dynamic_lookup -Wl,-install_name,/galaxydir/galaxy/datibility_version,2.7 -Wl,ibpython2.7.dylib Modules/getbuer/grammar1.o Parser/listnode.o Parser/o Parser/bitset.o Parser/metagrammar.o Parser/fimyreadline.o Parser/tokenizer.o Objects/abstract.o Objects/bbjects/bytearrayobject.o Objects/capsule.o Objects/cellobject.o Objects/clabjects/descrobject.o Objects/enumobject.o Objects/exceptions.o Objects/genobject.o Objects/fil Objects/iterobject.o Objects/listobject.o Objects/longobject.o Objects/dictobject.o Objects/memoryobject.o Objects/mects/sliceobject.o Objects/stringobject.o Objects/structseq.o Objects/tupleobject.o Objects/typeobject.o Objects/weakrefobject.o Objects/unicodeobjePython/codecs.o Python/errors.o Python/frozen.o Python/frozenmain.o Python/future.o Python/getargs.o Python/getcompiler.o Python/getcopyright.o Python/getplatform.o Python/getversion.ohon/pyfpe.o Python/pymath.o Python/pystate.o Python/pythonrun.o Python/random.o Python/structmember.o Python/symtable.o Python/sysmodule.o Python/traceback.o Python/getopt.o Python/pystrcmp.o Python/pystrtod.o Python/dtoa.o Pythonodules/posixmodule.o Modules/errnomodule.o Modules/pwdmodule.o Modules/_sre.o Modules/_codecsmodule.o Modules/_weakref.o Modules/zipimport.o Modules/symtablemodule.o Modules/xxsubtype.o -ldl -framework CoreFoundation ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,159 /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libpython2.7.a(pymath.o) has no symbols install_environment.STDOUT DEBUG 2017-11-18 17:02:28,219 Modules/python.o \ install_environment.STDOUT DEBUG 2017-11-18 17:02:28,255 E -S -m sysconfig --generate-posix-vars ;\ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,263 gcc -u _PyMac_Error -o python.exe \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,263 -L. -lpython2.7 -ldl -framework CoreFoundation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,264 Modules/python.o \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,264 DYLD_LIBRARY_PATH=/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 ./python.exe - if test $? -ne 0 ; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,264 echo "generate-posix-vars failed" ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,264 rm -f ./pybuilddir.txt ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,264 exit 1 ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,264 fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,264 E -S -m sysconfig --generate-posix-vars ;\ install_environment.STDOUT DEBUG 2017-11-18 17:02:28,569 running build_ext tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,571 running build tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,572 running build_ext install_environment.STDOUT DEBUG 2017-11-18 17:02:28,689 building '_struct' extension install_environment.STDOUT DEBUG 2017-11-18 17:02:28,689 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy install_environment.STDOUT DEBUG 2017-11-18 17:02:28,690 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,775 building dbm using ndbm tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,775 building '_struct' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,775 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,775 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,775 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,775 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,775 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,775 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,776 on-2.7.10/Modules tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:28,776 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/_struct.olshed-mtdP5qHBA/Python-2.7.10/Modules/_struct.o install_environment.STDOUT DEBUG 2017-11-18 17:02:29,062 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tc -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-togcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databosx-10.4-x86_64-2.7/_struct.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:29,078 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tc -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-togcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databosx-10.4-x86_64-2.7/_struct.so install_environment.STDOUT DEBUG 2017-11-18 17:02:29,106 xtension install_environment.STDOUT DEBUG 2017-11-18 17:02:29,106 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:29,179 xtension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:29,180 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:29,180 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_struct.o -L/usr/local/lib -L. -o build/lib.macbuilding '_ctypes_test' ecreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Modules/_ctypes/_ctypes_test.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/gal.7.10/Modules/_ctypes/_ctypes_test.o install_environment.STDOUT DEBUG 2017-11-18 17:02:29,314 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Paxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4es_test.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_ctypes_building 'array' extension install_environment.STDOUT DEBUG 2017-11-18 17:02:29,314 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/arraymodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/arraymodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:29,381 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/_ctyptest.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:29,381 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Paxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4es_test.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_ctypes_building 'array' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:29,382 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/arraymodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/arraymodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:29,790 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxgcc -bundle -undefined dyPython-2.7.10/Modules/arraymodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/array.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:29,790 building 'cmath' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:29,790 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/cmathmodp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cmathmodule.o install_environment.STDOUT DEBUG 2017-11-18 17:02:30,121 namic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/gcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmgcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydirsr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/datdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_math.c -o build/temp.macosx-10.4-x86_64-2.7/gp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_math.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,200 namic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/gcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmgcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydirsr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/datdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_math.c -o build/temp.macosx-10.4-x86_64-2.7/gp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_math.o install_environment.STDOUT DEBUG 2017-11-18 17:02:30,268 uild/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/_64-2.7/galaxydir/galaxy/ath.o -L/usr/local/lib -L. -o bbuilding 'math' extension install_environment.STDOUT DEBUG 2017-11-18 17:02:30,268 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/localaxy/database/tmp/tmp-toInclude -I/galaxydir/galaxy/dat-2.7.10 -c /galaxydir/galaxy/database/tmathmodule.c -o build/temp.macosx-10.4-x86_64-2.n-2.7.10/Modules/mathmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,304 /galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/uabase/tmp/tmp-toolshed-mtalaxydir/galaxy/database/tmp/tmgcc -bundle -undefined dynamic_lookup bModules/cmathmodule.o build/temp.macosx-10.4-x86database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_muild/lib.macosx-10.4-x86_64-2.7/cmath.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,304 uild/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/_64-2.7/galaxydir/galaxy/ath.o -L/usr/local/lib -L. -o bbuilding 'math' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,304 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/localaxy/database/tmp/tmp-toInclude -I/galaxydir/galaxy/dat-2.7.10 -c /galaxydir/galaxy/database/tmathmodule.c -o build/temp.macosx-10.4-x86_64-2.n-2.7.10/Modules/mathmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,304 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_math.c:25:21: warning: unused variable 'zero' [-Wunused-const-variable] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,305 static const double zero = 0.0; tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,305 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,305 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,615 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythogcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-protde -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pylaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5q.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_math.o install_environment.STDOUT DEBUG 2017-11-18 17:02:30,688 otypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IIncluthon-2.7.10/Include -I/gaHBA/Python-2.7.10/Modules/_mathgcc -bundle -undefined dynamic_lookup bModules/mathmodule.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_math.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/math.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,716 otypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IIncluthon-2.7.10/Include -I/gaHBA/Python-2.7.10/Modules/_mathgcc -bundle -undefined dynamic_lookup bModules/mathmodule.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_math.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/math.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,717 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_math.c:25:21: warning: unused variable 'zero' [-Wunused-const-variable] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,717 static const double zero = 0.0; tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,717 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,717 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:02:30,720 n install_environment.STDOUT DEBUG 2017-11-18 17:02:30,720 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/stropmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/stropmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,823 n tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:30,823 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/stropmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/stropmodule.o 127.0.0.1 - - [18/Nov/2017:17:02:30 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:31,131 uild/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/building 'strop' extensiogcc -fno-strict-aliasing -g -O2gcc -bundle -undefined dynamic_lookup bModules/stropmodule.o -L/usr/local/lib -L. -o bu4-2.7/strop.so install_environment.STDOUT DEBUG 2017-11-18 17:02:31,157 uild/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/ild/lib.macosx-10.4-x86_6building 'time' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:31,235 uild/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/ild/lib.macosx-10.4-x86_6building 'time' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:31,236 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxed-mtdP5qHBA/Python-2.7.10/Modules/timemodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/timemodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:31,336 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmb -L. -o build/lib.macosx-10.4-x86_64-2.7/time.so install_environment.STDOUT DEBUG 2017-11-18 17:02:31,351 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/timemodule.o -L/usr/local/ligcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydirsr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/datdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/datetimemodule.c -o build/temp.macosx-10.4-x86se/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/datetimemodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:31,441 building 'datetime' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:31,441 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/timemodule.o -L/usr/local/ligcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydirsr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/datdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/datetimemodule.c -o build/temp.macosx-10.4-x86se/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/datetimemodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:32,160 /galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/uabase/tmp/tmp-toolshed-mt_64-2.7/galaxydir/galaxy/databagcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Modules/timemodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databales/timemodule.o install_environment.STDOUT DEBUG 2017-11-18 17:02:32,300 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Pse/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modugcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4e.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/timemodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/datetime.so install_environment.STDOUT DEBUG 2017-11-18 17:02:32,338 nsion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:32,368 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Pse/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modugcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4e.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/timemodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/datetime.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:32,369 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/datetimemodulbuilding 'itertools' extegcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/itertoolsmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/itertoolsmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:32,369 nsion install_environment.STDOUT DEBUG 2017-11-18 17:02:33,036 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/itertoolsmodule.o -L/usr/local/lib -L. -o build/lib.mgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tuiltins.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmns.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:33,089 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmacosx-10.4-x86_64-2.7/itertools.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:33,089 building 'future_builtins' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:33,089 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/itertoolsmodule.o -L/usr/local/lib -L. -o build/lib.mgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tuiltins.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmns.o install_environment.STDOUT DEBUG 2017-11-18 17:02:33,160 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/future_builtins.o -L/usr/locgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-todule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:33,190 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/future_bp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/future_builtigcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/future_builtins.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:33,191 building '_random' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:33,191 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/future_builtins.o -L/usr/locgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-todule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/ install_environment.STDOUT DEBUG 2017-11-18 17:02:33,391 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_randommodule.o -L/usr/localgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tionsmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databasensmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:33,394 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/_randommtmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_randommodule.ogcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_random.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:33,395 building '_collections' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:33,395 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_randommodule.o -L/usr/localgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tionsmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databasensmodule.o install_environment.STDOUT DEBUG 2017-11-18 17:02:33,784 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_collectionsmodule.o -L/usr/building '_bisect' extensgcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_bisectmodydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_bisectmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:33,801 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/_collect/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_collectiogcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gallocal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_collections.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:33,801 ion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:33,801 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_collectionsmodule.o -L/usr/building '_bisect' extensgcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_bisectmodydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_bisectmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:33,906 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdInclude -I./Include -I/us/tmp-toolshed-mtdP5qHBA/Python--mtdP5qHBA/Python-2.7.10 -c /galaxydir/ule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_bisect.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,008 building '_heapq' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,008 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/_heapqmomp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_heapqmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,008 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_heapqmodule.c:595:21: warning: illegal character encoding in string literal [-Winvalid-source-encoding] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,008 [explanation by Fran<E7>ois Pinard]\n\ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,008 ^~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,009 Include/Python.h:171:60: note: expanded from macro 'PyDoc_STRVAR' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,009 #define PyDoc_STRVAR(name,str) PyDoc_VAR(name) = PyDoc_STR(str) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,009 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,009 Include/Python.h:173:24: note: expanded from macro 'PyDoc_STR' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,009 #define PyDoc_STR(str) str tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,009 ^ 127.0.0.1 - - [18/Nov/2017:17:02:34 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:02:34,124 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_bisectmodulegcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tdule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databb.macosx-10.4-x86_64-2.7/_heapq.so install_environment.STDOUT DEBUG 2017-11-18 17:02:34,158 building 'operator' extension install_environment.STDOUT DEBUG 2017-11-18 17:02:34,158 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Poolshed-mtdP5qHBA/Python-2.7.10/Modules/operator.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,218 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_bisectmodulegcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tdule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databb.macosx-10.4-x86_64-2.7/_heapq.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,218 building 'operator' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,218 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Poolshed-mtdP5qHBA/Python-2.7.10/Modules/operator.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,218 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,420 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_heapqmodule.o -L/usr/local/lib -L. -o build/ligcc -fno-strict-aliasing ython-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/operator.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-tgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databcosx-10.4-x86_64-2.7/operator.so install_environment.STDOUT DEBUG 2017-11-18 17:02:34,457 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/operator.o -L/usr/local/lib -L. -o build/lib.mabuilding '_io' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,522 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,522 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -IModules/_io -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/bufferedio.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/bufferedio.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,522 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/operator.o -L/usr/local/lib -L. -o build/lib.mabuilding '_io' extension install_environment.STDOUT DEBUG 2017-11-18 17:02:34,894 alaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Incl-I/galaxydir/galaxy/databPython-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/gal.7.10/Modules/_io/bytesio.c -o build/temp.macosxmtdP5qHBA/Python-2.7.10/Modules/_io/bytesio.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:34,937 alaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Incl-I/galaxydir/galaxy/databPython-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/gal.7.10/Modules/_io/bytesio.c -o build/temp.macosxmtdP5qHBA/Python-2.7.10/Modules/_io/bytesio.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:35,145 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -IModules/_io -I/gude -I/usr/local/include ase/tmp/tmp-toolshed-mtdP5qHBA/dir/galaxy/database/tmp/tmp-toolshed-mtaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-protde -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshe/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-t/Modules/_io/fileio.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/fileio.o install_environment.STDOUT DEBUG 2017-11-18 17:02:35,291 otypes -IModules/_io -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Includ-mtdP5qHBA/Python-2.7.10oolshed-mtdP5qHBA/Python-2.7.10gcc -fno-strict-aliasing -g -O2 -DNDEBUed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/iobase.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/iobase.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:35,347 otypes -IModules/_io -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Includ-mtdP5qHBA/Python-2.7.10oolshed-mtdP5qHBA/Python-2.7.10gcc -fno-strict-aliasing -g -O2 -DNDEBUed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/iobase.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/iobase.o install_environment.STDOUT DEBUG 2017-11-18 17:02:35,477 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -IModules/_io -I/galaxydir/galaxy/database/ule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:35,554 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -IModules/_io -I/galaxydir/galaxy/database/ule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:35,658 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -IModules/_io -I/galaxydir/galaxy/database/tmp/tmp-toolshgcc -fno-strict-aliasing tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/_iomodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/_iomodgcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -IModules/_io -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5tabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/stringio.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/stringio.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:35,867 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -IModules/_io -I/gtmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/textio.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/textio.o install_environment.STDOUT DEBUG 2017-11-18 17:02:36,375 qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/daalaxydir/galaxy/database/p/tmp-toolshed-mtdP5qHBA/Pythongcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Modules/_functoolsmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/0/Modules/_functoolsmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:36,379 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tm-2.7.10/Modules/_io/bufferedio.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/bytesio.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/fileio.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/iobase.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/_iomodule.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/stringio.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_io/textio.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_io.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:36,380 building '_functools' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:36,380 qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/daalaxydir/galaxy/database/p/tmp-toolshed-mtdP5qHBA/Pythongcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Modules/_functoolsmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/0/Modules/_functoolsmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:36,583 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Pdatabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.1gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4ule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_functools.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:36,584 building '_json' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:36,584 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/_json.c shed-mtdP5qHBA/Python-2.7.10/Modules/_json.o install_environment.STDOUT DEBUG 2017-11-18 17:02:37,076 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_functoolsmodgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-t-o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databx-10.4-x86_64-2.7/_json.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:37,099 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_functoolsmodgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-t-o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databx-10.4-x86_64-2.7/_json.so install_environment.STDOUT DEBUG 2017-11-18 17:02:37,119 nsion 127.0.0.1 - - [18/Nov/2017:17:02:37 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:37,200 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_json.o -L/usr/local/lib -L. -o build/lib.macosbuilding '_testcapi' extegcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_testcapimodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_testcapimodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:37,200 nsion install_environment.STDOUT DEBUG 2017-11-18 17:02:37,581 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_testcapimodule.o -L/usr/local/lib -L. -o build/lib.mstcapi.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:37,612 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_testcapimodule.o -L/usr/local/lib -L. -o build/lib.mstcapi.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:37,716 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmacosx-10.4-x86_64-2.7/_tebuilding '_hotshot' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:37,716 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/localaxy/database/tmp/tmp-toInclude -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_hotshot.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_hotshot.o install_environment.STDOUT DEBUG 2017-11-18 17:02:38,018 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwr.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/inclutabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mod4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_lsprof.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:38,024 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmModules/_hotshot.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_hotshot.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:38,025 building '_lsprof' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:38,025 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwr.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/inclutabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mod4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_lsprof.o install_environment.STDOUT DEBUG 2017-11-18 17:02:38,176 apv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7ydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/rotatingtree.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:38,232 apv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7ydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/rotatingtree.o install_environment.STDOUT DEBUG 2017-11-18 17:02:38,274 _lsprof.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pytbuilding 'unicodedata' exgcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/unicodedatir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/unicodedata.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:38,340 apv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7de -I/galaxydir/galaxy/da/database/tmp/tmp-toolshed-mtdPules/_lsprof.c -o build/temp.macosx-10.gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwr.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/rotatingtree.c -o build/temp.macosx-10.4-x86_64-2.7/galaxgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/hon-2.7.10/Modules/rotatingtree.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_lsprof.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:38,340 tension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:38,341 _lsprof.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pytbuilding 'unicodedata' exgcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/unicodedatir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/unicodedata.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,161 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdInclude -I./Include -I/us/tmp-toolshed-mtdP5qHBA/Python--mtdP5qHBA/Python-2.7.10 -c /galaxydir/a.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4 -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/unicodedata.so install_environment.STDOUT DEBUG 2017-11-18 17:02:39,169 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/unicodedata.ogcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-todule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,266 building '_locale' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,267 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/unicodedata.ogcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-todule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,371 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/_localemtmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_localemodule.ogcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_locale.so -framework CoreFoundation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,476 building 'fcntl' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,476 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/fcntlmodp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/fcntlmodule.o install_environment.STDOUT DEBUG 2017-11-18 17:02:39,518 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_localemodule.o -L/usr/localgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datab.macosx-10.4-x86_64-2.7/fcntl.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,582 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_localemodule.o -L/usr/localgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datab.macosx-10.4-x86_64-2.7/fcntl.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,582 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/fcntlmodule.o -L/usr/local/lib -L. -o build/libbuilding 'grp' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,582 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/localaxy/database/tmp/tmp-toInclude -I/galaxydir/galaxy/dat-2.7.10 -c /galaxydir/galaxy/database/tgrpmodule.c -o build/temp.macosx-10.4-x86_64-2.7-2.7.10/Modules/grpmodule.o install_environment.STDOUT DEBUG 2017-11-18 17:02:39,656 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules//galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythongcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gal -L. -o build/lib.macosx-10.4-x86_64-2.7/grp.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,685 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules//galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythongcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gal -L. -o build/lib.macosx-10.4-x86_64-2.7/grp.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,685 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/grpmodule.c:102:17: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,685 if (gid < 0) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,685 ~~~ ^ ~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,685 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:02:39,687 on install_environment.STDOUT DEBUG 2017-11-18 17:02:39,687 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/selectmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/selectmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,789 on tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,789 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/selectmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/selectmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,992 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/grpmodule.o -L/usr/local/libbuilding 'select' extensigcc -fno-strict-aliasing -g -O2gcc -bundle -undefined dynamic_lookup bModules/selectmodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/select.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,992 building 'parser' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:39,993 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/parsermomp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/parsermodule.o 127.0.0.1 - - [18/Nov/2017:17:02:40 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:02:41,049 uild/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/gcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tdule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databb.macosx-10.4-x86_64-2.7/parser.so install_environment.STDOUT DEBUG 2017-11-18 17:02:41,090 nsion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:41,127 uild/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/gcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tdule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databb.macosx-10.4-x86_64-2.7/parser.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:41,127 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/parsermodule.o -L/usr/local/lib -L. -o build/libuilding 'cStringIO' extegcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cStringIO.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cStringIO.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:41,128 nsion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:41,336 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tm10.4-x86_64-2.7/cStringIO.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:41,336 building 'cPickle' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:41,337 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/cPickle.olshed-mtdP5qHBA/Python-2.7.10/Modules/cPickle.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:41,442 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cPickle.c:3451:20: warning: shifting a negative signed value is undefined [-Wshift-negative-value] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:41,442 l |= (~0L) << 32; tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:41,442 ~~~~~ ^ install_environment.STDOUT DEBUG 2017-11-18 17:02:42,721 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cStringIO.o -L/usr/local/lib -L. -o build/lib.macosx-gcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tc -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-togcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databosx-10.4-x86_64-2.7/cPickle.so install_environment.STDOUT DEBUG 2017-11-18 17:02:42,764 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:42,781 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cStringIO.o -L/usr/local/lib -L. -o build/lib.macosx-gcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tc -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-togcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databosx-10.4-x86_64-2.7/cPickle.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:42,781 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:42,882 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cPickle.o -L/usr/local/lib -L. -o build/lib.macbuilding 'mmap' extensiongcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/mmapmoduler/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/mmapmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:42,882 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/mmapmodule.c:639:17: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:42,882 if (cnt < 0 || (cnt + dest) < cnt || (cnt + src) < cnt || tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:42,882 ~~~ ^ ~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:42,882 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/mmapmodule.c:640:16: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:42,883 src < 0 || src > self->size || (src + cnt) > self->size || tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:42,883 ~~~ ^ ~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:42,883 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/mmapmodule.c:641:17: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:42,883 dest < 0 || dest > self->size || (dest + cnt) > self->size) { tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:42,883 ~~~~ ^ ~ install_environment.STDOUT DEBUG 2017-11-18 17:02:42,980 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdInclude -I./Include -I/us/tmp-toolshed-mtdP5qHBA/Python--mtdP5qHBA/Python-2.7.10 -c /galaxydir/.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydigcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/mmap.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:42,984 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdInclude -I./Include -I/us/tmp-toolshed-mtdP5qHBA/Python--mtdP5qHBA/Python-2.7.10 -c /galaxydir/.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydigcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/mmap.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:42,984 3 warnings generated. install_environment.STDOUT DEBUG 2017-11-18 17:02:43,011 on tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:43,087 on tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:43,088 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/mmapmodule.o building 'syslog' extensigcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/syslogmodudir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/syslogmodule.o install_environment.STDOUT DEBUG 2017-11-18 17:02:43,112 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdInclude -I./Include -I/us/tmp-toolshed-mtdP5qHBA/Python--mtdP5qHBA/Python-2.7.10 -c /galaxydir/le.c -o build/temp.macosx-10.4-x86_64-2.7/galaxygcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/syslog.so install_environment.STDOUT DEBUG 2017-11-18 17:02:43,148 ion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:43,199 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdInclude -I./Include -I/us/tmp-toolshed-mtdP5qHBA/Python--mtdP5qHBA/Python-2.7.10 -c /galaxydir/le.c -o build/temp.macosx-10.4-x86_64-2.7/galaxygcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/syslog.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:43,202 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/syslogmodule.building 'audioop' extensgcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/audioop.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/audioop.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:43,202 ion 127.0.0.1 - - [18/Nov/2017:17:02:43 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:43,608 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tm.4-x86_64-2.7/audioop.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:43,713 building 'readline' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:43,713 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/readlineoolshed-mtdP5qHBA/Python-2.7.10/Modules/readline.o install_environment.STDOUT DEBUG 2017-11-18 17:02:43,789 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/audioop.o -L/usr/local/lib -L. -o build/lib.macosx-10gcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-t.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-tgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datab-L. -lreadline -lncurses -o build/lib.macosx-10.4-x86_64-2.7/readline.so -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:43,817 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/audioop.o -L/usr/local/lib -L. -o build/lib.macosx-10gcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-t.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-tgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datab-L. -lreadline -lncurses -o build/lib.macosx-10.4-x86_64-2.7/readline.so -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:43,817 ld: warning: directory not found for option '-L/usr/lib/termcap' install_environment.STDOUT DEBUG 2017-11-18 17:02:43,829 n tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:43,918 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/readline.o -L/usr/lib/termcap -L/usr/local/lib building 'crypt' extensiogcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cryptmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cryptmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:43,918 n tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:43,919 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmx-10.4-x86_64-2.7/crypt.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:44,020 building '_csv' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:44,020 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/_csv.c -hed-mtdP5qHBA/Python-2.7.10/Modules/_csv.o install_environment.STDOUT DEBUG 2017-11-18 17:02:44,214 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cryptmodule.o -L/usr/local/lib -L. -o build/lib.macosgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-to build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolsgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datab-10.4-x86_64-2.7/_csv.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:44,222 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cryptmodule.o -L/usr/local/lib -L. -o build/lib.macosgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-to build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolsgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datab-10.4-x86_64-2.7/_csv.so install_environment.STDOUT DEBUG 2017-11-18 17:02:44,247 ion install_environment.STDOUT DEBUG 2017-11-18 17:02:44,247 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/socketmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/socketmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:44,323 ion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:44,323 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/socketmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/socketmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:44,735 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_csv.o -L/usr/local/lib -L. -o build/lib.macosxbuilding '_socket' extensgcc -fno-strict-aliasing -g -O2gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Modules/timemodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databales/timemodule.o install_environment.STDOUT DEBUG 2017-11-18 17:02:44,832 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Pse/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modugcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/timemodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_socket.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:44,840 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Pse/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modugcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/timemodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_socket.so install_environment.STDOUT DEBUG 2017-11-18 17:02:44,872 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:44,943 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/socketmodule.building '_sha' extensiongcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/shamodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/shamodule.o install_environment.STDOUT DEBUG 2017-11-18 17:02:45,224 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/shamodule.o -L/usr/local/lib -L. -o build/lib.macosx-building '_md5' extensiongcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/md5module./galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/md5module.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:45,253 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tm10.4-x86_64-2.7/_sha.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:45,355 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/shamodule.o -L/usr/local/lib -L. -o build/lib.macosx-building '_md5' extensiongcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/md5module./galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/md5module.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:45,355 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdInclude -I./Include -I/us/tmp-toolshed-mtdP5qHBA/Python--mtdP5qHBA/Python-2.7.10 -c /galaxydir/c -o build/temp.macosx-10.4-x86_64-2.7/galaxydirgcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Walude -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/md5.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/md5.o install_environment.STDOUT DEBUG 2017-11-18 17:02:45,542 l -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Inclp/tmp-toolshed-mtdP5qHBA/gcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/sha256modudir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/sha256module.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:45,559 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmPython-2.7.10/Modules/md5module.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/md5.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_md5.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:45,559 building '_sha256' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:45,559 l -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Inclp/tmp-toolshed-mtdP5qHBA/gcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/sha256modudir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/sha256module.o install_environment.STDOUT DEBUG 2017-11-18 17:02:46,137 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/sha256module.building '_sha512' extensgcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/sha512modudir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/sha512module.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:46,174 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdInclude -I./Include -I/us/tmp-toolshed-mtdP5qHBA/Python--mtdP5qHBA/Python-2.7.10 -c /galaxydir/le.c -o build/temp.macosx-10.4-x86_64-2.7/galaxygcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_sha256.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:46,175 ion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:46,175 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/sha256module.building '_sha512' extensgcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/sha512modudir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/sha512module.o 127.0.0.1 - - [18/Nov/2017:17:02:46 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:46,786 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdInclude -I./Include -I/us/tmp-toolshed-mtdP5qHBA/Python--mtdP5qHBA/Python-2.7.10 -c /galaxydir/le.c -o build/temp.macosx-10.4-x86_64-2.7/galaxygcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_sha512.so install_environment.STDOUT DEBUG 2017-11-18 17:02:46,793 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/sha512module.creating build/temp.macos tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:46,890 building '_sqlite3' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:46,890 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/sha512module.creating build/temp.macos tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:46,890 x-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlitegcc -fno-strict-aliasing EXTENSION=1 -IModules/_sqlite -r/galaxy/database/tmp/tmp-toolshed-mtdP -I. -IInclude -I./Include -I/usr/local/include olshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/d -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modlaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/cache.o install_environment.STDOUT DEBUG 2017-11-18 17:02:46,911 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DMODULE_NAME="sqlite3" -DSQLITE_OMIT_LOAD_I/usr/include -I/galaxydi5qHBA/Python-2.7.10/Mac/Include-I/galaxydir/galaxy/database/tmp/tmp-toatabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10ules/_sqlite/cache.c -o build/temp.macosx-10.4-x86_64-2.7/gagcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-protlaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/connection.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/connection.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:46,991 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DMODULE_NAME="sqlite3" -DSQLITE_OMIT_LOAD_I/usr/include -I/galaxydi5qHBA/Python-2.7.10/Mac/Include-I/galaxydir/galaxy/database/tmp/tmp-toatabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10ules/_sqlite/cache.c -o build/temp.macosx-10.4-x86_64-2.7/gagcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-protlaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/connection.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/connection.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:47,298 otypes -DMODULE_NAME="sqlite3" -DSQLITE_OMIT_LOAD_EXTENSION=1 -IModules/_sqlite -I/usr/include -I/gagcc -fno-strict-aliasing EXTENSION=1 -IModules/_sqlite -r/galaxy/database/tmp/tmp-toolshed-mtdP -I. -IInclude -I./Include -I/usr/local/include olshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/d -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modalaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/cursor.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:47,505 otypes -DMODULE_NAME="sqlite3" -DSQLITE_OMIT_LOAD_EXTENSION=1 -IModules/_sqlite -I/usr/include -I/gamicroprotocols.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/microprotocols.o install_environment.STDOUT DEBUG 2017-11-18 17:02:47,586 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DMODULE_NAME="sqlite3" -DSQLITE_OMIT_LOAD_I/usr/include -I/galaxydi5qHBA/Python-2.7.10/Mac/Include-I/galaxydir/galaxy/database/tmp/tmp-toatabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10ules/_sqlite/cursor.c -o build/temp.macosx-10.4-x86_64-2.7/ggcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-protlaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DMODULE_NAME="sqlite3" -DSQLITE_OMIT_LOAD_EXTENSION=1 -IModules/_sqlite -I/usr/include -I/galaxydir/g/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7e.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/module.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:47,610 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DMODULE_NAME="sqlite3" -DSQLITE_OMIT_LOAD_I/usr/include -I/galaxydi5qHBA/Python-2.7.10/Mac/Include-I/galaxydir/galaxy/database/tmp/tmp-toatabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10ules/_sqlite/cursor.c -o build/temp.macosx-10.4-x86_64-2.7/ggcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-protlaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DMODULE_NAME="sqlite3" -DSQLITE_OMIT_LOAD_EXTENSION=1 -IModules/_sqlite -I/usr/include -I/galaxydir/g/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7e.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/module.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:47,711 alaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr.10/Modules/_sqlite/modulgcc -fno-strict-aliasing -g -O2ION=1 -IModules/_sqlite -I/usr/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/prepare_protocol.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/prepare_protocol.o install_environment.STDOUT DEBUG 2017-11-18 17:02:47,778 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DMODULE_NAME="sqlite3" -DSQLITE_OMIT_LOAD_EXTENSgcc -fno-strict-aliasing EXTENSION=1 -IModules/_sqlite -r/galaxy/database/tmp/tmp-toolshed-mtdP -I. -IInclude -I./Include -I/usr/local/include olshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/d -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/row.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:47,813 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DMODULE_NAME="sqlite3" -DSQLITE_OMIT_LOAD_EXTENSgcc -fno-strict-aliasing EXTENSION=1 -IModules/_sqlite -r/galaxy/database/tmp/tmp-toolshed-mtdP -I. -IInclude -I./Include -I/usr/local/include olshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/d -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/row.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:47,916 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DMODULE_NAME="sqlite3" -DSQLITE_OMIT_LOAD_I/usr/include -I/galaxydi5qHBA/Python-2.7.10/Mac/Include-I/galaxydir/galaxy/database/tmp/tmp-toatabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10ules/_sqlite/row.c -o build/temp.macosx-10.4-x86_64-2.7/galagcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-protlaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/statement.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/statement.o install_environment.STDOUT DEBUG 2017-11-18 17:02:48,074 otypes -DMODULE_NAME="sqlite3" -DSQLITE_OMIT_LOAD_EXTENSION=1 -IModules/_sqlite -I/usr/include -I/gaite3" -DSQLITE_OMIT_LOAD_lite -I/usr/include -I/galaxydihed-mtdP5qHBA/Python-2.7.10/Mac/Include/include -I/galaxydir/galaxy/database/tmp/tmp-todir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10thon-2.7.10/Modules/_sqlite/util.c -o build/temp.macosx-10.4-x86_64-2.7/gallite/util.o 127.0.0.1 - - [18/Nov/2017:17:02:48 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/datasets/error?dataset_id=a799d38679e985db&__identifer=9nms4ovms1v" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:48,124 otypes -DMODULE_NAME="sqlite3" -DSQLITE_OMIT_LOAD_EXTENSION=1 -IModules/_sqlite -I/usr/include -I/gaite3" -DSQLITE_OMIT_LOAD_lite -I/usr/include -I/galaxydihed-mtdP5qHBA/Python-2.7.10/Mac/Include/include -I/galaxydir/galaxy/database/tmp/tmp-todir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10thon-2.7.10/Modules/_sqlite/util.c -o build/temp.macosx-10.4-x86_64-2.7/gallite/util.o install_environment.STDOUT DEBUG 2017-11-18 17:02:48,206 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/cache.o build/temp.macosx-10.4-x86_64-20.4-x86_64-2.7/galaxydir/mp-toolshed-mtdP5qHBA/Python-2..4-x86_64-2.7/galaxydir/galaxy/database2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:48,224 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/cache.o build/temp.macosx-10.4-x86_64-20.4-x86_64-2.7/galaxydir/mp-toolshed-mtdP5qHBA/Python-2..4-x86_64-2.7/galaxydir/galaxy/database2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mt 127.0.0.1 - - [18/Nov/2017:17:02:48 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:02:48 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:48,328 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DMODULE_NAME="sqlEXTENSION=1 -IModules/_sqr/galaxy/database/tmp/tmp-tools -I. -IInclude -I./Include -I/usr/localolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxy -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pyaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datab.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/connection.o build/temp.macosx-1galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/cursor.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/t7.10/Modules/_sqlite/microprotocols.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/module.o build/temp.macosx-10/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/prepare_protocol.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/row.o build/temp.macosx-10.4-x86_64-tdP5qHBA/Python-2.7.10/Modules/_sqlite/statement.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_sqlite/util.o -L/usr/lib -L/usr/local/lib -L. -lsqlite3 -o build/lib.macosx-10.4-x86_64-2.7/_sqlite3.so -Wl,-search_paths_firsbuilding 'bsddb185' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:48,328 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/localaxy/database/tmp/tmp-toInclude -I/galaxydir/galaxy/dat-2.7.10 -c /galaxydir/galaxy/database/tbsddbmodule.c -o build/temp.macosx-10.4-x86_64-2on-2.7.10/Modules/bsddbmodule.o 127.0.0.1 - - [18/Nov/2017:17:02:48 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:02:48 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:02:48,621 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galib -L. -o build/lib.macosx-10.4-x86_64-2.7/bsddb185.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:48,636 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galib -L. -o build/lib.macosx-10.4-x86_64-2.7/bsddb185.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:48,738 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/bsddbmodule.o -L/usr/local/lbuilding 'dbm' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:48,738 alaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Incl-I/galaxydir/galaxy/databPython-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/gal.7.10/Modules/dbmmodule.c -o build/temp.macosx-1dP5qHBA/Python-2.7.10/Modules/dbmmodule.o install_environment.STDOUT DEBUG 2017-11-18 17:02:48,809 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_NDBM_H -I/gude -I/usr/local/include ase/tmp/tmp-toolshed-mtdP5qHBA/dir/galaxy/database/tmp/tmp-toolshed-mtaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-20.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gal -L. -o build/lib.macosx-10.4-x86_64-2.7/dbm.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:48,842 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_NDBM_H -I/gude -I/usr/local/include ase/tmp/tmp-toolshed-mtdP5qHBA/dir/galaxy/database/tmp/tmp-toolshed-mtaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-20.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gal -L. -o build/lib.macosx-10.4-x86_64-2.7/dbm.so install_environment.STDOUT DEBUG 2017-11-18 17:02:48,843 ion install_environment.STDOUT DEBUG 2017-11-18 17:02:48,843 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/termios.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/termios.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:48,946 ion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:48,946 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/termios.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/termios.o install_environment.STDOUT DEBUG 2017-11-18 17:02:48,985 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmModules/termios.o -L/usr/7/termios.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:49,047 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmModules/termios.o -L/usr/7/termios.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:49,047 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/dbmmodule.o -L/usr/local/libbuilding 'termios' extensgcc -fno-strict-aliasing -g -O2p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.building 'resource' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:49,047 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/localaxy/database/tmp/tmp-toInclude -I/galaxydir/galaxy/dat-2.7.10 -c /galaxydir/galaxy/database/tresource.c -o build/temp.macosx-10.4-x86_64-2.7/2.7.10/Modules/resource.o install_environment.STDOUT DEBUG 2017-11-18 17:02:49,147 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gal-L. -o build/lib.macosx-10.4-x86_64-2.7/resource.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:49,152 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gal-L. -o build/lib.macosx-10.4-x86_64-2.7/resource.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:49,256 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/resource.o -L/usr/local/lib building 'nis' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:49,256 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/localaxy/database/tmp/tmp-toInclude -I/galaxydir/galaxy/dat-2.7.10 -c /galaxydir/galaxy/database/tnismodule.c -o build/temp.macosx-10.4-x86_64-2.7-2.7.10/Modules/nismodule.o install_environment.STDOUT DEBUG 2017-11-18 17:02:49,352 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules//galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythongcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gal -L. -o build/lib.macosx-10.4-x86_64-2.7/nis.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:49,357 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules//galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythongcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gal -L. -o build/lib.macosx-10.4-x86_64-2.7/nis.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:49,357 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/nismodule.c:404:15: warning: explicitly assigning value of variable of type 'nismaplist *' (aka 'struct nismaplist *') to itself [-Wself-assign] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:49,357 for (maps = maps; maps; maps = maps->next) { tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:49,357 ~~~~ ^ ~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:49,357 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:02:49,388 ion install_environment.STDOUT DEBUG 2017-11-18 17:02:49,389 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_cursesmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_cursesmodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:49,457 ion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:49,458 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_cursesmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_cursesmodule.o install_environment.STDOUT DEBUG 2017-11-18 17:02:50,144 uild/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/curses -o build/lib.macosbuilding '_curses_panel' extensgcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Modules/_curses_panel.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datodules/_curses_panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:50,178 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/nismodule.o -L/usr/local/libbuilding '_curses' extensgcc -fno-strict-aliasing -g -O2gcc -bundle -undefined dynamic_lookup bModules/_cursesmodule.o -L/usr/local/lib -L. -lnx-10.4-x86_64-2.7/_curses.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:50,178 ion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:50,178 uild/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/curses -o build/lib.macosbuilding '_curses_panel' extensgcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Modules/_curses_panel.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datodules/_curses_panel.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:50,386 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Pabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4.o -L/usr/local/lib -L. -lpanel -lncurses -o build/lib.macosx-10.4-x86_64-2.7/_curses_panel.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:50,386 building 'zlib' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:50,386 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/zlibmodu-toolshed-mtdP5qHBA/Python-2.7.10/Modules/zlibmodule.o install_environment.STDOUT DEBUG 2017-11-18 17:02:50,569 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_curses_panelgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tle.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmpgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datablib.macosx-10.4-x86_64-2.7/zlib.so -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:50,587 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_curses_panelgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tle.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmpgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datablib.macosx-10.4-x86_64-2.7/zlib.so -Wl,-search_paths_first install_environment.STDOUT DEBUG 2017-11-18 17:02:50,603 sion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:50,688 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/zlibmodule.o -L/usr/local/lib -L. -lz -o build/building 'binascii' extengcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/binascii.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/binascii.o -DUSE_ZLIB_CRC32 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:50,688 sion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:51,003 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmsx-10.4-x86_64-2.7/binascii.so -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:51,003 building 'bz2' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:51,003 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/bz2modultoolshed-mtdP5qHBA/Python-2.7.10/Modules/bz2module.o install_environment.STDOUT DEBUG 2017-11-18 17:02:51,319 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/binascii.o -L/usr/local/lib -L. -lz -o build/lib.macogcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-te.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datab/lib.macosx-10.4-x86_64-2.7/bz2.so -Wl,-search_paths_first install_environment.STDOUT DEBUG 2017-11-18 17:02:51,362 ion install_environment.STDOUT DEBUG 2017-11-18 17:02:51,362 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/expat tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:51,416 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/binascii.o -L/usr/local/lib -L. -lz -o build/lib.macogcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-te.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datab/lib.macosx-10.4-x86_64-2.7/bz2.so -Wl,-search_paths_first tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:51,416 ion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:51,417 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/expat tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:51,417 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/bz2module.o -L/usr/local/lib -L. -lbz2 -o buildbuilding 'pyexpat' extenscreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/PythonI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I.lude -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydihon-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/pyexpat.c -o build/temp.macod-mtdP5qHBA/Python-2.7.10/Modules/pyexpat.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:51,417 ld: warning: object file (/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source/libbz2.a(bzlib.o)) was built for newer OSX version (10.11) than being linked (10.4) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:51,417 ld: warning: object file (/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source/libbz2.a(compress.o)) was built for newer OSX version (10.11) than being linked (10.4) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:51,417 ld: warning: object file (/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source/libbz2.a(crctable.o)) was built for newer OSX version (10.11) than being linked (10.4) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:51,417 ld: warning: object file (/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source/libbz2.a(decompress.o)) was built for newer OSX version (10.11) than being linked (10.4) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:51,417 ld: warning: object file (/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source/libbz2.a(randtable.o)) was built for newer OSX version (10.11) than being linked (10.4) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:51,417 ld: warning: object file (/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source/libbz2.a(blocksort.o)) was built for newer OSX version (10.11) than being linked (10.4) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:51,418 ld: warning: object file (/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source/libbz2.a(huffman.o)) was built for newer OSX version (10.11) than being linked (10.4) install_environment.STDOUT DEBUG 2017-11-18 17:02:52,032 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_EXPAT_CONFIG_H=1 -DUSE_PYEXPAT_CAPI -I/galaxydir/g-2.7.10/./Modules/expat -n-2.7.10/Mac/Include -I/galaxyd -IInclude -I./Include -I/usr/local/incr/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pytsx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshegcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prot5qHBA/Python-2.7.10/./Modules/expat -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/PyI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/locaatabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Modules/expat/xmlparse.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/expat/xmlparse.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:52,036 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_EXPAT_CONFIG_H=1 -DUSE_PYEXPAT_CAPI -I/galaxydir/g-2.7.10/./Modules/expat -n-2.7.10/Mac/Include -I/galaxyd -IInclude -I./Include -I/usr/local/incr/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pytsx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshegcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prot5qHBA/Python-2.7.10/./Modules/expat -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/PyI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/locaatabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Modules/expat/xmlparse.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/expat/xmlparse.o 127.0.0.1 - - [18/Nov/2017:17:02:53 -0400] "GET /admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04 HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:53,583 otypes -DHAVE_EXPAT_CONFIG_H=1 -DUSE_PYEXPAT_CAPI -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdPthon-2.7.10/Mac/Include -l/include -I/galaxydir/galaxy/d/database/tmp/tmp-toolshed-mtdP5qHBA/Pygcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/./Modules/exptabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/gamtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydi5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy10/Modules/expat/xmlrole.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/expat/xmlrole.o 127.0.0.1 - - [18/Nov/2017:17:02:53 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:53,792 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_EXPAT_CONFIp-toolshed-mtdP5qHBA/Python-2.7.10/./Modules/expat -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/ee/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/expat/xmltok.o install_environment.STDOUT DEBUG 2017-11-18 17:02:55,089 apv -O3 -Wall -Wstrict-prototypes -DHAVE_EXPAT_CONFIG_H=1 -DUSE_PYEXPAT_CAPI -I/galaxydir/galaxy/datat -I/galaxydir/galaxy/dalaxy/database/tmp/tmp-toolshed-r/galaxy/database/tmp/tmp-toolshed-mtdP/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.G_H=1 -DUSE_PYEXPAT_CAPI -I/galaxydir/galaxy/database/tmp/tmxpat/xmltok.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databasgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/expat/xmlparse.o build/temp.macosx-10.4-x86_64abase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/expat/xmlrole.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolsheds/expat/xmltok.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/pyexpat.so install_environment.STDOUT DEBUG 2017-11-18 17:02:55,132 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_EXPAT_CONFIules/expat -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10//database/tmp/tmp-toolshed-mtdP5qHBA/PyI./Include -I/usr/local/include -I/galaxydir/gal.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-p-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_elementtree.c -o build/temp.macthon-2.7.10/Modules/_elementtree.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:55,133 apv -O3 -Wall -Wstrict-prototypes -DHAVE_EXPAT_CONFIG_H=1 -DUSE_PYEXPAT_CAPI -I/galaxydir/galaxy/datat -I/galaxydir/galaxy/dalaxy/database/tmp/tmp-toolshed-r/galaxy/database/tmp/tmp-toolshed-mtdP/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.G_H=1 -DUSE_PYEXPAT_CAPI -I/galaxydir/galaxy/database/tmp/tmxpat/xmltok.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databasgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/expat/xmlparse.o build/temp.macosx-10.4-x86_64abase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/expat/xmlrole.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolsheds/expat/xmltok.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/pyexpat.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:55,133 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/pyexpat.o build/temp.macosx-10.4-x86_64-2.7/gal-2.7/galaxydir/galaxy/dat-mtdP5qHBA/Python-2.7.10/Modulebuilding '_elementtree' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:55,133 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_EXPAT_CONFIules/expat -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10//database/tmp/tmp-toolshed-mtdP5qHBA/PyI./Include -I/usr/local/include -I/galaxydir/gal.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-p-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_elementtree.c -o build/temp.macthon-2.7.10/Modules/_elementtree.o install_environment.STDOUT DEBUG 2017-11-18 17:02:55,722 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_elementtree.o -L/usr/local/lib -L. -o build/libuilding '_multibytecodeccreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/multibytecodec.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/multibytecodec.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:55,749 G_H=1 -DUSE_PYEXPAT_CAPI -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/./Modalaxy/database/tmp/tmp-toMac/Include -I/galaxydir/galaxython-2.7.10/Mac/Include -I. -IInclude -axy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pygcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databb.macosx-10.4-x86_64-2.7/_elementtree.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:55,749 ' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:55,749 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:55,750 ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_elementtree.o -L/usr/local/lib -L. -o build/libuilding '_multibytecodeccreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/multibytecodec.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/multibytecodec.o install_environment.STDOUT DEBUG 2017-11-18 17:02:56,096 namic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/gcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-ts/_codecs_kr.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databas/_codecs_kr.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:56,162 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pgcc -bundle -undefined dyPython-2.7.10/Modules/cjkcodecs/multibytecodec.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_multibytecodec.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:56,162 building '_codecs_kr' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:56,162 namic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/gcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-ts/_codecs_kr.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databas/_codecs_kr.o install_environment.STDOUT DEBUG 2017-11-18 17:02:56,422 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecs_kr.o -L/usgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-ts/_codecs_jp.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databas/_codecs_jp.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:56,468 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecse/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_codecs_kr.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:56,468 building '_codecs_jp' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:56,468 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecs_kr.o -L/usgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-ts/_codecs_jp.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databas/_codecs_jp.o 127.0.0.1 - - [18/Nov/2017:17:02:56 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:02:56,968 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecs_jp.o -L/usgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-ts/_codecs_cn.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databas/_codecs_cn.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:56,986 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecse/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_codecs_jp.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:56,986 building '_codecs_cn' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:56,986 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecs_jp.o -L/usgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-ts/_codecs_cn.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databas/_codecs_cn.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:57,398 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecse/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_codecs_cn.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:57,398 ension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:57,398 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdInclude -I./Include -I/us/tmp-toolshed-mtdP5qHBA/Python--mtdP5qHBA/Python-2.7.10 -c /galaxydir/_codecs_tw.c -o build/temp.macosx-10.4-x86_64-2._tw.o install_environment.STDOUT DEBUG 2017-11-18 17:02:57,545 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecs_cn.o -L/usbuilding '_codecs_tw' extgcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecsgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtd6_64-2.7/_codecs_tw.so install_environment.STDOUT DEBUG 2017-11-18 17:02:57,577 ension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:57,600 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecs_cn.o -L/usbuilding '_codecs_tw' extgcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecsgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtd6_64-2.7/_codecs_tw.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:57,600 P5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecs_tw.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x8building '_codecs_hk' extgcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecs_hk.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecs_hk.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:57,600 ension install_environment.STDOUT DEBUG 2017-11-18 17:02:57,895 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecs_hk.o -L/usr/local/lib -L. -o build/gcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-ts/_codecs_iso2022.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/dcodecs/_codecs_iso2022.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:57,907 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmlib.macosx-10.4-x86_64-2.7/_codecs_hk.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:57,907 building '_codecs_iso2022' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:57,907 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecs_hk.o -L/usr/local/lib -L. -o build/gcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-ts/_codecs_iso2022.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/dcodecs/_codecs_iso2022.o install_environment.STDOUT DEBUG 2017-11-18 17:02:58,161 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecs_iso2022.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_codecs_iso2022.so install_environment.STDOUT DEBUG 2017-11-18 17:02:58,194 building '_multiprocessing' extension install_environment.STDOUT DEBUG 2017-11-18 17:02:58,194 A/Python-2.7.10/Modules/_multiprocessing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,213 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecs/_codecs_iso2022.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_codecs_iso2022.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,213 building '_multiprocessing' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,213 A/Python-2.7.10/Modules/_multiprocessing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,213 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkcodecatabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/cjkgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galcreating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBgcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -IModules/_multiprocessing -I/galaxyI/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdgalaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_multiprocessing/multiprocessing.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-tooodules/_multiprocessing/multiprocessing.o install_environment.STDOUT DEBUG 2017-11-18 17:02:58,314 dir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -P5qHBA/Python-2.7.10 -c /lshed-mtdP5qHBA/Python-2.7.10/Mgcc -fno-strict-aliasing -g -O2 -DNDEBUmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Incllude -I/usr/local/include -I/galaxydir/galaxy/database/tmp/t7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_multiprocessing/socket_connection.c -o build/abase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_multiprocessing/socket_connection.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,316 dir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -P5qHBA/Python-2.7.10 -c /lshed-mtdP5qHBA/Python-2.7.10/Mgcc -fno-strict-aliasing -g -O2 -DNDEBUmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Incllude -I/usr/local/include -I/galaxydir/galaxy/database/tmp/t7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_multiprocessing/socket_connection.c -o build/abase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_multiprocessing/socket_connection.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,524 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -IModules/_multiprocessing -I/galaxydir/galaxy/database/tude -I. -IInclude -I./Incmp-toolshed-mtdP5qHBA/Python-2.-2.7.10 -c /galaxydir/galaxy/database/ttemp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datgcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -WalqHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_multiprocessing/semaphore.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_multiprocessing/semaphore.o install_environment.STDOUT DEBUG 2017-11-18 17:02:58,601 l -Wstrict-prototypes -IModules/_multiprocessing -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5gcc -bundle -undefined dyPython-2.7.10/Modules/_multiprocessing/multiprocessing.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_multiprocessing/socket_connection.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_multiprocessing/semaphore.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_multiprocessing.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,629 l -Wstrict-prototypes -IModules/_multiprocessing -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5gcc -bundle -undefined dyPython-2.7.10/Modules/_multiprocessing/multiprocessing.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_multiprocessing/socket_connection.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_multiprocessing/semaphore.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_multiprocessing.so install_environment.STDOUT DEBUG 2017-11-18 17:02:58,682 sion install_environment.STDOUT DEBUG 2017-11-18 17:02:58,682 -x86_64-2.7/Mac install_environment.STDOUT DEBUG 2017-11-18 17:02:58,682 creating build/temp.macosx-10.4-x86_64-2.7/Mac/Modules install_environment.STDOUT DEBUG 2017-11-18 17:02:58,682 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c ./Mac/Modules/_scproxy.c -o build/temp.macosx-10.4-x86_64-2.7/./Mac/Modules/_scproxy.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,730 sion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,731 -x86_64-2.7/Mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,731 creating build/temp.macosx-10.4-x86_64-2.7/Mac/Modules tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,731 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c ./Mac/Modules/_scproxy.c -o build/temp.macosx-10.4-x86_64-2.7/./Mac/Modules/_scproxy.o install_environment.STDOUT DEBUG 2017-11-18 17:02:58,905 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/./Mac/Modules/_scproxy.o -L/4-2.7/_scproxy.so -framework SystemConfiguration -framework CoreFoundation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,939 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/./Mac/Modules/_scproxy.o -L/4-2.7/_scproxy.so -framework SystemConfiguration -framework CoreFoundation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,939 ./Mac/Modules/_scproxy.c:67:10: warning: comparison of address of 'kSCPropNetProxiesExcludeSimpleHostnames' not equal to a null pointer is always true [-Wtautological-pointer-compare] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,939 if (&kSCPropNetProxiesExcludeSimpleHostnames != NULL) { tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,939 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,939 /System/Library/Frameworks/SystemConfiguration.framework/Headers/SCSchemaDefinitions.h:2153:49: note: expanded from macro 'kSCPropNetProxiesExcludeSimpleHostnames' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,939 #define kSCPropNetProxiesExcludeSimpleHostnames kSCPropNetProxiesExcludeSimpleHostnames tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,940 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:58,940 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:02:58,946 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythcreating build/temp.macoscreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Mac/Modules/cf/_CFmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/0/Mac/Modules/cf/_CFmodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,041 namic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/building '_scproxy' extencreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUusr/local/lib -L. -o build/lib.macosx-10.4-x86_6building '_CF' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,041 on-2.7.10/Mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,041 x-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,041 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cf tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,041 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythcreating build/temp.macoscreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Mac/Modules/cf/_CFmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/0/Mac/Modules/cf/_CFmodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,343 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cf/_CFmodule.c:1837:18: warning: incompatible pointer types initializing 'UniChar *' (aka 'unsigned short *') with an expression of type 'Py_UNICODE *' (aka 'unsigned int *') [-Wincompatible-pointer-types] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,344 UniChar *unichars = PyUnicode_AsUnicode(v); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,344 ^ ~~~~~~~~~~~~~~~~~~~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,344 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cf/_CFmodule.c:2368:52: warning: incompatible pointer types passing 'Py_UNICODE *' (aka 'unsigned int *') to parameter of type 'UniChar *' (aka 'unsigned short *') [-Wincompatible-pointer-types] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,344 CFStringGetCharacters(_self->ob_itself, range, data); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,344 ^~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,344 /System/Library/Frameworks/CoreFoundation.framework/Headers/CFString.h:262:75: note: passing argument to parameter 'buffer' here tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,344 void CFStringGetCharacters(CFStringRef theString, CFRange range, UniChar *buffer); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,344 ^ 127.0.0.1 - - [18/Nov/2017:17:02:59 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,860 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Pdatabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.1gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Walude -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/dataP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.ase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cf/pycfbridge.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydi5qHBA/Python-2.7.10/Mac/Modules/cf/pycfbridge.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:02:59,860 2 warnings generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,175 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cf/pycfbridge.c:136:39: warning: incompatible pointer types passing 'Py_UNICODE *' (aka 'unsigned int *') to parameter of type 'UniChar *' (aka 'unsigned short *') [-Wincompatible-pointer-types] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,175 CFStringGetCharacters(src, range, data); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,175 ^~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,175 /System/Library/Frameworks/CoreFoundation.framework/Headers/CFString.h:262:75: note: passing argument to parameter 'buffer' here tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,175 void CFStringGetCharacters(CFStringRef theString, CFRange range, UniChar *buffer); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,176 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,176 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cf/pycfbridge.c:294:23: warning: incompatible pointer types assigning to 'UniChar *' (aka 'unsigned short *') from 'Py_UNICODE *' (aka 'unsigned int *') [-Wincompatible-pointer-types] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,176 if ((unichars = PyUnicode_AsUnicode(src)) == NULL ) goto err; tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,176 ^ ~~~~~~~~~~~~~~~~~~~~~~~~ install_environment.STDOUT DEBUG 2017-11-18 17:03:00,201 l -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Inclbase/tmp/tmp-toolshed-mtd7.10 -c /galaxydir/galaxy/databr/galaxy/database/tmp/tmp-toolshed-mtdPgcc -bundle -undefined dynamic_lookup build/tempes/cf/_CFmodule.o build/temp.macosx-10.4-x86_64-2.7/galaxydi-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cf/pycfbridge.o -L/usr/local/4-x86_64-2.7/_CF.so -framework CoreFoundation install_environment.STDOUT DEBUG 2017-11-18 17:03:00,270 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modu.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pyth tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,277 l -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Inclbase/tmp/tmp-toolshed-mtd7.10 -c /galaxydir/galaxy/databr/galaxy/database/tmp/tmp-toolshed-mtdPgcc -bundle -undefined dynamic_lookup build/tempes/cf/_CFmodule.o build/temp.macosx-10.4-x86_64-2.7/galaxydi-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cf/pycfbridge.o -L/usr/local/4-x86_64-2.7/_CF.so -framework CoreFoundation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,277 .macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modulr/galaxy/database/tmp/tmplib -L. -o build/lib.macosx-10.building 'autoGIL' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,277 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modu.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pyth tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,277 2 warnings generated. install_environment.STDOUT DEBUG 2017-11-18 17:03:00,421 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/autoGIL.o -L/usr/local/lgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-trPickermodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databorPickermodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,478 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/localaxy/database/tmp/tmp-toInclude -I/galaxydir/galaxy/dat-2.7.10 -c /galaxydir/galaxy/database/tles/autoGIL.c -o build/temp.macosx-10.4-x86_64-2on-2.7.10/Mac/Modules/autoGIL.o -Wno-deprecated-declarationsgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galib -L. -o build/lib.macosx-10.4-x86_64-2.7/autoGIL.so -framework CoreFoundation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,479 building 'ColorPicker' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,479 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/autoGIL.o -L/usr/local/lgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-trPickermodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databorPickermodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:00,884 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/Coloase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/Colgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galsr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/ColorPicker.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:01,086 building 'gestalt' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:01,086 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/gestaltmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/gestaltmodule.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:01,451 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ColorPickermodule.o -L/ugcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac/gcc -bundle -undefined dynamic_lookup bMac/Modules/gestaltmodule.o -L/usr/local/lib -L.-x86_64-2.7/gestalt.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:01,498 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ColorPickermodule.o -L/ugcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac/gcc -bundle -undefined dynamic_lookup bMac/Modules/gestaltmodule.o -L/usr/local/lib -L.-x86_64-2.7/gestalt.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:01,599 uild/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/ -o build/lib.macosx-10.4building 'MacOS' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:01,599 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/localaxy/database/tmp/tmp-toInclude -I/galaxydir/galaxy/dat-2.7.10 -c /galaxydir/galaxy/database/tles/MacOS.c -o build/temp.macosx-10.4-x86_64-2.7-2.7.10/Mac/Modules/MacOS.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:01,912 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modu/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythongcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gal -L. -o build/lib.macosx-10.4-x86_64-2.7/MacOS.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:01,914 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modu/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythongcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gal -L. -o build/lib.macosx-10.4-x86_64-2.7/MacOS.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:02,017 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/MacOS.o -L/usr/local/libbuilding 'Nav' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:02,017 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/localaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/Nav.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/Nav.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:02,315 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/gp/tmp-toolshed-mtdP5qHBA/Python -L/usr/local/lib -L. -o build/lib.macoework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:02,324 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/gp/tmp-toolshed-mtdP5qHBA/Python -L/usr/local/lib -L. -o build/lib.macoework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:02,372 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modu86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHd-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:02,426 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tm-2.7.10/Mac/Modules/Nav.osx-10.4-x86_64-2.7/Nav.so -frambuilding 'OSATerminology' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:02,426 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxal/include -I/galaxydir/golshed-mtdP5qHBA/Python-2.7.10/abase/tmp/tmp-toolshed-mtdP5qHBA/Pythonmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modu86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHd-declarations 127.0.0.1 - - [18/Nov/2017:17:03:02 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:02,837 y/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/localaxy/database/tmp/tmp-toInclude -I/galaxydir/galaxy/dat-2.7.10 -c /galaxydir/galaxy/database/tles/OSATerminology.c -o build/temp.macosx-10.4-xBA/Python-2.7.10/Mac/Modules/OSATerminology.o -Wno-deprecategcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gallocal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/OSATerminology.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:02,837 on tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:02,837 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdInclude -I./Include -I/us/tmp-toolshed-mtdP5qHBA/Python--mtdP5qHBA/Python-2.7.10 -c /galaxydir/module.c -o build/temp.macosx-10.4-x86_64-2.7/gano-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:03,194 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/OSATerminology.o -L/usr/building 'icglue' extensigcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/icgluelaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/icgluemodule.o -Wgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtd-2.7/icglue.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:03,252 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/OSATerminology.o -L/usr/building 'icglue' extensigcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/icgluelaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/icgluemodule.o -Wgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtd-2.7/icglue.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:03,252 P5qHBA/Python-2.7.10/Mac/Modules/icgluemodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64building '_AE' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:03,252 on-2.7.10/Mac/Modules/ae tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:03,252 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.s install_environment.STDOUT DEBUG 2017-11-18 17:03:03,822 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ae/_AEmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ae/_AEmodule.o -Wno-deprecated-declarationp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ae/_AEmodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_AE.so -framework Carbonbuilding '_AH' extension install_environment.STDOUT DEBUG 2017-11-18 17:03:03,823 on-2.7.10/Mac/Modules/ah tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:03,869 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tm tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:03,870 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ae/_AEmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ae/_AEmodule.o -Wno-deprecated-declarationp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ae/_AEmodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_AE.so -framework Carbonbuilding '_AH' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:03,870 on-2.7.10/Mac/Modules/ah tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:03,871 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tAHmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tdule.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:04,198 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ah/_mp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ah/_AHmogcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galcal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_AH.so -framework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:04,251 install_environment.STDOUT DEBUG 2017-11-18 17:03:04,252 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/app tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,279 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ah/_mp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ah/_AHmogcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galcal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_AH.so -framework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:04,379 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Py/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4odule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_App.so -fbuilding '_CarbonEvt' extension install_environment.STDOUT DEBUG 2017-11-18 17:03:04,379 on-2.7.10/Mac/Modules/carbonevt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,379 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/app tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,379 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ah/_AHmodule.o -L/usr/lobuilding '_App' extensioncreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Mac/Modules/app/_Appmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galax.10/Mac/Modules/app/_Appmodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,380 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/app/_Appmramework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,380 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Py/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4odule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_App.so -fbuilding '_CarbonEvt' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,380 on-2.7.10/Mac/Modules/carbonevt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,380 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/carbonevt/_CarbonEvtmodule.c -o build/temp.macosx-10.4- -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:04,457 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/carbonevt/_CarbonEvtmodule.ogcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4/_CarbonEvtmodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.k Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,482 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/carbonevt/_CarbonEvtmodule.ogcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4/_CarbonEvtmodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.k Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:04,507 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tCmmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tdule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,587 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/carbonevt7/_CarbonEvt.so -frameworbuilding '_Cm' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,587 on-2.7.10/Mac/Modules/cm tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,587 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tCmmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tdule.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:04,970 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cm/_Cmmodule.o -L/usr/locreating build/temp.macos install_environment.STDOUT DEBUG 2017-11-18 17:03:04,970 4-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ctl/_Ctlmodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,992 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cm/_mp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cm/_Cmmogcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galcal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Cm.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,993 building '_Ctl' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,993 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cm/_Cmmodule.o -L/usr/locreating build/temp.macos tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:04,993 4-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ctl/_Ctlmodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:05,096 x-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ctlgcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ctl/_Ctlmodule.c -o build/temp.macosx-10.4-x86_6gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modubon install_environment.STDOUT DEBUG 2017-11-18 17:03:05,097 les/ctl/_Ctlmodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Ctl.so -framework Carbuilding '_Dlg' extensioncreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/dlg/_Dlgmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/dlg/_Dlgmodule.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:05,292 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmPython-2.7.10/Mac/Modules/dlg/_Dlgmodule.o -L/usr/local/creating build/temp.macosx-10.4-x86_64-gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwr.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/inclutabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Macmp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/drag/_Dragmodgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/ModuCarbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:05,301 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/dlg tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:05,301 les/ctl/_Ctlmodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Ctl.so -framework Carbuilding '_Dlg' extensioncreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/dlg/_Dlgmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/dlg/_Dlgmodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:05,301 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pp/tmp-toolshed-mtdP5qHBA/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Dlg.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:05,301 building '_Drag' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:05,301 2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/drag tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:05,302 apv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7de -I/galaxydir/galaxy/da/database/tmp/tmp-toolshed-mtdP/Modules/drag/_Dragmodule.c -o build/teule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:05,302 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmPython-2.7.10/Mac/Modules/dlg/_Dlgmodule.o -L/usr/local/creating build/temp.macosx-10.4-x86_64-gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwr.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/inclutabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Macmp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/drag/_Dragmodgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/ModuCarbon install_environment.STDOUT DEBUG 2017-11-18 17:03:05,342 install_environment.STDOUT DEBUG 2017-11-18 17:03:05,343 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/evt install_environment.STDOUT DEBUG 2017-11-18 17:03:05,467 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Pp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modulr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Evt.so building '_File' extension install_environment.STDOUT DEBUG 2017-11-18 17:03:05,467 on-2.7.10/Mac/Modules/file tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:05,508 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/evt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:05,508 les/drag/_Dragmodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Drag.so -framework building '_Evt' extensioncreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Mac/Modules/evt/_Evtmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/evt/_Evtmodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:05,509 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmes/evt/_Evtmodule.o -L/us-framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:05,509 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Pp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modulr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Evt.so building '_File' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:05,509 on-2.7.10/Mac/Modules/file tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:05,509 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-t/_Filemodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databa/_Filemodule.o -Wno-deprecated-declarations 127.0.0.1 - - [18/Nov/2017:17:03:05 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:03:06,010 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/filese/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/filegcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_File.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:06,027 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/filese/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/filegcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_File.so -framework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:06,069 ion install_environment.STDOUT DEBUG 2017-11-18 17:03:06,069 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/folder install_environment.STDOUT DEBUG 2017-11-18 17:03:06,070 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/folder/_Foldermodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/folder/_Foldermodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:06,128 ion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:06,128 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/folder tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:06,129 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/folder/_Foldermodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/folder/_Foldermodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:06,545 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/file/_Filemodule.o -L/usbuilding '_Folder' extenscreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBU-I. -IInclude -I./Include -I/usr/local/include -gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4oldermodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Folder.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:06,545 building '_Fm' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:06,545 x-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/fm tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:06,545 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdInclude -I./Include -I/us/tmp-toolshed-mtdP5qHBA/Python--mtdP5qHBA/Python-2.7.10 -c /galaxydir/module.c -o build/temp.macosx-10.4-x86_64-2.7/gano-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:06,860 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/folder/_Fcreating build/temp.macosgcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/fm/_Fmlaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/fm/_Fmmodule.o -Wgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtd-2.7/_Fm.so -framework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:06,914 n install_environment.STDOUT DEBUG 2017-11-18 17:03:06,914 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/help tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:06,950 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/folder/_Fcreating build/temp.macosgcc -fno-strict-aliasing -g -O2P5qHBA/Python-2.7.10/Mac/Include -I. -Ir/local/include -I/galaxydir/galaxy/database/tmp2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshedgalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/fm/_Fmlaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/fm/_Fmmodule.o -Wgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtd-2.7/_Fm.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:06,951 n tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:06,951 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/help tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:06,951 P5qHBA/Python-2.7.10/Mac/Modules/fm/_Fmmodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64building '_Help' extensiocreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Mac/Modules/help/_Helpmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/gal.7.10/Mac/Modules/help/_Helpmodule.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:06,995 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Paxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/help/_Helb -L. -o build/lib.macosx-10.4-x86_64-2.7/_Help.so -framework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:07,052 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-t_Icnmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databasecnmodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,054 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Paxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/help/_Helb -L. -o build/lib.macosx-10.4-x86_64-2.7/_Help.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,054 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmpmodule.o -L/usr/local/libuilding '_Icn' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,055 on-2.7.10/Mac/Modules/icn tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,055 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-t_Icnmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databasecnmodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,155 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/icn//tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/icn/_Igcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gallocal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Icn.so -framework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:07,190 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/icn/_Icnmodule.o -L/usr/creating build/temp.macosarbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,259 building '_IBCarbon' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,259 x-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ibcgcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ibcarbon/_IBCarbon.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ibcarbon/_IBCarbon.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,259 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/icn/_Icnmodule.o -L/usr/creating build/temp.macosarbon install_environment.STDOUT DEBUG 2017-11-18 17:03:07,324 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ibcarbon/_IBCarbon.o -L/usr/local/lib -L. -o builcreating build/temp.macost tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,364 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmd/lib.macosx-10.4-x86_64-2.7/_IBCarbon.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,364 building '_List' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,365 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/ibcarbon/_IBCarbon.o -L/usr/local/lib -L. -o builcreating build/temp.macost tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,365 x-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/lisgcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/list/_Listmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/list/_Listmodule.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:07,406 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmlib.macosx-10.4-x86_64-2.7/_List.so -framework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:07,457 n install_environment.STDOUT DEBUG 2017-11-18 17:03:07,457 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/menu tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,469 gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmlib.macosx-10.4-x86_64-2.7/_List.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,469 n tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,469 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/menu tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,470 p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/list/_Listmodule.o -L/usr/local/lib -L. -o build/building '_Menu' extensiocreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Mac/Modules/menu/_Menumodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/gal.7.10/Mac/Modules/menu/_Menumodule.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:07,554 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Paxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4umodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Menu.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,573 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Paxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4umodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Menu.so -framework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:07,607 n install_environment.STDOUT DEBUG 2017-11-18 17:03:07,607 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/mlte tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,677 n tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,677 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/mlte tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,678 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/menu/_Menbuilding '_Mlte' extensiocreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Mac/Modules/mlte/_Mltemodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/gal.7.10/Mac/Modules/mlte/_Mltemodule.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:07,686 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Paxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4emodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Mlte.so -framework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:07,738 install_environment.STDOUT DEBUG 2017-11-18 17:03:07,738 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/osa tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,783 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Paxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4emodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Mlte.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,883 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/osa tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:07,883 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/mlte/_Mltbuilding '_OSA' extensioncreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Mac/Modules/osa/_OSAmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galax.10/Mac/Modules/osa/_OSAmodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:08,189 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/osa/_OSAmramework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:08,209 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Py/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4odule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_OSA.so -fbuilding '_Res' extension install_environment.STDOUT DEBUG 2017-11-18 17:03:08,209 on-2.7.10/Mac/Modules/res tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:08,292 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Py/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4odule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_OSA.so -fbuilding '_Res' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:08,294 on-2.7.10/Mac/Modules/res tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:08,296 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-t_Resmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databaseesmodule.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:08,696 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/res//tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/res/_Rgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gallocal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Res.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:08,712 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/res//tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/res/_Rgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/gallocal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Res.so -framework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:08,755 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing s 127.0.0.1 - - [18/Nov/2017:17:03:08 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:08,817 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/res/_Resmodule.o -L/usr/building '_Qd' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:08,817 on-2.7.10/Mac/Modules/qd tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:08,817 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing s tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,122 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/qd/_Qdmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/qd/_Qdmodule.o -Wno-deprecated-declarationgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modu install_environment.STDOUT DEBUG 2017-11-18 17:03:09,175 les/qd/_Qdmodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Qd.so -framework Carbonbuilding '_Qdoffs' extenscreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Mac/Modules/qdoffs/_Qdoffsmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydiron-2.7.10/Mac/Modules/qdoffs/_Qdoffsmodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,223 ion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,223 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/qdoffs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,223 les/qd/_Qdmodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Qd.so -framework Carbonbuilding '_Qdoffs' extenscreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Mac/Modules/qdoffs/_Qdoffsmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydiron-2.7.10/Mac/Modules/qdoffs/_Qdoffsmodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,532 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/P/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4doffsmodule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Qdoffs.so -framework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:09,578 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/qdoffs/_Qcreating build/temp.macosap tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,636 building '_Scrap' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,637 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/qdoffs/_Qcreating build/temp.macosap tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,637 x-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/scrgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tp/_Scrapmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/datarap/_Scrapmodule.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:09,658 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/scrabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/scgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galusr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Scrap.so -framework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:09,710 install_environment.STDOUT DEBUG 2017-11-18 17:03:09,710 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/snd tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,739 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/scrabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/scgcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galusr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Scrap.so -framework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:09,834 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Py/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4odule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Snd.so -fbuilding '_TE' extension install_environment.STDOUT DEBUG 2017-11-18 17:03:09,834 on-2.7.10/Mac/Modules/te tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,843 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/snd tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,843 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/scrap/_Scrapmodule.o -L/building '_Snd' extensioncreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Mac/Modules/snd/_Sndmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galax.10/Mac/Modules/snd/_Sndmodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,843 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/snd/_Sndmramework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,843 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Py/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4odule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Snd.so -fbuilding '_TE' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,843 on-2.7.10/Mac/Modules/te tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,843 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tTEmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tdule.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:09,912 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/te/_mp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/te/_TEmogcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galcal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_TE.so -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:09,948 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/te/_mp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/te/_TEmogcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galcal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_TE.so -framework Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:09,963 install_environment.STDOUT DEBUG 2017-11-18 17:03:09,963 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/win install_environment.STDOUT DEBUG 2017-11-18 17:03:10,093 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Py/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4odule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Win.so -fbuilding '_Launch' extension install_environment.STDOUT DEBUG 2017-11-18 17:03:10,094 on-2.7.10/Mac/Modules/launch tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:10,160 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/win tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:10,165 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/te/_TEmodule.o -L/usr/lobuilding '_Win' extensioncreating build/temp.macosx-10.4gcc -fno-strict-aliasing -g -O2 -DNDEBUython-2.7.10/Mac/Include -I. -IInclude -I./IncluI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythoalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxython-2.7.10/Mac/Modules/win/_Winmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galax.10/Mac/Modules/win/_Winmodule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:10,165 -x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/win/_Winmramework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:10,165 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pde -I/usr/local/include -n-2.7.10/Include -I/galaxydir/gy/database/tmp/tmp-toolshed-mtdP5qHBA/Py/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4odule.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Win.so -fbuilding '_Launch' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:10,165 on-2.7.10/Mac/Modules/launch tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:10,165 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tch/_Launchmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/dalaunch/_Launchmodule.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:10,503 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/launtabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galL/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Launch.so -framework ApplicationServices install_environment.STDOUT DEBUG 2017-11-18 17:03:10,562 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tCGmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tdule.o -Wno-deprecated-declarations tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:10,577 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/launtabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galL/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Launch.so -framework ApplicationServices tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:10,577 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/launch/_Launchmodule.o -building '_CG' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:10,577 on-2.7.10/Mac/Modules/cg tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:10,577 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tCGmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tdule.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:11,078 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cg/_CGmodule.o -L/usr/lobuilding '_Qt' extension install_environment.STDOUT DEBUG 2017-11-18 17:03:11,078 on-2.7.10/Mac/Modules/qt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,091 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cg/_mp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cg/_CGmogcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galcal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_CG.so -framework ApplicationServices tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,091 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/cg/_CGmodule.o -L/usr/lobuilding '_Qt' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,091 on-2.7.10/Mac/Modules/qt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,091 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythgcc -fno-strict-aliasing ed-mtdP5qHBA/Python-2.7.10/Mac//Include -I/usr/local/include -I/galaxylshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-tQtmodule.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tdule.o -Wno-deprecated-declarations install_environment.STDOUT DEBUG 2017-11-18 17:03:11,160 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/qt/_mp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/qt/_Qtmogcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galcal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Qt.so -framework QuickTime -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,195 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/galaxydir/galaxy/database/tmp/tmp-toolshInclude -I. -IInclude -I.dir/galaxy/database/tmp/tmp-tooir/galaxy/database/tmp/tmp-toolshed-mtdoolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/qt/_mp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/qt/_Qtmogcc -bundle -undefined dynamic_lookup build/temp.macosx-10.4-x86_64-2.7/galcal/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_Qt.so -framework QuickTime -framework Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,196 ld: warning: ignoring file /System/Library/Frameworks//QuickTime.framework/QuickTime, file was built for i386 which is not the architecture being linked (x86_64): /System/Library/Frameworks//QuickTime.framework/QuickTime install_environment.STDOUT DEBUG 2017-11-18 17:03:11,219 sion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,301 sion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,301 axydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Modules/qt/_Qtmodule.o -L/usr/lobuilding '_tkinter' extengcc -fno-strict-aliasing -g -O2.framework/Headers -I/System/Library/Frrsions/Current/PrivateHeaders -I/System/Library/ -I/System/Library/Frameworks/Tk.framework/Versions/Current/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Inclde -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir//galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_tkinter.c -o build/temp.macosx-10.4-x86_6dules/_tkinter.o -framework Tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,301 clang: warning: -framework Tk: 'linker' input unused tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,407 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_tkinter.c:1178:38: warning: incompatible pointer types passing 'Py_UNICODE *' (aka 'unsigned int *') to parameter of type 'const Tcl_UniChar *' (aka 'const unsigned short *') [-Wincompatible-pointer-types] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,407 return Tcl_NewUnicodeObj(inbuf, size); tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,407 ^~~~~ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,407 /System/Library/Frameworks/Tcl.framework/Headers/tclDecls.h:2238:55: note: passing argument to parameter 'unicode' here tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,407 EXTERN Tcl_Obj * Tcl_NewUnicodeObj(CONST Tcl_UniChar *unicode, tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,407 ^ 127.0.0.1 - - [18/Nov/2017:17:03:11 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:03:11,884 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DWITH_APPINIT=1 -I/System/Library/Frameworks/Tclameworks/Tcl.framework/VeFrameworks/Tk.framework/HeadersPrivateHeaders -I/usr/X11R6/include -I/ude -I. -IInclude -I./Include -I/usr/local/inclugalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c 4-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mogcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DWITH_APPINersions/Current/PrivateHeaders -I/System/Library/Frameworks/Tk.framework/Headers -I/System/Library/Frameworks/Tk.framevateHeaders -I/usr/X11R6/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/tkappinit.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/tkappinit.o -framework Tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,926 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DWITH_APPINIT=1 -I/System/Library/Frameworks/Tclameworks/Tcl.framework/VeFrameworks/Tk.framework/HeadersPrivateHeaders -I/usr/X11R6/include -I/ude -I. -IInclude -I./Include -I/usr/local/inclugalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c 4-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mogcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DWITH_APPINersions/Current/PrivateHeaders -I/System/Library/Frameworks/Tk.framework/Headers -I/System/Library/Frameworks/Tk.framevateHeaders -I/usr/X11R6/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/tkappinit.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/tkappinit.o -framework Tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,926 1 warning generated. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:11,926 clang: warning: -framework Tk: 'linker' input unused tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:12,030 IT=1 -I/System/Library/Frameworks/Tcl.framework/Headers -I/System/Library/Frameworks/Tcl.framework/Vwork/Versions/Current/Prigcc -bundle -undefined dynamic_-2.7.10/Modules/_tkinter.o build/temp.maxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBit.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2. Tk install_environment.STDOUT DEBUG 2017-11-18 17:03:12,052 lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythonacosx-10.4-x86_64-2.7/galA/Python-2.7.10/Modules/tkappin7/_tkinter.so -framework Tcl -frameworkbuilding '_ctypes' extension install_environment.STDOUT DEBUG 2017-11-18 17:03:12,053 on-2.7.10/Modules/_ctypes/darwin install_environment.STDOUT DEBUG 2017-11-18 17:03:12,053 x-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypescreating build/temp.macos/libffi_osx/x86 install_environment.STDOUT DEBUG 2017-11-18 17:03:12,054 x-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypesgcc -fno-strict-aliasing se/tmp/tmp-toolshed-mtdP5qHBA/P-I/galaxydir/galaxy/database/tmp/tmp-toModules/_ctypes/libffi_osx/include -I/galaxydir/HBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IIydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/ga7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/_ctmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/_ctypes.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:12,131 lookup build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythonacosx-10.4-x86_64-2.7/galA/Python-2.7.10/Modules/tkappin7/_tkinter.so -framework Tcl -frameworkbuilding '_ctypes' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:12,131 on-2.7.10/Modules/_ctypes/darwin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:12,131 creating build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pythcreating build/temp.macos/libffi_osx tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:12,131 x-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypescreating build/temp.macos/libffi_osx/x86 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:12,131 x-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypescreating build/temp.macos/libffi_osx/powerpc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:12,131 x-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypesgcc -fno-strict-aliasing se/tmp/tmp-toolshed-mtdP5qHBA/P-I/galaxydir/galaxy/database/tmp/tmp-toModules/_ctypes/libffi_osx/include -I/galaxydir/HBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IIydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/ga7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/_ctmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/_ctypes.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:12,847 -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -I/galaxydir/galaxy/databaython-2.7.10/Mac/Include olshed-mtdP5qHBA/Python-2.7.10/galaxy/database/tmp/tmp-toolshed-mtdP5qnclude -I./Include -I/usr/local/include -I/galaxlaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.types.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/dagalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/include -I/galaxydir/galaxy/databaqHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/callbacks.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/callbacks.o -DMACOSX install_environment.STDOUT DEBUG 2017-11-18 17:03:12,942 rwin -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/se/tmp/tmp-toolshed-mtdP5I/galaxydir/galaxy/database/tmpython-2.7.10/Mac/Include -I/galaxydir/g-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_e/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/lsr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pylshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-xydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/callproc.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:12,950 rwin -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/se/tmp/tmp-toolshed-mtdP5I/galaxydir/galaxy/database/tmpython-2.7.10/Mac/Include -I/galaxydir/g-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_e/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/lsr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pylshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-xydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/callproc.o -DMACOSX install_environment.STDOUT DEBUG 2017-11-18 17:03:13,157 rwin -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/se/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/stgdict.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/stgdict.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:13,258 rwin -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/se/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/stgdict.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/stgdict.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:13,360 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -/tmp-toolshed-mtdP5qHBA/Palaxy/database/tmp/tmp-toolshedosx/include -I/galaxydir/galaxy/databasibffi_osx/powerpc -I. -IInclude -I./Include -I/uthon-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-too2.7.10/Modules/_ctypes/callproc.c -o build/temp.macosx-10.4-x86_64-2.7/galagcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/dagalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/include -I/galaxydir/galaxy/databagcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mt.10/Modules/_ctypes/libffi_osx/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/cfield.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/cfield.o -DMACOSX install_environment.STDOUT DEBUG 2017-11-18 17:03:13,634 dP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7I/galaxydir/galaxy/databahon-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/malloc_closure.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/malloc_closure.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:13,668 dP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7I/galaxydir/galaxy/databahon-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/malloc_closure.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/malloc_closure.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:13,772 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -se/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pytgcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -I/galaxydir/galaxytoolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/darwin/dlfcn_simple.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/darwin/dlfcn_simple.o -DMACOSX install_environment.STDOUT DEBUG 2017-11-18 17:03:13,778 /database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-I/galaxydir/galaxy/databa/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/ffi.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/ffi.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:13,874 /database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-I/galaxydir/galaxy/databa/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/ffi.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/ffi.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:13,874 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -se/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/databasegcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mt.10/Modules/_ctypes/libffi_osx/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/x86/darwin64.S -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/x86/darwin64.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:13,874 /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/ffi.c:107:1: warning: unused function 'struct_on_stack' [-Wunused-function] tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:13,874 struct_on_stack( tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:13,874 ^ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:13,874 1 warning generated. install_environment.STDOUT DEBUG 2017-11-18 17:03:13,924 dP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7I/galaxydir/galaxy/databaibffi_osx/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/databaseI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp--2.7.10/Modules/_ctypes/libffi_osx/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/x86/x86-ffi_darwin.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2./x86/x86-ffi_darwin.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:13,976 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -se/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/l/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/x86/x86-darwin.S -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/x86/x86-darwin.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:13,976 dP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7I/galaxydir/galaxy/databaibffi_osx/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/databaseI/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp--2.7.10/Modules/_ctypes/libffi_osx/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/x86/x86-ffi_darwin.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2./x86/x86-ffi_darwin.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:13,976 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -toolshed-mtdP5qHBA/Python7.10/Modules/_ctypes/libffi_osxgcc -fno-strict-aliasing -g -O2 -DNDEBUlshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/x86/x86-ffi64.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/x86/x86-ffi64.o -DMACOSX install_environment.STDOUT DEBUG 2017-11-18 17:03:14,122 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -I/galaxydir/galaxy/database/tmp/tmp-tooI/galaxydir/galaxy/databaqHBA/Python-2.7.10/Mac/Include p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/alaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qerpc -I. -IInclude -I./Include -I/usr/local/include -I/galax0/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2./Modules/_ctypes/libffi_osx/powerpc/ppc-darwin.S -o build/temp.macosx-10.4-x86_64-2.7/galaxydippc-darwin.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,178 G -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -I/galaxydir/galaxy/database/tmp/tmp-tooI/galaxydir/galaxy/databaqHBA/Python-2.7.10/Mac/Include p/tmp-toolshed-mtdP5qHBA/Python-2.7.10/alaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qerpc -I. -IInclude -I./Include -I/usr/local/include -I/galax0/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2./Modules/_ctypes/libffi_osx/powerpc/ppc-darwin.S -o build/temp.macosx-10.4-x86_64-2.7/galaxydippc-darwin.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,178 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -se/tmp/tmp-toolshed-mtdP5-I/galaxydir/galaxy/database/tmModules/_ctypes/libffi_osx/include -I/gHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.17.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10r/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -I/galaxydir/galaxytoolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc/ppc-darwin_closure.S -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc/ppc-darwin_closure.o -DMACOSX install_environment.STDOUT DEBUG 2017-11-18 17:03:14,191 /database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-I/galaxydir/galaxy/databahon-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc/ppc-ffi_darwin.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc/ppc-ffi_darwin.o -DMACOSX install_environment.STDOUT DEBUG 2017-11-18 17:03:14,257 /database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-ctypes/libffi_osx/powerpcthon-2.7.10 -c /galaxydir/galaxlibffi_osx/powerpc/ppc64-darwin_closuregcc -bundle -undefined dynamic_lookup build/tempctypes/_ctypes.o build/temp.macosx-10.4-x86_64-2.7/galaxydirtoolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/callbacks.o build/temp.macalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/callproc.o build/temp./database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/stgdict.o build/temp.macosx-10.4-x86_64-2.7/galaxydthon-2.7.10/Modules/_ctypes/cfield.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_laxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/darwin/dlfcn_simple.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/x86/darwin64.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/e/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/x86/x86-ffi_darwin.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/x86/x86-ffi64.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/d4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc/ppc-darwin_closure.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc/ppc-ffi_darwin.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toctypes.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,283 /database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-I/galaxydir/galaxy/databahon-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 -c /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc/ppc-ffi_darwin.c -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc/ppc-ffi_darwin.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,285 gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -se/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pytgcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I_ctypes/darwin -I/galaxydir/galaxytoolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ -I. -IInclude -I./Include -I/usr/local/include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Include -I/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pyy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc/ppc64-darwin_closure.S -o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/.o -DMACOSX tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,285 /database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Mac/Include -I/galaxydir/galaxy/database/tmp/tmp-ctypes/libffi_osx/powerpcthon-2.7.10 -c /galaxydir/galaxlibffi_osx/powerpc/ppc64-darwin_closuregcc -bundle -undefined dynamic_lookup build/tempctypes/_ctypes.o build/temp.macosx-10.4-x86_64-2.7/galaxydirtoolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/callbacks.o build/temp.macalaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/callproc.o build/temp./database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/stgdict.o build/temp.macosx-10.4-x86_64-2.7/galaxydthon-2.7.10/Modules/_ctypes/cfield.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_laxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/darwin/dlfcn_simple.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/x86/darwin64.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/e/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/x86/x86-ffi_darwin.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/x86/x86-ffi64.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/d4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc/ppc-darwin_closure.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc/ppc-ffi_darwin.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toctypes.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,286 ld: warning: could not create compact unwind for _ffi_call_unix64: does not use RBP or RSP based frame install_environment.STDOUT DEBUG 2017-11-18 17:03:14,304 Python build finished, but the necessary bits to build these modules were not found: install_environment.STDOUT DEBUG 2017-11-18 17:03:14,307 copying and adjusting /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Tools/scricopying and adjusting /ga-2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:14,308 copying and adjusting /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Tools/scri-2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:14,309 r/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Lib/smtpd.py -> build/scripts-2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:14,309 changing mode of build/scripts-2.7/pydoc from 644 to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:14,309 changing mode of build/scripts-2.7/idle from 644 to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:14,309 changing mode of build/scripts-2.7/2to3 from 644 to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:14,309 changing mode of build/scripts-2.7/smtpd.py from 644 to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:14,323 /usr/bin/install -c -m 644 ./Tools/gdb/libpython.py python.exe-gdb.py install_environment.STDOUT DEBUG 2017-11-18 17:03:14,376 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin install_environment.STDOUT DEBUG 2017-11-18 17:03:14,379 pendencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib install_environment.STDOUT DEBUG 2017-11-18 17:03:14,382 pendencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:14,386 if test -n "" ; then \ install_environment.STDOUT DEBUG 2017-11-18 17:03:14,386 _2_7/8b09fe018cac/bin; \ install_environment.STDOUT DEBUG 2017-11-18 17:03:14,386 /usr/bin/install -c -m 555 libpython2.7.dylib /galaxydir/galaxy/database/dependencies/python/2.7/ if test libpython2.7.d (cd /galaxydir/galaxy/databthon2.7.dylib) \ install_environment.STDOUT DEBUG 2017-11-18 17:03:14,387 fi; \ install_environment.STDOUT DEBUG 2017-11-18 17:03:14,387 fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,390 .macosx-10.4-x86_64-2.7/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_/galaxy/database/tmp/tmp-osx-10.4-x86_64-2.7/galaxydir/gmacosx-10.4-x86_64-2.7/galaxydir/galaxyir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Pyctypes/malloc_closure.o build/temp.macosx-10.4-x86_64-2.7/ga5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/ffi.o build/temp.macosx-10.4_ctypes/libffi_osx/x86/x86-darwin.o build/temp.macosx-10.4-x86_64-2.7/galaxydir/galaxy/databasatabase/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc/ppc-darwin.o build/temp.macosx-10.olshed-mtdP5qHBA/Python-2.7.10/Modules/_ctypes/libffi_osx/powerpc/ppc64-darwin_closure.o -L/usr/local/lib -L. -o build/lib.macosx-10.4-x86_64-2.7/_ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,390 _bsddb _ssl dl tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,390 gdbm imageop linuxaudiodev tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,391 ossaudiodev spwd sunaudiodev tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,391 To find the necessary bits, look in setup.py in detect_modules() for the module's name. install_environment.STDOUT DEBUG 2017-11-18 17:03:14,466 running build_ext tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,493 running build_scripts tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,493 Python build finished, but the necessary bits to build these modules were not found: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,493 creating build/scripts-2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,494 pts/pydoc -> build/scripts-2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,494 copying and adjusting /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Tools/scricopying and adjusting /ga-2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,494 copying and adjusting /galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Tools/scri-2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,494 r/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Lib/smtpd.py -> build/scripts-2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,494 changing mode of build/scripts-2.7/pydoc from 644 to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,494 changing mode of build/scripts-2.7/idle from 644 to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,494 changing mode of build/scripts-2.7/2to3 from 644 to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,494 changing mode of build/scripts-2.7/smtpd.py from 644 to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,494 /usr/bin/install -c -m 644 ./Tools/gdb/libpython.py python.exe-gdb.py tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,494 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,494 pendencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,495 pendencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,495 laxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10/Tools/scripts/idle -> build/scriptspts/2to3 -> build/scriptscopying and adjusting /galaxydiCreating directory /galaxydir/galaxy/daCreating directory /galaxydir/galaxy/database/de/usr/bin/install -c python.exe /galaxydir/galaxy/database/deif test -f libpython2.7.dylib; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,495 if test -n "" ; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,495 _2_7/8b09fe018cac/bin; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,495 /usr/bin/install -c -m 555 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python else \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,495 iuc/package_python_2_7/8b09fe018cac/lib/libpython2.7.dylib; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,495 ylib != libpython2.7.dylib; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,495 /usr/bin/install -c -m 555 libpython2.7.dylib /galaxydir/galaxy/database/dependencies/python/2.7/ if test libpython2.7.d (cd /galaxydir/galaxy/databthon2.7.dylib) \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,495 ase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib; ln -sf libpython2.7.dylib libpy fi \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,495 fi; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,495 else true; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,496 fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,496 running build tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,496 running build_ext install_environment.STDOUT DEBUG 2017-11-18 17:03:14,639 install_environment.STDOUT DEBUG 2017-11-18 17:03:14,657 Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0Creating directory /galaxk install_environment.STDOUT DEBUG 2017-11-18 17:03:14,662 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tCreating directory /galaxk/test/test_tkinter install_environment.STDOUT DEBUG 2017-11-18 17:03:14,670 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tCreating directory /galaxpackages install_environment.STDOUT DEBUG 2017-11-18 17:03:14,675 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:14,683 alaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/audiodCreating directory /galaxcapath install_environment.STDOUT DEBUG 2017-11-18 17:03:14,692 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/Creating directory /galaxcjkencodings install_environment.STDOUT DEBUG 2017-11-18 17:03:14,701 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/Creating directory /galaxxmltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,701 building dbm using ndbm tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,701 Python build finished, but the necessary bits to build these modules were not found: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,701 _bsddb _ssl dl tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,702 gdbm imageop linuxaudiodev tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,702 ossaudiodev spwd sunaudiodev tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,702 To find the necessary bits, look in setup.py in detect_modules() for the module's name. install_environment.STDOUT DEBUG 2017-11-18 17:03:14,709 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/Creating directory /galaxsubprocessdata install_environment.STDOUT DEBUG 2017-11-18 17:03:14,720 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/Creating directory /galaxings install_environment.STDOUT DEBUG 2017-11-18 17:03:14,729 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/compiCreating directory /galaxot install_environment.STDOUT DEBUG 2017-11-18 17:03:14,738 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/emailCreating directory /galax/mime install_environment.STDOUT DEBUG 2017-11-18 17:03:14,748 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/emailCreating directory /galax/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:14,757 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ensurCreating directory /galaxepip/_bundled install_environment.STDOUT DEBUG 2017-11-18 17:03:14,761 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/json install_environment.STDOUT DEBUG 2017-11-18 17:03:14,765 alaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/json/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:14,769 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/sqlite3 install_environment.STDOUT DEBUG 2017-11-18 17:03:14,773 pendencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/sqlite3/test install_environment.STDOUT DEBUG 2017-11-18 17:03:14,776 ython/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/logging install_environment.STDOUT DEBUG 2017-11-18 17:03:14,780 ackage_python_2_7/8b09fe018cac/lib/python2.7/bsddb install_environment.STDOUT DEBUG 2017-11-18 17:03:14,782 b09fe018cac/lib/python2.7/bsddb/test install_environment.STDOUT DEBUG 2017-11-18 17:03:14,786 7/importlib install_environment.STDOUT DEBUG 2017-11-18 17:03:14,800 Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0Creating directory /galaxo3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:14,810 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2tCreating directory /galaxo3/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:14,819 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2tCreating directory /galaxo3/tests/data/fixers install_environment.STDOUT DEBUG 2017-11-18 17:03:14,829 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2tCreating directory /galaxs install_environment.STDOUT DEBUG 2017-11-18 17:03:14,835 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ctypeCreating directory /galaxs/macholib install_environment.STDOUT DEBUG 2017-11-18 17:03:14,844 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelCreating directory /galaxib/Icons install_environment.STDOUT DEBUG 2017-11-18 17:03:14,860 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelCreating directory /galax18cac/lib/python2.7/distutils/command install_environment.STDOUT DEBUG 2017-11-18 17:03:14,867 18cac/lib/python2.7/xml install_environment.STDOUT DEBUG 2017-11-18 17:03:14,878 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/dCreating directory /galaxtree install_environment.STDOUT DEBUG 2017-11-18 17:03:14,880 Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0arsers install_environment.STDOUT DEBUG 2017-11-18 17:03:14,883 alaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/sax install_environment.STDOUT DEBUG 2017-11-18 17:03:14,889 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/multiprocessing install_environment.STDOUT DEBUG 2017-11-18 17:03:14,894 pendencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/multiprocessing/dummy install_environment.STDOUT DEBUG 2017-11-18 17:03:14,899 ython/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest install_environment.STDOUT DEBUG 2017-11-18 17:03:14,904 ackage_python_2_7/8b09fe018cac/lib/python2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,909 running build_scripts tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,909 18cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,909 Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0Creating directory /galaxk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,909 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tCreating directory /galaxk/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,910 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tCreating directory /galaxk/test/test_tkinter tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,910 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tCreating directory /galaxk/test/test_ttk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,912 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tCreating directory /galaxpackages tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,912 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,912 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-Creating directory /galaxCreating directory /galaxydir/gata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,912 alaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/audiodCreating directory /galaxcapath tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,912 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/Creating directory /galaxdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,912 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/Creating directory /galaxcjkencodings install_environment.STDOUT DEBUG 2017-11-18 17:03:14,912 b09fe018cac/lib/python2.7/curses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,913 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/Creating directory /galaxdecimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,913 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/Creating directory /galaxxmltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,913 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/Creating directory /galaximghdrdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,913 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/Creating directory /galaxsubprocessdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,913 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/Creating directory /galaxtracedmodules tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,913 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/Creating directory /galaxings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,913 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodCreating directory /galaxler tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,914 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/compiCreating directory /galaxot tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,914 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hotshCreating directory /galax tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,914 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/emailCreating directory /galax/mime tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,914 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/emailCreating directory /galax/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,914 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/emailCreating directory /galax/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,914 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/emailCreating directory /galaxepip tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,914 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ensurCreating directory /galaxepip/_bundled tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,914 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/json tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,914 alaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,914 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/sqlite3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,914 pendencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/sqlite3/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,915 ython/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/logging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,915 ackage_python_2_7/8b09fe018cac/lib/python2.7/bsddb tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,915 b09fe018cac/lib/python2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,915 7/importlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,915 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ensurCreating directory /galaxCreating directory /galaxydir/gCreating directory /galaxydir/galaxy/daCreating directory /galaxydir/galaxy/database/deCreating directory /galaxydir/galaxy/database/dependencies/pCreating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pCreating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/wsgiref tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,915 18cac/lib/python2.7/lib2to3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,915 Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0Creating directory /galaxo3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,915 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2tCreating directory /galaxo3/pgen2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,915 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2tCreating directory /galaxo3/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,915 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2tCreating directory /galaxo3/tests/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,915 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2tCreating directory /galaxo3/tests/data/fixers tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,916 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2tCreating directory /galaxo3/tests/data/fixers/myfixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,916 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2tCreating directory /galaxs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,916 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ctypeCreating directory /galaxs/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,916 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ctypeCreating directory /galaxs/macholib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,916 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ctypeCreating directory /galaxib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,916 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelCreating directory /galaxib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,916 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelCreating directory /galaxib/idle_test install_environment.STDOUT DEBUG 2017-11-18 17:03:14,920 7/pydoc_data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,920 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,920 Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,921 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelCreating directory /galax18cac/lib/python2.7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,921 18cac/lib/python2.7/xml tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,921 Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0Creating directory /galaxom tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,921 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/dCreating directory /galaxtree tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,921 Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0arsers tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,921 alaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/sax 127.0.0.1 - - [18/Nov/2017:17:03:14 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,923 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/multiprocessing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,923 pendencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/multiprocessing/dummy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,923 ython/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,925 ackage_python_2_7/8b09fe018cac/lib/python2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,925 b09fe018cac/lib/python2.7/curses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:14,925 7/pydoc_data install_environment.STDOUT DEBUG 2017-11-18 17:03:14,936 Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0Creating directory /galaxmac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:14,951 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-Creating directory /galaxmac/lib-scriptpackages/_builtinCreating directory /galaxydir/galaxy/dapackages/CodeWarrior install_environment.STDOUT DEBUG 2017-11-18 17:03:14,957 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat- install_environment.STDOUT DEBUG 2017-11-18 17:03:14,971 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptCreating directory /galaxmac/lib-scriptpackages/NetscapeCreating directory /galaxydir/galaxy/dapackages/StdSuites install_environment.STDOUT DEBUG 2017-11-18 17:03:14,974 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-ents install_environment.STDOUT DEBUG 2017-11-18 17:03:14,998 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-script/usr/bin/install -c -m 648b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,009 4 ./Lib/Bastion.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,019 4 ./Lib/ConfigParser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,029 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/e18cac/lib/python2.7/xml/pCreating directory /galaxydir/gCreating directory /galaxydir/galaxy/daCreating directory /galaxydir/galaxy/database/deCreating directory /galaxydir/galaxy/database/dependencies/pCreating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pCreating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-darwin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,029 18cac/lib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,029 Creating directory /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0Creating directory /galaxmac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,029 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-Creating directory /galaxmac/lib-scriptpackages tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,029 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-Suites tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,030 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-Creating directory /galaxmac/lib-scriptpackages/_builtinCreating directory /galaxydir/galaxy/dapackages/CodeWarrior tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,030 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat- tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,030 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptCreating directory /galaxmac/lib-scriptpackages/ExplorerCreating directory /galaxydir/galaxy/dapackages/Finder tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,030 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat- tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,030 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptCreating directory /galaxmac/lib-scriptpackages/NetscapeCreating directory /galaxydir/galaxy/dapackages/StdSuites tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,030 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-ents tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,030 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptCreating directory /galaxmac/lib-scriptpackages/SystemEvCreating directory /galaxydir/galaxy/dapackages/Terminal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,030 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-script/usr/bin/install -c -m 648b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,030 4 ./Lib/BaseHTTPServer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,031 4 ./Lib/Bastion.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,031 4 ./Lib/CGIHTTPServer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 6409fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,031 4 ./Lib/ConfigParser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,031 4 ./Lib/Cookie.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,031 4 ./Lib/HTMLParser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,035 4 ./Lib/DocXMLRPCServer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64/usr/bin/install -c -m 644 ./Liac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,046 4 ./Lib/Queue.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,057 4 ./Lib/SimpleXMLRPCServer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_/usr/bin/install -c -m 6409fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,064 4 ./Lib/StringIO.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,071 4 ./Lib/UserList.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c ./Libc/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,078 4 ./Lib/_LWPCookieJar.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,084 4 ./Lib/__future__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 648b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,094 4 ./Lib/_abcoll.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 6409fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,102 4 ./Lib/_pyio.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64e018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,109 4 ./Lib/_threading_local.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/usr/bin/install -c -m 649fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,115 4 ./Lib/abc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64ac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,122 4 ./Lib/antigravity.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 648cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,130 4 ./Lib/argparse.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64c/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,136 4 ./Lib/DocXMLRPCServer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64/usr/bin/install -c -m 644 ./Liac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,137 b/MimeWriter.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,137 4 ./Lib/Queue.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,137 4 ./Lib/SimpleHTTPServer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,137 4 ./Lib/SimpleXMLRPCServer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_/usr/bin/install -c -m 6409fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,137 4 ./Lib/asynchat.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,137 4 ./Lib/SocketServer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,137 4 ./Lib/StringIO.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/UserDict.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/UserList.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c ./Libc/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 /UserString.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/_LWPCookieJar.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/_MozillaCookieJar.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/usr/bin/install -c -m 64fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/__future__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 648b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/__phello__.foo.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/_abcoll.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 6409fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/_osx_support.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/_pyio.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/_strptime.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/_threading_local.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/usr/bin/install -c -m 649fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/_weakrefset.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64c/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/abc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64ac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/aifc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 649fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/antigravity.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/anydbm.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/argparse.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64c/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,138 4 ./Lib/ast.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,139 4 ./Lib/asynchat.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,143 4 ./Lib/atexit.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,151 /base64.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64c/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,159 4 ./Lib/binhex.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 648cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,165 /cProfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,171 /cgi.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 64cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,177 4 ./Lib/chunk.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64c/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,186 4 ./Lib/code.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 648cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,195 4 ./Lib/codeop.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 649fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,204 4 ./Lib/colorsys.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,211 4 ./Lib/compileall.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,216 4 ./Lib/cookielib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64ac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,222 4 ./Lib/copy_reg.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64c/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,230 4 ./Lib/dbhash.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 6418cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,238 4 ./Lib/difflib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,241 4 ./Lib/asyncore.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,241 4 ./Lib/atexit.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,241 4 ./Lib/audiodev.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c ./Libb/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,241 /base64.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64c/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,242 4 ./Lib/bdb.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,242 4 ./Lib/binhex.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,242 4 ./Lib/bisect.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c ./Liblib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,242 /cProfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,242 4 ./Lib/calendar.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c ./Libython2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,242 /cgi.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 64cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,242 4 ./Lib/cgitb.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,242 4 ./Lib/chunk.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64c/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,242 4 ./Lib/cmd.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64ac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,242 4 ./Lib/code.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/codecs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/codeop.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 649fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/collections.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/colorsys.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/commands.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/compileall.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/contextlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/cookielib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64ac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/copy.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/copy_reg.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64c/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/csv.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/dbhash.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/decimal.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/difflib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,243 4 ./Lib/dircache.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64c/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,248 4 ./Lib/dis.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018caackage_python_2_7/8b09fe0/usr/bin/install -c -m 644 ./Lilib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,257 4 ./Lib/dummy_thread.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,268 4 ./Lib/filecmp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/package_python_2_7/8b09f/usr/bin/install -c -m 644 ./Lilib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,276 4 ./Lib/formatter.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,281 4 ./Lib/fractions.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 648cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,284 /usr/bin/install -c -m 644 ./Lib/functools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuce018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,303 b/genericpath.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64ackage_python_2_7/8b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,309 4 ./Lib/glob.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64ac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,318 4 ./Lib/hashlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,327 4 ./Lib/hmac.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 648b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,333 4 ./Lib/htmllib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 6418cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,341 4 ./Lib/ihooks.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,346 /usr/bin/install -c -m 644 ./Lib/doctest.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/p18cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,346 4 ./Lib/dis.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018caackage_python_2_7/8b09fe0/usr/bin/install -c -m 644 ./Lilib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,346 b/dumbdbm.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 6409fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,346 4 ./Lib/dummy_thread.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,346 4 ./Lib/dummy_threading.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,346 /usr/bin/install -c -m 644 ./Lib/fileinput.py /galaxydir/galaxy/database/dependencies/python/2.7/iuce018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,346 4 ./Lib/filecmp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/package_python_2_7/8b09f/usr/bin/install -c -m 644 ./Lilib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,347 b/fnmatch.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,347 4 ./Lib/formatter.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,347 4 ./Lib/fpformat.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,347 4 ./Lib/fractions.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,347 /usr/bin/install -c -m 644 ./Lib/functools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuce018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,347 4 ./Lib/ftplib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/package_python_2_7/8b09f/usr/bin/install -c -m 644 ./Licac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,347 4 ./Lib/getopt.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,348 /usr/bin/install -c -m 644 ./Lib/getpass.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,348 b/genericpath.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64ackage_python_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,348 /usr/bin/install -c -m 644 ./Lib/gettext.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/p/usr/bin/install -c -m 64ac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,348 4 ./Lib/glob.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64ac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,348 4 ./Lib/gzip.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,349 4 ./Lib/hashlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,349 4 ./Lib/heapq.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64ac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,349 4 ./Lib/hmac.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 648b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,349 4 ./Lib/imghdr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,349 4 ./Lib/htmlentitydefs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,349 4 ./Lib/htmllib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,349 4 ./Lib/httplib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,349 4 ./Lib/ihooks.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,350 4 ./Lib/imaplib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,350 4 ./Lib/imghdr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 6418cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,359 4 ./Lib/inspect.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,367 /keyword.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64e018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,375 4 ./Lib/locale.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 6418cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,392 4 ./Lib/macurl2path.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64ackage_python_2_7/8b09fe018cac//usr/bin/install -c -m 644 ./Lib/markupython2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,406 4 ./Lib/md5.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,412 4 ./Lib/mimetools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64e018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,418 /mimify.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 6409fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,424 4 ./Lib/multifile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,430 4 ./Lib/netrc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64c/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,438 4 ./Lib/nntplib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 648cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,444 4 ./Lib/nturl2path.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 6418cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,452 4 ./Lib/opcode.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,454 4 ./Lib/imputil.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,454 4 ./Lib/inspect.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,454 4 ./Lib/io.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c ./Libib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,454 /keyword.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,455 4 ./Lib/linecache.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,455 4 ./Lib/locale.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,455 4 ./Lib/macpath.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 649fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,455 4 ./Lib/mailbox.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,455 /usr/bin/install -c -m 644 ./Lib/mailcap.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/plib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,455 4 ./Lib/macurl2path.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64ackage_python_2_7/8b09fe018cac//usr/bin/install -c -m 644 ./Lib/markupython2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,455 base.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 64c/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,455 4 ./Lib/md5.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,456 4 ./Lib/mhlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,456 4 ./Lib/mimetools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,456 4 ./Lib/mimetypes.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c ./Libb/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,456 /mimify.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 6409fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,456 4 ./Lib/modulefinder.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,457 4 ./Lib/multifile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,457 4 ./Lib/mutex.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,457 4 ./Lib/netrc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64c/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,457 4 ./Lib/new.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,457 4 ./Lib/nntplib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,457 4 ./Lib/ntpath.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,457 4 ./Lib/nturl2path.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,457 4 ./Lib/numbers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,457 4 ./Lib/opcode.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,457 4 ./Lib/optparse.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,465 4 ./Lib/os.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cacc/package_python_2_7/8b09/usr/bin/install -c ./Lib/pdb.p.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,471 4 ./Lib/pickle.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 649fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,476 4 ./Lib/pipes.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 6418cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,484 /platform.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,492 4 ./Lib/popen2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 648cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,499 4 ./Lib/posixfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64e018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,508 4 ./Lib/pprint.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c ./Libib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,516 4 ./Lib/pstats.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64c/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,523 4 ./Lib/py_compile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 648cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,532 /pydoc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c ./Libb/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,542 4 ./Lib/random.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,550 4 ./Lib/repr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,558 4 ./Lib/rfc822.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 649fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,560 /usr/bin/install -c -m 644 ./Lib/os2emxpath.py /galaxydir/galaxy/database/dependencies/python/2.7/iufe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,560 4 ./Lib/os.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cacc/package_python_2_7/8b09/usr/bin/install -c ./Lib/pdb.p.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,560 y /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,560 4 ./Lib/pickle.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 649fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,560 4 ./Lib/pickletools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,561 4 ./Lib/pipes.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,561 4 ./Lib/pkgutil.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c ./Liblib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,561 /platform.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,561 4 ./Lib/plistlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,561 4 ./Lib/popen2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,561 4 ./Lib/poplib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,561 4 ./Lib/posixfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,562 4 ./Lib/posixpath.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,562 4 ./Lib/pprint.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c ./Libib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,562 /profile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,562 4 ./Lib/pstats.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64c/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,562 4 ./Lib/pty.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,562 4 ./Lib/py_compile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,562 4 ./Lib/pyclbr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c ./Lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,562 /pydoc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c ./Libb/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,562 /quopri.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,562 4 ./Lib/random.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,563 4 ./Lib/re.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64ac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,563 4 ./Lib/repr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,563 4 ./Lib/rexec.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,563 4 ./Lib/rfc822.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 649fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,563 4 ./Lib/rlcompleter.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 649fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,570 4 ./Lib/robotparser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0kage_python_2_7/8b09fe018/usr/bin/install -c -m 644 ./Lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,576 4 ./Lib/sets.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 6418cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,581 4 ./Lib/sha.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 648cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,589 4 ./Lib/shlex.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 648cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,592 4 ./Lib/site.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,599 /usr/bin/install -c ./Lib/smtpd.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,603 alaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,607 xydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,611 /database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,614 cies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,617 /2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,620 n_2_7/8b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,630 /usr/bin/install -c -m 644 ./Lib/ssl.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa/usr/bin/install -c -m 64ac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,638 4 ./Lib/statvfs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 648cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,645 4 ./Lib/stringold.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,650 4 ./Lib/struct.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,658 4 ./Lib/sunau.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,664 /symbol.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,669 /usr/bin/install -c -m 644 ./Lib/runpy.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/paccac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,669 4 ./Lib/robotparser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0kage_python_2_7/8b09fe018/usr/bin/install -c -m 644 ./Lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,670 b/sched.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64ac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,670 4 ./Lib/sets.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,670 4 ./Lib/sgmllib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64c/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,670 4 ./Lib/sha.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,670 4 ./Lib/shelve.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,670 4 ./Lib/shlex.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,670 4 ./Lib/site.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,671 /usr/bin/install -c ./Lib/smtpd.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,671 alaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,671 xydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,671 /database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,671 cies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,671 /2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,671 n_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,671 4 ./Lib/shutil.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c ./Lib/smtplib.py /g/usr/bin/install -c -m 644 ./Lib/sndhdr.py /gala/usr/bin/install -c -m 644 ./Lib/socket.py /galaxydir/galaxy/usr/bin/install -c -m 644 ./Lib/sre.py /galaxydir/galaxy/database/dependen/usr/bin/install -c -m 644 ./Lib/sre_compile.py /galaxydir/galaxy/database/dependencies/python/usr/bin/install -c -m 644 ./Lib/sre_constants.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho/usr/bin/install -c -m 644 ./Lib/sre_parse.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,671 ge_python_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,671 /usr/bin/install -c -m 644 ./Lib/ssl.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa/usr/bin/install -c -m 64ac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,671 4 ./Lib/stat.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,672 4 ./Lib/statvfs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,672 4 ./Lib/string.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,672 4 ./Lib/stringold.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,672 4 ./Lib/stringprep.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,672 4 ./Lib/struct.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,672 4 ./Lib/subprocess.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,672 4 ./Lib/sunau.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,672 4 ./Lib/sunaudio.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c ./Libb/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,672 /symbol.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,672 4 ./Lib/symtable.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64e018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,678 4 ./Lib/sysconfig.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f_python_2_7/8b09fe018cac//usr/bin/install -c -m 644 ./Lilib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,686 4 ./Lib/telnetlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,694 4 ./Lib/textwrap.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64ac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,700 4 ./Lib/threading.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c ./Libb/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,706 4 ./Lib/toaiff.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,715 4 ./Lib/tokenize.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c ./Lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,726 4 ./Lib/traceback.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fge_python_2_7/8b09fe018ca/usr/bin/install -c -m 644 ./Lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,736 4 ./Lib/urllib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01ackage_python_2_7/8b09fe0/usr/bin/install -c -m 644 ./Li/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,743 4 ./Lib/user.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c ./Libthon2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,749 4 ./Lib/uuid.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,758 4 ./Lib/wave.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 6418cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,765 /webbrowser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,773 /usr/bin/install -c ./Lib/tabnanny.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagelib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,773 4 ./Lib/sysconfig.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f_python_2_7/8b09fe018cac//usr/bin/install -c -m 644 ./Lilib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,773 b/tarfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,774 4 ./Lib/telnetlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,774 4 ./Lib/tempfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,774 4 ./Lib/textwrap.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64ac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,774 4 ./Lib/this.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,774 4 ./Lib/threading.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c ./Libb/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,774 /timeit.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,774 4 ./Lib/toaiff.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,774 4 ./Lib/token.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,774 4 ./Lib/tokenize.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c ./Lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,774 /trace.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,774 /usr/bin/install -c -m 644 ./Lib/tty.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,775 4 ./Lib/traceback.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fge_python_2_7/8b09fe018ca/usr/bin/install -c -m 644 ./Lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,775 b/types.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,775 /usr/bin/install -c -m 644 ./Lib/urllib2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/p18cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,775 4 ./Lib/urllib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01ackage_python_2_7/8b09fe0/usr/bin/install -c -m 644 ./Li/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,775 b/urlparse.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64ac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,775 4 ./Lib/user.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c ./Libthon2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,775 /uu.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 64ac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,775 4 ./Lib/uuid.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,775 4 ./Lib/warnings.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64ac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,776 4 ./Lib/wave.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,776 4 ./Lib/weakref.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c ./Libc/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,776 /webbrowser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,776 4 ./Lib/whichdb.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 648cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,776 4 ./Lib/xdrlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 648cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,783 4 ./Lib/xmlrpclib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 6418cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,786 4 build/lib.macosx-10.4-x86_64-2.7/_sysconfigdata.py /galaxydir/galaxy/database/dependencies/python/fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,795 c /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 64b09fe018cac/lib/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:15,808 4 ./Lib/lib-tk/Canvas.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8k install_environment.STDOUT DEBUG 2017-11-18 17:03:15,815 /Dialog.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tk install_environment.STDOUT DEBUG 2017-11-18 17:03:15,826 /usr/bin/install -c -m 644 ./Lib/lib-tk/FileDialog.py /galaxydir/galaxy/database/dependencies/pythoniuc/package_python_2_7/8blib-tk install_environment.STDOUT DEBUG 2017-11-18 17:03:15,833 b/lib-tk/ScrolledText.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/lib-tk install_environment.STDOUT DEBUG 2017-11-18 17:03:15,846 4 ./Lib/lib-tk/Tix.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 644 ./Lib/lib-tk/Tkinter.2.7/lib-tk install_environment.STDOUT DEBUG 2017-11-18 17:03:15,849 4 ./Lib/lib-tk/tkColorChooser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/lib-tk install_environment.STDOUT DEBUG 2017-11-18 17:03:15,866 /tkCommonDialog.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0on/2.7/iuc/package_python/iuc/package_python_2_7/8b09fe0on/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 644 ./Lib/lib-tk/tkSimple/python2.7/lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,880 4 ./Lib/xdrlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 648cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,880 4 ./Lib/xmllib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64e018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,880 4 ./Lib/xmlrpclib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 6418cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,880 4 build/lib.macosx-10.4-x86_64-2.7/_sysconfigdata.py /galaxydir/galaxy/database/dependencies/python/fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,880 4 ./Lib/zipfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 642.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 644 ./Lib/pdb.do.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,880 c /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 64b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,880 4 ./Lib/lib-tk/Canvas.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8k tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,881 /Dialog.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,881 4 ./Lib/wsgiref.egg-info /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/lib-t/usr/bin/install -c -m 644 ./Lib/lib-tk/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,881 /usr/bin/install -c -m 644 ./Lib/lib-tk/FileDialog.py /galaxydir/galaxy/database/dependencies/pythoniuc/package_python_2_7/8blib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,881 /usr/bin/install -c -m 644 ./Lib/lib-tk/FixTk.py /galaxydir/galaxy/database/dependencies/python/2.7/09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib09fe018cac/lib/python2.7/lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,881 b/lib-tk/ScrolledText.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,881 4 ./Lib/lib-tk/SimpleDialog.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/usr/bin/install -c -m 64fe018cac/lib/python2.7/lib-tk install_environment.STDOUT DEBUG 2017-11-18 17:03:15,881 4 ./Lib/lib-tk/ttk.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/lib-t/usr/bin/install -c -m 644 ./Lib/lib-tklib/python2.7/lib-tk/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,881 4 ./Lib/lib-tk/Tkconstants.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,881 /usr/bin/install -c -m 644 ./Lib/lib-tk/Tkdnd.py /galaxydir/galaxy/database/dependencies/python/2.7//python2.7/lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,882 4 ./Lib/lib-tk/Tix.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 644 ./Lib/lib-tk/Tkinter.2.7/lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,882 4 ./Lib/lib-tk/tkColorChooser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,882 py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/lib-tk18cac/lib/python2.7/lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,882 /usr/bin/install -c -m 644 ./Lib/lib-tk/tkFileDialog.py /galaxydir/galaxy/database/dependencies/pyth_2_7/8b09fe018cac/lib/python2.7/lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,882 /usr/bin/install -c -m 644 ./Lib/lib-tk/tkFont.py /galaxydir/galaxy/database/dependencies/python/2.718cac/lib/python2.7/lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,882 /usr/bin/install -c -m 644 ./Lib/lib-tk/tkMessageBox.py /galaxydir/galaxy/database/dependencies/pythcac/lib/python2.7/lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,882 /tkCommonDialog.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0on/2.7/iuc/package_python/iuc/package_python_2_7/8b09fe0on/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 644 ./Lib/lib-tk/tkSimple/python2.7/lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,882 Dialog.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 64fe018cac/lib/python2.7/lib-tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,882 4 ./Lib/lib-tk/turtle.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8k tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,882 4 ./Lib/lib-tk/ttk.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/lib-t/usr/bin/install -c -m 644 ./Lib/lib-tklib/python2.7/lib-tk/test install_environment.STDOUT DEBUG 2017-11-18 17:03:15,885 4 ./Lib/lib-tk/test/runtktests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/lib-tk/test install_environment.STDOUT DEBUG 2017-11-18 17:03:15,897 /test/widget_tests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64package_python_2_7/8b09fe018cact/test_tkinter install_environment.STDOUT DEBUG 2017-11-18 17:03:15,902 b/lib-tk/test/test_tkinter/test_font.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/lib-tk/test/test_tkinte/usr/bin/install -c -m 644 ./Li2.7/iuc/package_python_2_7/8b09fe018cact/test_tkinter install_environment.STDOUT DEBUG 2017-11-18 17:03:15,909 b/lib-tk/test/test_tkinter/test_images.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pac2.7/lib-tk/test/test_tkin/usr/bin/install -c -m 644 ./Likage_python_2_7/8b09fe018cac/lib/pythonter install_environment.STDOUT DEBUG 2017-11-18 17:03:15,917 b/lib-tk/test/test_tkinter/test_text.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/lib-tk/test/test_tkinte/usr/bin/install -c -m 644 ./Lipackage_python_2_7/8b09fe018cac/lib/pytkinter install_environment.STDOUT DEBUG 2017-11-18 17:03:15,929 b/lib-tk/test/test_tkinter/test_widgets.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pan2.7/lib-tk/test/test_tki/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/lib-tk/test/test_ttk install_environment.STDOUT DEBUG 2017-11-18 17:03:15,932 /usr/bin/install -c -m 644 ./Lib/lib-tk/test/test_ttk/support.py /galaxydir/galaxy/database/dependenge_python_2_7/8b09fe018cat_ttk install_environment.STDOUT DEBUG 2017-11-18 17:03:15,945 /test/test_ttk/test_extensions.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytependencies/python/2.7/iufe018cac/lib/python2.7/lib-tk/t/usr/bin/install -c -m 644 ./Lib/lib-tk_7/8b09fe018cac/lib/python2.7/lib-tk/test/test_t/usr/bin/install -c -m 644 ./Lib/lib-tk/test/test_ttk/test_w/python2.7/lib-tk/test/test_ttk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,982 4 ./Lib/lib-tk/test/runtktests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/lib-tk/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,983 /test/README /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/lib-tkfe018cac/lib/python2.7/lib-tk/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,983 /test/widget_tests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64package_python_2_7/8b09fe018cact/test_tkinter tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,983 4 ./Lib/lib-tk/test/test_tkinter/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc//lib/python2.7/lib-tk/tes/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2.r tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,983 b/lib-tk/test/test_tkinter/test_font.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/lib-tk/test/test_tkinte/usr/bin/install -c -m 644 ./Li2.7/iuc/package_python_2_7/8b09fe018cact/test_tkinter tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,983 b/lib-tk/test/test_tkinter/test_geometry_managers.py /galaxydir/galaxy/database/dependencies/python//lib/python2.7/lib-tk/tes/usr/bin/install -c -m 644 ./Likage_python_2_7/8b09fe018cac/lib/pythonter tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,983 b/lib-tk/test/test_tkinter/test_images.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pac2.7/lib-tk/test/test_tkin/usr/bin/install -c -m 644 ./Likage_python_2_7/8b09fe018cac/lib/pythonter tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,983 b/lib-tk/test/test_tkinter/test_loadtk.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pac2.7/lib-tk/test/test_tkin/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2.r tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,984 b/lib-tk/test/test_tkinter/test_text.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/lib-tk/test/test_tkinte/usr/bin/install -c -m 644 ./Lipackage_python_2_7/8b09fe018cac/lib/pytkinter tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,984 b/lib-tk/test/test_tkinter/test_variables.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/hon2.7/lib-tk/test/test_t/usr/bin/install -c -m 644 ./Lickage_python_2_7/8b09fe018cac/lib/pythonter tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,984 b/lib-tk/test/test_tkinter/test_widgets.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pan2.7/lib-tk/test/test_tki/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/lib-tk/test/test_ttk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,984 /usr/bin/install -c -m 644 ./Lib/lib-tk/test/test_ttk/support.py /galaxydir/galaxy/database/dependenge_python_2_7/8b09fe018cat_ttk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,984 b/lib-tk/test/test_ttk/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pycies/python/2.7/iuc/packac/lib/python2.7/lib-tk/test/tes/usr/bin/install -c -m 644 ./Lib/lib-tkhon_2_7/8b09fe018cac/lib/python2.7/lib-tk/test/test_ttk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,984 /usr/bin/install -c -m 644 ./Lib/lib-tk/test/test_ttk/test_functions.py /galaxydir/galaxy/database/dc/package_python_2_7/8b09est/test_ttk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,984 /test/test_ttk/test_style.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2tk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,984 /test/test_ttk/test_extensions.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytependencies/python/2.7/iufe018cac/lib/python2.7/lib-tk/t/usr/bin/install -c -m 644 ./Lib/lib-tk_7/8b09fe018cac/lib/python2.7/lib-tk/test/test_t/usr/bin/install -c -m 644 ./Lib/lib-tk/test/test_ttk/test_w/python2.7/lib-tk/test/test_ttk tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,984 idgets.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/site-packages tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:15,984 /usr/bin/install -c -m 644 ./Lib/test/185test.db /galaxydir/galaxy/database/dependencies/python/2.7/09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:15,983 4 ./Lib/site-packages/README /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2iuc/package_python_2_7/8bpython/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:15,990 4 ./Lib/test/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8on/2.7/iuc/package_pythonhon2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:15,996 b/test/audiotest.au /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,005 4 ./Lib/test/autotest.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/b/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,009 4 ./Lib/test/bad_coding3.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st install_environment.STDOUT DEBUG 2017-11-18 17:03:16,018 adcert.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 6409fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,024 4 ./Lib/test/badsyntax_future3.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,038 adsyntax_future4.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/b018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,043 4 ./Lib/test/badsyntax_future7.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,052 adsyntax_future8.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/b018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,055 4 ./Lib/test/buffer_tests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est install_environment.STDOUT DEBUG 2017-11-18 17:03:16,061 fgparser.1 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,064 4 ./Lib/test/cmath_testcases.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,072 ests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 6409fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,075 4 ./Lib/test/doctest_aliases.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,085 ouble_const.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 649fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,089 4 ./Lib/site-packages/README /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2iuc/package_python_2_7/8bpython/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,089 /usr/bin/install -c -m 644 ./Lib/test/Sine-1000Hz-300ms.aif /galaxydir/galaxy/database/dependencies//usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,089 4 ./Lib/test/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8on/2.7/iuc/package_pythonhon2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,090 /usr/bin/install -c -m 644 ./Lib/test/_mock_backport.py /galaxydir/galaxy/database/dependencies/pyth_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Li018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,090 b/test/audiotest.au /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,090 4 ./Lib/test/audiotests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,090 4 ./Lib/test/bad_coding.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,091 4 ./Lib/test/autotest.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/b/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,091 4 ./Lib/test/bad_coding3.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,091 ad_coding2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/bb/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,091 adcert.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 6409fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,091 4 ./Lib/test/badsyntax_future3.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,091 4 ./Lib/test/badkey.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/b018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,091 4 ./Lib/test/badsyntax_future5.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,091 adsyntax_future4.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/b018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,092 4 ./Lib/test/badsyntax_future7.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,092 adsyntax_future6.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/b018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,092 4 ./Lib/test/badsyntax_future9.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,092 adsyntax_future8.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/b018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,092 4 ./Lib/test/buffer_tests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,092 adsyntax_nocaret.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/cb/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,092 fgparser.1 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,092 4 ./Lib/test/cmath_testcases.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,092 4 ./Lib/test/check_soundcard.vbs /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c ./Lib/test/curses_tython2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,092 ests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 6409fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,093 4 ./Lib/test/doctest_aliases.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,093 4 ./Lib/test/exception_hierarchy.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_thon/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,093 4 ./Lib/test/dh1024.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/dc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,093 ouble_const.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 649fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,093 4 ./Lib/test/empty.vbs /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,093 4 ./Lib/test/exception_hierarchy.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_thon/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,096 4 ./Lib/test/fork_wait.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ install_environment.STDOUT DEBUG 2017-11-18 17:03:16,102 ormatfloat_testcases.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,111 4 ./Lib/test/greyrgb.uue /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64ckage_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 644 ./Lib/test/ib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,114 4 ./Lib/test/infinite_reload.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,126 nspect_fodder.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/k8cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,136 4 ./Lib/test/keycert.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/kib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,141 4 ./Lib/test/keycert4.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ install_environment.STDOUT DEBUG 2017-11-18 17:03:16,152 ist_tests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/mcac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,156 4 ./Lib/test/mapping_tests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,166 ath_testcases.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/npython2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,170 4 ./Lib/test/nullbytecert.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,184 ullcert.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/pc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,195 4 ./Lib/test/fork_wait.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,195 /usr/bin/install -c -m 644 ./Lib/test/floating_points.txt /galaxydir/galaxy/database/dependencies/py/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/fb09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,195 ormatfloat_testcases.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,195 4 ./Lib/test/gdb_sample.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,195 4 ./Lib/test/https_svn_python_org_root.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/paib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,195 4 ./Lib/test/greyrgb.uue /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64ckage_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 644 ./Lib/test/ib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,195 4 ./Lib/test/infinite_reload.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,195 eee754.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/icac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,195 4 ./Lib/test/inspect_fodder2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,196 nspect_fodder.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/k8cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,196 eycert.passwd.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,196 4 ./Lib/test/keycert2.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,196 4 ./Lib/test/keycert.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/kib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,196 4 ./Lib/test/keycert4.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,196 eycert3.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/llib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,196 4 ./Lib/test/lock_tests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,197 ist_tests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/mcac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,197 4 ./Lib/test/mapping_tests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,197 ake_ssl_certs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/m8cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,197 4 ./Lib/test/mp_fork_bomb.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,197 ath_testcases.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/npython2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,197 4 ./Lib/test/nullbytecert.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,197 okia.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/nib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,197 4 ./Lib/test/outstanding_bugs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,197 ullcert.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/pc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,197 ickletester.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,197 4 ./Lib/test/pycacert.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,198 yclbr_input.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,199 4 ./Lib/test/profilee.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/p/usr/bin/install -c -m 644 ./Lib/test/pydoc_mod.2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,205 /usr/bin/install -c -m 644 ./Lib/test/pydocfodder.py /galaxydir/galaxy/database/dependencies/python/7/8b09fe018cac/lib/python/usr/bin/install -c ./Lib/test/b/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,210 4 ./Lib/test/randv2_32.pck /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t install_environment.STDOUT DEBUG 2017-11-18 17:03:16,216 andv2_64.pck /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 6409fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,223 /test/re_tests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c ./Lib8cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,227 4 ./Lib/test/relimport.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ install_environment.STDOUT DEBUG 2017-11-18 17:03:16,239 eperf.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/scac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,247 4 ./Lib/test/sample_doctest_no_docstrings.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/dencies/python/2.7/iuc/pa8cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,262 b/test/script_helper.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8bendencies/python/2.7/iuc/7/iuc/package_python_2_7/8b09fe/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 644 ./Lib/test/sha256.pem7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,273 4 ./Lib/test/sortperf.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/s8cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,284 4 ./Lib/test/ssl_key.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/sc/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,288 4 ./Lib/test/symlink_support.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,298 /usr/bin/install -c -m 644 ./Lib/test/test_MimeWriter.py /galaxydir/galaxy/database/dependencies/pyt8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lin_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,298 4 ./Lib/test/profilee.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/p/usr/bin/install -c -m 644 ./Lib/test/pydoc_mod.2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,298 py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/iuc/package_python_2_2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,299 /usr/bin/install -c -m 644 ./Lib/test/pydocfodder.py /galaxydir/galaxy/database/dependencies/python/7/8b09fe018cac/lib/python/usr/bin/install -c ./Lib/test/b/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,299 4 ./Lib/test/randv2_32.pck /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,299 pystone.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/rlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,299 andv2_64.pck /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 6409fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,299 4 ./Lib/test/randv3.pck /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c ./Lib8cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,299 /test/re_tests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c ./Lib8cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,299 4 ./Lib/test/relimport.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,299 /test/regrtest.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/rpython2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,299 4 ./Lib/test/revocation.crl /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,299 eperf.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/scac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,299 ample_doctest.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,299 4 ./Lib/test/sample_doctest_no_docstrings.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/dencies/python/2.7/iuc/pa8cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,300 /usr/bin/install -c -m 644 ./Lib/test/sample_doctest_no_doctests.py /galaxydir/galaxy/database/depenckage_python_2_7/8b09fe01/usr/bin/install -c -m 644 ./Li09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,300 /usr/bin/install -c -m 644 ./Lib/test/selfsigned_pythontestdotnet.pem /galaxydir/galaxy/database/deppackage_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,300 /usr/bin/install -c -m 644 ./Lib/test/seq_tests.py /galaxydir/galaxy/database/dependencies/python/2.018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,300 /usr/bin/install -c -m 644 ./Lib/test/sgml_input.html /galaxydir/galaxy/database/dependencies/pythonc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,300 b/test/script_helper.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8bendencies/python/2.7/iuc/7/iuc/package_python_2_7/8b09fe/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 644 ./Lib/test/sha256.pem7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,300 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,300 4 ./Lib/test/ssl_cert.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,300 4 ./Lib/test/sortperf.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/s8cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,300 sl_key.passwd.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,300 4 ./Lib/test/ssl_servers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,300 4 ./Lib/test/ssl_key.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/sc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,300 4 ./Lib/test/symlink_support.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,301 tring_tests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64hon/2.7/iuc/package_python_2_7/7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,301 /usr/bin/install -c -m 644 ./Lib/test/test_MimeWriter.py /galaxydir/galaxy/database/dependencies/pyt8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lin_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,302 4 ./Lib/test/test_StringIO.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,315 est___all__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,319 4 ./Lib/test/test__osx_support.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,346 est_abc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 642.7/iuc/package_python_2_7/8b097/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 644 ./Lib/test/test_al.py7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,361 /usr/bin/install -c -m 644 ./Lib/test/test_anydbm.py /galaxydir/galaxy/database/dependencies/python/7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lin/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 644 ./Lib/test/test_arrayn2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,370 4 ./Lib/test/test_ascii_formatd.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_py/iuc/package_python_2_7/8n/2.7/iuc/package_python_2_7/8btest install_environment.STDOUT DEBUG 2017-11-18 17:03:16,376 b/test/test_asyncore.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,384 /usr/bin/install -c -m 644 ./Lib/test/test_audioop.py /galaxydir/galaxy/database/dependencies/python_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,388 4 ./Lib/test/test_base64.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st install_environment.STDOUT DEBUG 2017-11-18 17:03:16,403 est_bastion.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 642.7/iuc/package_python_2_7/8b09st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,404 4 ./Lib/test/test_StringIO.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,404 b/test/test_SimpleHTTPServer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,404 4 ./Lib/test/test___future__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,404 est___all__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,405 4 ./Lib/test/test__osx_support.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,405 est__locale.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,405 4 ./Lib/test/test_abstract_numbers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,405 /usr/bin/install -c -m 644 ./Lib/test/test_aepack.py /galaxydir/galaxy/database/dependencies/python/fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,405 /usr/bin/install -c -m 644 ./Lib/test/test_aifc.py /galaxydir/galaxy/database/dependencies/python/2.ib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,405 est_abc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 642.7/iuc/package_python_2_7/8b097/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 644 ./Lib/test/test_al.py7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,405 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.2.7/iuc/package_python_2_2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,406 b/test/test_applesingle.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,406 /usr/bin/install -c -m 644 ./Lib/test/test_argparse.py /galaxydir/galaxy/database/dependencies/pythoac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,406 /usr/bin/install -c -m 644 ./Lib/test/test_anydbm.py /galaxydir/galaxy/database/dependencies/python/7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lin/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 644 ./Lib/test/test_arrayn2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,406 .py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,407 /usr/bin/install -c -m 644 ./Lib/test/test_ast.py /galaxydir/galaxy/database/dependencies/python/2.7b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,407 4 ./Lib/test/test_ascii_formatd.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_py/iuc/package_python_2_7/8n/2.7/iuc/package_python_2_7/8btest tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,408 /usr/bin/install -c -m 644 ./Lib/test/test_asynchat.py /galaxydir/galaxy/database/dependencies/pytho09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Li09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,408 b/test/test_asyncore.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,408 4 ./Lib/test/test_atexit.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/2.7/iuc/package_python_2n2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,408 /usr/bin/install -c -m 644 ./Lib/test/test_audioop.py /galaxydir/galaxy/database/dependencies/python_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,409 b/test/test_binascii.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,409 4 ./Lib/test/test_base64.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,409 b/test/test_augassign.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,410 4 ./Lib/test/test_bigaddrspace.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,410 est_bastion.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 642.7/iuc/package_python_2_7/8b09st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,410 b/test/test_binascii.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,413 /usr/bin/install -c -m 644 ./Lib/test/test_binhex.py /galaxydir/galaxy/database/dependencies/python//lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,415 /usr/bin/install -c -m 644 ./Lib/test/test_binop.py /galaxydir/galaxy/database/dependencies/python/2n2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,419 dir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,422 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,425 thon/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,428 python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,431 hon2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,445 /usr/bin/install -c -m 644 ./Lib/test/test_bufio.py /galaxydir/galaxy/database/dependencies/python/2/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,451 4 ./Lib/test/test_bz2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,457 4 ./Lib/test/test_call.py 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/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/t9fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,500 4 ./Lib/test/test_code.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//python/2.7/iuc/package_pb/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,510 /usr/bin/install -c -m 644 ./Lib/test/test_binhex.py /galaxydir/galaxy/database/dependencies/python//lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,510 /usr/bin/install -c -m 644 ./Lib/test/test_binop.py /galaxydir/galaxy/database/dependencies/python/2n2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,510 dir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,510 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,511 thon/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,511 b/test/test_codecencodings_cn.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/test/ton2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,511 python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,511 hon2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,511 /usr/bin/install -c -m 644 ./Lib/test/test_bigmem.py /galaxydir/galaxy/database/dependencies/python/fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Li2.7/iuc/package_python_2_7/8b09fe018cac.7/iuc/package_python_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/test/test_bisect.py /galaxy/usr/bin/install -c -m 644 ./Lib/test/test_bool.py /galaxydir/galaxy/databa/usr/bin/install -c -m 644 ./Lib/test/test_bsddb.py /galaxydir/galaxy/database/dependencies/py/usr/bin/install -c -m 644 ./Lib/test/test_bsddb185.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_/usr/bin/install -c -m 644 ./Lib/test/test_bsddb3.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/test/test_buffer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,511 .7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,511 4 ./Lib/test/test_builtin.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,511 /usr/bin/install -c -m 644 ./Lib/test/test_bufio.py /galaxydir/galaxy/database/dependencies/python/2/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,511 est_bytes.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,512 4 ./Lib/test/test_bz2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,512 4 ./Lib/test/test_calendar.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,512 4 ./Lib/test/test_call.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/7/iuc/package_python_2_7/7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,512 /usr/bin/install -c -m 644 ./Lib/test/test_capi.py /galaxydir/galaxy/database/dependencies/python/2.8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Li8cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,512 b/test/test_cd.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01on/2.7/iuc/package_pythonhon2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,512 /usr/bin/install -c -m 644 ./Lib/test/test_cfgparser.py /galaxydir/galaxy/database/dependencies/pyth_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Li18cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,512 b/test/test_cgi.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,512 4 ./Lib/test/test_charmapcodec.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt/usr/bin/install -c -m 6409fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,512 4 ./Lib/test/test_cl.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,512 4 ./Lib/test/test_cmath.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,512 4 ./Lib/test/test_class.py 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DEBUG 2017-11-18 17:03:16,644 est_cprofile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,648 4 ./Lib/test/test_ctypes.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st install_environment.STDOUT DEBUG 2017-11-18 17:03:16,658 est_curses.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,662 4 ./Lib/test/test_decimal.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est install_environment.STDOUT DEBUG 2017-11-18 17:03:16,671 est_decorators.py 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2017-11-18 17:03:16,841 /usr/bin/install -c -m 644 ./Lib/test/test_file.py /galaxydir/galaxy/database/dependencies/python/2.018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,847 4 ./Lib/test/test_extcall.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2.7/iuc/package_python_2_77/iuc/package_python_2_7/8b09fe2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 644 ./Lib/test/test_file_python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,851 4 ./Lib/test/test_filecmp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est install_environment.STDOUT DEBUG 2017-11-18 17:03:16,862 est_fileinput.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,865 4 ./Lib/test/test_fnmatch.py 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647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,945 4 ./Lib/test/test_getargs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,946 4 ./Lib/test/test_fnmatch.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,946 est_float.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,946 4 ./Lib/test/test_format.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,946 /usr/bin/install -c -m 644 ./Lib/test/test_fpformat.py /galaxydir/galaxy/database/dependencies/pythoac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,946 est_fork1.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/ten/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 644 ./Lib/test/test_fractython2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,946 4 ./Lib/test/test_frozen.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,946 ions.py 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,947 est_functools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,947 est_future1.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,947 4 ./Lib/test/test_future3.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,947 4 ./Lib/test/test_future2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,947 4 ./Lib/test/test_future5.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,947 est_future4.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/t9fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,947 est_future_builtins.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 6409fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,947 4 ./Lib/test/test_gc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,947 4 ./Lib/test/test_gdbm.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,947 4 ./Lib/test/test_gdb.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/t8cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,947 4 ./Lib/test/test_genericpath.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,947 est_generators.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:16,947 4 ./Lib/test/test_getargs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est install_environment.STDOUT DEBUG 2017-11-18 17:03:16,955 est_getargs2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,966 4 ./Lib/test/test_gl.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,968 4 ./Lib/test/test_grammar.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est install_environment.STDOUT DEBUG 2017-11-18 17:03:16,975 est_grp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,981 /usr/bin/install -c -m 644 ./Lib/test/test_hash.py /galaxydir/galaxy/database/dependencies/python/2.8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Li9fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:16,984 4 ./Lib/test/test_heapq.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t install_environment.STDOUT DEBUG 2017-11-18 17:03:16,997 est_hmac.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,000 4 ./Lib/test/test_htmlparser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,012 est_httplib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/tib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,016 4 ./Lib/test/test_imageop.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est install_environment.STDOUT DEBUG 2017-11-18 17:03:17,031 est_imaplib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,048 est_genexps.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,048 4 ./Lib/test/test_getopt.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,049 est_getargs2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,049 est_gettext.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 6409fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,049 4 ./Lib/test/test_glob.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,049 4 ./Lib/test/test_gl.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,049 4 ./Lib/test/test_grammar.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,049 est_global.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,049 est_grp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,050 4 ./Lib/test/test_gzip.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/7/iuc/package_python_2_7/7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,050 /usr/bin/install -c -m 644 ./Lib/test/test_hash.py /galaxydir/galaxy/database/dependencies/python/2.8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Li9fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,050 4 ./Lib/test/test_heapq.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,050 b/test/test_hashlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/tib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,050 4 ./Lib/test/test_hotshot.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,050 est_hmac.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,050 4 ./Lib/test/test_htmlparser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,050 est_htmllib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,050 4 ./Lib/test/test_httpservers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,050 est_httplib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/tib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,050 4 ./Lib/test/test_imageop.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,051 est_idle.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,051 4 ./Lib/test/test_imgfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,051 est_imaplib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,051 est_imghdr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,051 4 ./Lib/test/test_import.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st install_environment.STDOUT DEBUG 2017-11-18 17:03:17,049 4 ./Lib/test/test_imp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t18cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,056 4 ./Lib/test/test_importlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,069 est_index.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,072 4 ./Lib/test/test_int_literal.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,083 est_io.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/t8cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,086 4 ./Lib/test/test_iter.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ install_environment.STDOUT DEBUG 2017-11-18 17:03:17,096 est_iterlen.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/tib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,101 4 ./Lib/test/test_kqueue.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st install_environment.STDOUT DEBUG 2017-11-18 17:03:17,113 est_largefile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tcac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,117 4 ./Lib/test/test_linuxaudiodev.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,129 est_list.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,134 4 ./Lib/test/test_long.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ install_environment.STDOUT DEBUG 2017-11-18 17:03:17,148 est_long_future.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,153 4 ./Lib/test/test_macostools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,153 4 ./Lib/test/test_imp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t18cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,153 4 ./Lib/test/test_importlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,153 est_importhooks.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,153 4 ./Lib/test/test_inspect.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,153 est_index.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,153 4 ./Lib/test/test_int_literal.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,153 est_int.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/t/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,153 4 ./Lib/test/test_ioctl.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,154 est_io.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/t8cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,154 4 ./Lib/test/test_iter.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,154 est_isinstance.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,154 4 ./Lib/test/test_itertools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,154 est_iterlen.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/tib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,154 4 ./Lib/test/test_kqueue.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,154 est_json.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tcac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,154 4 ./Lib/test/test_lib2to3.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,154 est_largefile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tcac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,154 4 ./Lib/test/test_linuxaudiodev.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,154 est_linecache.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/test/tib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,154 4 ./Lib/test/test_locale.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,154 est_list.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,155 4 ./Lib/test/test_long.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,155 est_logging.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/t18cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,155 4 ./Lib/test/test_longexp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,155 est_long_future.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,155 4 ./Lib/test/test_macostools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,164 est_macpath.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,167 4 ./Lib/test/test_marshal.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est install_environment.STDOUT DEBUG 2017-11-18 17:03:17,174 est_math.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,178 4 ./Lib/test/test_memoryio.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,184 est_memoryview.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01.7/iuc/package_python_2_7.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,195 b/test/test_mimetools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,198 4 ./Lib/test/test_mmap.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ install_environment.STDOUT DEBUG 2017-11-18 17:03:17,214 est_module.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,218 4 ./Lib/test/test_multibytecodec.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,229 est_multibytecodec_support.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/t9fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,233 4 ./Lib/test/test_mutants.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est install_environment.STDOUT DEBUG 2017-11-18 17:03:17,246 est_mutex.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,256 est_macos.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,256 4 ./Lib/test/test_macurl2path.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,256 est_macpath.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,257 4 ./Lib/test/test_marshal.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,257 est_mailbox.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,257 est_math.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,257 4 ./Lib/test/test_memoryio.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,257 4 ./Lib/test/test_md5.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/t8cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,257 est_memoryview.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01.7/iuc/package_python_2_7.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,257 /usr/bin/install -c -m 644 ./Lib/test/test_mhlib.py /galaxydir/galaxy/database/dependencies/python/2/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,257 4 ./Lib/test/test_mimetypes.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,257 b/test/test_mimetools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,258 4 ./Lib/test/test_mmap.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,258 est_minidom.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,258 4 ./Lib/test/test_nis.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/te018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,258 4 ./Lib/test/test_modulefinder.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,258 est_module.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,258 4 ./Lib/test/test_multibytecodec.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,258 est_msilib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/test/t2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,258 4 ./Lib/test/test_multifile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,258 est_multibytecodec_support.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/t9fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,259 4 ./Lib/test/test_mutants.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,259 est_multiprocessing.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,259 4 ./Lib/test/test_netrc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,259 est_mutex.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,259 est_new.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,259 4 ./Lib/test/test_nntplib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,259 4 ./Lib/test/test_nis.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/te018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,263 4 ./Lib/test/test_ntpath.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st install_environment.STDOUT DEBUG 2017-11-18 17:03:17,273 est_old_mailbox.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,277 4 ./Lib/test/test_operator.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,284 est_optparse.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 6409fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,287 4 ./Lib/test/test_ossaudiodev.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,298 est_parser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64on/2.7/iuc/package_python_2_7/8/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,313 b/test/test_pep247.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,316 4 ./Lib/test/test_pep292.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st install_environment.STDOUT DEBUG 2017-11-18 17:03:17,326 est_pep352.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t18cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,331 4 ./Lib/test/test_pipes.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t install_environment.STDOUT DEBUG 2017-11-18 17:03:17,343 est_pkg.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,348 4 ./Lib/test/test_platform.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,359 4 ./Lib/test/test_ntpath.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,360 est_normalization.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t18cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,360 4 ./Lib/test/test_opcodes.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,360 est_old_mailbox.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,360 4 ./Lib/test/test_operator.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,360 est_openpty.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/tac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,360 est_optparse.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 6409fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,360 4 ./Lib/test/test_ossaudiodev.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,360 4 ./Lib/test/test_os.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,360 4 ./Lib/test/test_pdb.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,361 est_parser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64on/2.7/iuc/package_python_2_7/8/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,361 /usr/bin/install -c -m 644 ./Lib/test/test_peepholer.py /galaxydir/galaxy/database/dependencies/pythb09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Life018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,361 4 ./Lib/test/test_pep263.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,361 b/test/test_pep247.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,361 4 ./Lib/test/test_pep292.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,361 est_pep277.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,361 4 ./Lib/test/test_pickle.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,361 est_pep352.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t18cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,361 4 ./Lib/test/test_pipes.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,361 est_pickletools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,362 4 ./Lib/test/test_pkgimport.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,362 est_pkg.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,362 4 ./Lib/test/test_platform.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,362 est_pkgutil.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/tac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,362 4 ./Lib/test/test_poll.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ install_environment.STDOUT DEBUG 2017-11-18 17:03:17,363 est_plistlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,373 4 ./Lib/test/test_popen2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,385 /usr/bin/install -c -m 644 ./Lib/test/test_poplib.py /galaxydir/galaxy/database/dependencies/python/fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Li/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,394 /usr/bin/install -c -m 644 ./Lib/test/test_pprint.py /galaxydir/galaxy/database/dependencies/python/7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lie018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,400 4 ./Lib/test/test_profile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est install_environment.STDOUT DEBUG 2017-11-18 17:03:17,408 est_property.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 642.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,418 b/test/test_pty.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,422 4 ./Lib/test/test_py3kwarn.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,430 est_py_compile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 642.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,445 b/test/test_pydoc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,449 4 ./Lib/test/test_quopri.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st install_environment.STDOUT DEBUG 2017-11-18 17:03:17,458 est_random.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 6409fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,462 4 ./Lib/test/test_readline.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,465 est_plistlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,465 4 ./Lib/test/test_popen2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,465 est_popen.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 642.7/iuc/package_python_2_7/8b09st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,465 b/test/test_posix.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,466 /usr/bin/install -c -m 644 ./Lib/test/test_posixpath.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,466 /usr/bin/install -c -m 644 ./Lib/test/test_poplib.py /galaxydir/galaxy/database/dependencies/python/fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Li/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,466 /usr/bin/install -c -m 644 ./Lib/test/test_pow.py /galaxydir/galaxy/database/dependencies/python/2.72.7/iuc/package_python_2_2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,466 /usr/bin/install -c -m 644 ./Lib/test/test_pprint.py /galaxydir/galaxy/database/dependencies/python/7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lie018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,466 4 ./Lib/test/test_profile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,466 b/test/test_print.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,466 est_property.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 642.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,466 4 ./Lib/test/test_pstats.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Li18cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,467 b/test/test_pty.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,467 4 ./Lib/test/test_py3kwarn.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,467 4 ./Lib/test/test_pwd.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/t8cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,467 est_py_compile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 642.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,467 4 ./Lib/test/test_pyclbr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lie018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,467 4 ./Lib/test/test_pyexpat.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,467 b/test/test_pydoc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,467 4 ./Lib/test/test_quopri.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,467 est_queue.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,467 est_random.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 6409fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,467 4 ./Lib/test/test_readline.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,467 4 ./Lib/test/test_re.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/tib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,470 est_repr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/ln/2.7/iuc/package_python_on2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,480 b/test/test_rfc822.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/t18cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,483 4 ./Lib/test/test_robotparser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,490 est_runpy.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,498 4 ./Lib/test/test_scope.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t install_environment.STDOUT DEBUG 2017-11-18 17:03:17,508 est_scriptpackages.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,513 4 ./Lib/test/test_setcomps.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,523 est_sets.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,526 4 ./Lib/test/test_shelve.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st install_environment.STDOUT DEBUG 2017-11-18 17:03:17,541 est_shlex.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,546 4 ./Lib/test/test_site.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ install_environment.STDOUT DEBUG 2017-11-18 17:03:17,561 est_slice.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,565 4 ./Lib/test/test_socket.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,571 est_repr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/ln/2.7/iuc/package_python_on2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,571 /usr/bin/install -c -m 644 ./Lib/test/test_resource.py /galaxydir/galaxy/database/dependencies/pytho2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Life018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,571 est_socketserver.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,571 4 ./Lib/test/test_richcmp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,571 b/test/test_rfc822.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/t18cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,571 4 ./Lib/test/test_robotparser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,572 est_rlcompleter.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,572 est_runpy.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,572 4 ./Lib/test/test_scope.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,572 4 ./Lib/test/test_sax.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/tfe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,572 4 ./Lib/test/test_select.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,572 est_scriptpackages.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,572 4 ./Lib/test/test_setcomps.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,572 est_set.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/tib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,572 4 ./Lib/test/test_sgmllib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,572 est_sets.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,572 4 ./Lib/test/test_shelve.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,572 est_sha.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,572 4 ./Lib/test/test_shutil.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,573 est_shlex.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,573 4 ./Lib/test/test_site.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,573 est_signal.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,573 4 ./Lib/test/test_smtplib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,573 est_slice.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,573 4 ./Lib/test/test_socket.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,573 est_smtpnet.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,573 est_socketserver.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,577 4 ./Lib/test/test_sort.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ install_environment.STDOUT DEBUG 2017-11-18 17:03:17,587 est_spwd.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,592 4 ./Lib/test/test_startfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,600 est_stat.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,604 4 ./Lib/test/test_strftime.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,620 est_string.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,624 4 ./Lib/test/test_strptime.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,635 est_strtod.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/te018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,639 4 ./Lib/test/test_structseq.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,648 est_subprocess.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/t18cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,656 4 ./Lib/test/test_sundry.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/2.7/iuc/package_python_2n2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,667 b/test/test_symtable.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,670 4 ./Lib/test/test_sys_setprofile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,673 4 ./Lib/test/test_sort.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,674 4 ./Lib/test/test_softspace.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/tib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,674 4 ./Lib/test/test_sqlite.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,674 est_spwd.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,674 4 ./Lib/test/test_startfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,674 est_ssl.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/tib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,674 est_stat.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,674 4 ./Lib/test/test_strftime.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,674 4 ./Lib/test/test_str.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,674 4 ./Lib/test/test_stringprep.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,674 est_string.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,674 4 ./Lib/test/test_strptime.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,675 est_strop.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,675 4 ./Lib/test/test_struct.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,675 est_strtod.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/te018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,675 4 ./Lib/test/test_structseq.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,675 est_structmembers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/t8cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,675 4 ./Lib/test/test_sunau.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,675 est_subprocess.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/t18cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,675 est_sunaudiodev.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,675 4 ./Lib/test/test_sundry.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/2.7/iuc/package_python_2n2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,676 /usr/bin/install -c -m 644 ./Lib/test/test_support.py /galaxydir/galaxy/database/dependencies/python_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Li09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,676 4 ./Lib/test/test_syntax.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,676 b/test/test_symtable.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tb/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,676 4 ./Lib/test/test_sys_setprofile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,676 est_sys.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/test/t018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,681 est_sys_settrace.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,689 4 ./Lib/test/test_tcl.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,693 4 ./Lib/test/test_tempfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,702 est_textwrap.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t9fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,706 4 ./Lib/test/test_threadedtempfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,717 est_threading.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/test/te018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,720 4 ./Lib/test/test_time.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ install_environment.STDOUT DEBUG 2017-11-18 17:03:17,732 est_timeit.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/t/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,736 4 ./Lib/test/test_tokenize.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,752 est_tools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/tcac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,759 4 ./Lib/test/test_transformer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,772 est_ttk_guionly.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,776 4 ./Lib/test/test_typechecks.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,776 4 ./Lib/test/test_sysconfig.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,777 est_sys_settrace.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,777 est_tarfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,777 4 ./Lib/test/test_tcl.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,777 4 ./Lib/test/test_tempfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,777 4 ./Lib/test/test_telnetlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/tac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,778 4 ./Lib/test/test_thread.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,778 est_textwrap.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t9fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,778 4 ./Lib/test/test_threadedtempfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/test 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./Lib/test/test_time.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,779 est_threadsignals.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,779 4 ./Lib/test/test_timeout.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,779 est_timeit.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/t/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,779 4 ./Lib/test/test_tokenize.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,780 est_tk.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,780 4 ./Lib/test/test_trace.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,780 est_tools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/tcac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,780 4 ./Lib/test/test_transformer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,780 est_traceback.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/t18cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,780 4 ./Lib/test/test_ttk_textonly.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,780 est_ttk_guionly.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,780 4 ./Lib/test/test_typechecks.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,784 est_types.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,787 4 ./Lib/test/test_unary.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t install_environment.STDOUT DEBUG 2017-11-18 17:03:17,793 est_undocumented_details.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/2.7/iuc/package_python_2n2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,802 b/test/test_unicode_file.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_thon/2.7/iuc/package_pythn/2.7/iuc/package_python_2_7/8btest install_environment.STDOUT DEBUG 2017-11-18 17:03:17,808 b/test/test_univnewlines.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/python/2.7/iuc/package_pb/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,820 b/test/test_unpack.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,828 4 ./Lib/test/test_urllib2_localnet.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagehon/2.7/iuc/package_pythothon2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,838 b/test/test_urllibnet.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/tac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,841 4 ./Lib/test/test_userlist.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,849 est_userstring.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,854 /usr/bin/install -c -m 644 ./Lib/test/test_uuid.py /galaxydir/galaxy/database/dependencies/python/2. install_environment.STDOUT DEBUG 2017-11-18 17:03:17,866 est_wait3.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/tac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,870 4 ./Lib/test/test_wave.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,881 est_tuple.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,881 est_types.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,881 4 ./Lib/test/test_unary.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,881 4 ./Lib/test/test_ucn.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/t7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,881 est_undocumented_details.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/2.7/iuc/package_python_2n2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,881 /usr/bin/install -c -m 644 ./Lib/test/test_unicode.py /galaxydir/galaxy/database/dependencies/python_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Li7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,882 /usr/bin/install -c -m 644 ./Lib/test/test_unicodedata.py /galaxydir/galaxy/database/dependencies/pyon_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,882 b/test/test_unicode_file.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_thon/2.7/iuc/package_pythn/2.7/iuc/package_python_2_7/8btest tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,882 /usr/bin/install -c -m 644 ./Lib/test/test_unittest.py /galaxydir/galaxy/database/dependencies/pytho09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Li7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,882 b/test/test_univnewlines.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/python/2.7/iuc/package_pb/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,882 /usr/bin/install -c -m 644 ./Lib/test/test_univnewlines2k.py /galaxydir/galaxy/database/dependenciesython_2_7/8b09fe018cac/li/usr/bin/install -c -m 644 ./Life018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,882 4 ./Lib/test/test_urllib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,882 b/test/test_unpack.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,882 est_urllib2.py 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17:03:17,882 b/test/test_urllibnet.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/tac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,882 4 ./Lib/test/test_userlist.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,883 est_userdict.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/t8cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,883 est_userstring.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,883 /usr/bin/install -c -m 644 ./Lib/test/test_uuid.py /galaxydir/galaxy/database/dependencies/python/2. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,883 /usr/bin/install -c -m 644 ./Lib/test/test_uu.py /galaxydir/galaxy/database/dependencies/python/2.7/7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/tlib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,883 4 ./Lib/test/test_wait4.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,883 est_wait3.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/tac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,883 4 ./Lib/test/test_wave.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,883 est_warnings.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/tc/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,883 4 ./Lib/test/test_weakset.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,883 est_whichdb.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,888 est_weakref.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/t2.7/iuc/package_python_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/test/test_winsound.py /gala install_environment.STDOUT DEBUG 2017-11-18 17:03:17,895 4 ./Lib/test/test_with.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//2.7/iuc/package_python_2n2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,904 b/test/test_xdrlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/t18cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,907 4 ./Lib/test/test_xmllib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st install_environment.STDOUT DEBUG 2017-11-18 17:03:17,915 est_xmlrpc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,918 /usr/bin/install -c -m 644 ./Lib/test/test_xrange.py /galaxydir/galaxy/database/dependencies/python/7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,921 /usr/bin/install -c -m 644 ./Lib/test/test_zipfile.py /galaxydir/galaxy/database/dependencies/python9fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,938 est_zipfile64.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/t7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,950 7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,960 4 ./Lib/test/testimg.uue /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 644 ./Lib/test/testimgr.uue /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,966 /usr/bin/install -c -m 644 ./Lib/test/testrgb.uue /galaxydir/galaxy/database/dependencies/python/2.7/usr/bin/install -c -m 64/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,984 b/test/tf_inherit_check.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 644 ./Lib/test/thon/2.7/iuc/package_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 644 ./Lib/test/warning_tests.py /gala 127.0.0.1 - - [18/Nov/2017:17:03:17 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,988 /usr/bin/install -c -m 644 ./Lib/test/test_winreg.py /galaxydir/galaxy/database/dependencies/python/on2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,988 4 ./Lib/test/win_console_handler.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,988 est_weakref.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/t2.7/iuc/package_python_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/test/test_winsound.py /gala tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,989 xydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,989 4 ./Lib/test/test_with.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//2.7/iuc/package_python_2n2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,989 /usr/bin/install -c -m 644 ./Lib/test/test_wsgiref.py /galaxydir/galaxy/database/dependencies/python_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Life018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,989 4 ./Lib/test/test_xml_etree.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,990 b/test/test_xdrlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/t18cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,990 4 ./Lib/test/test_xmllib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,990 est_xml_etree_c.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/t/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,991 est_xmlrpc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,991 /usr/bin/install -c -m 644 ./Lib/test/test_xrange.py /galaxydir/galaxy/database/dependencies/python/7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,991 /usr/bin/install -c -m 644 ./Lib/test/test_zipfile.py /galaxydir/galaxy/database/dependencies/python9fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,991 4 ./Lib/test/test_xpickle.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_22.7/iuc/package_python_2_/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 644 ./Lib/test/tcac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,991 4 ./Lib/test/test_zipimport.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,991 est_zipimport_support.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,992 /usr/bin/install -c -m 644 ./Lib/test/test_zlib.py /galaxydir/galaxy/database/dependencies/python/2./usr/bin/install -c -m 644 ./Lib/test/testall.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,992 est_zipfile64.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/t7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,992 7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,992 4 ./Lib/test/testimg.uue /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 644 ./Lib/test/testimgr.uue /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,992 /usr/bin/install -c -m 644 ./Lib/test/testcodec.py /galaxydir/galaxy/database/dependencies/python/2./usr/bin/install -c -m 64b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,992 /iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,992 /usr/bin/install -c -m 644 ./Lib/test/testrgb.uue /galaxydir/galaxy/database/dependencies/python/2.7/usr/bin/install -c -m 64/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,992 4 ./Lib/test/testtar.tar /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Li/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,993 4 ./Lib/test/threaded_import_hangers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packapython2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,993 ime_hashlib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,993 /usr/bin/install -c -m 644 ./Lib/test/tokenize_tests.txt /galaxydir/galaxy/database/dependencies/pytpython2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,993 b/test/tf_inherit_check.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 644 ./Lib/test/thon/2.7/iuc/package_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 644 ./Lib/test/warning_tests.py /gala tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,993 4 ./Lib/test/win_console_handler.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:17,993 xydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/test/wlib/python2.7/test install_environment.STDOUT DEBUG 2017-11-18 17:03:17,997 rongcert.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//iuc/package_python_2_7/8/test install_environment.STDOUT DEBUG 2017-11-18 17:03:18,016 b/test/zipdir.zip /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 644 ./Lib/test/a09fe018cac/lib/python2.7/test/audiodata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,020 4 ./Lib/test/audiodata/pluck-pcm16.wav /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/test/audiodata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,030 udiodata/pluck-pcm24.aiff /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/test/a8b09fe018cac/lib/python2.7/test/audiodata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,034 4 ./Lib/test/audiodata/pluck-pcm32.au /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/test/audiodata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,049 udiodata/pluck-pcm32.wav /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/test/a9fe018cac/lib/python2.7/test/audiodata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,054 4 ./Lib/test/audiodata/pluck-pcm8.wav /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/test/audiodata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,073 udiodata/pluck-ulaw.aifc /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/test/ccac/lib/python2.7/test/capath install_environment.STDOUT DEBUG 2017-11-18 17:03:18,077 4 ./Lib/test/capath/5ed36f99.0 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test/capath install_environment.STDOUT DEBUG 2017-11-18 17:03:18,084 apath/6e88d7b8.0 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018on/2.7/iuc/package_pythonhon2.7/test/capath tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,095 rongcert.pem /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//iuc/package_python_2_7/8/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,096 /usr/bin/install -c -m 644 ./Lib/test/xmltests.py /galaxydir/galaxy/database/dependencies/python/2.7b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Li8cac/lib/python2.7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,096 4 ./Lib/test/audiodata/pluck-pcm16.aiff /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packapython2.7/test/audiodata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,096 b/test/zipdir.zip /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 644 ./Lib/test/a09fe018cac/lib/python2.7/test/audiodata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,096 4 ./Lib/test/audiodata/pluck-pcm16.wav /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/test/audiodata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,096 udiodata/pluck-pcm16.au /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/test/a8b09fe018cac/lib/python2.7/test/audiodata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,096 4 ./Lib/test/audiodata/pluck-pcm24.wav /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/test/audiodata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,096 udiodata/pluck-pcm24.aiff /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/test/a8b09fe018cac/lib/python2.7/test/audiodata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,097 4 ./Lib/test/audiodata/pluck-pcm32.au /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/test/audiodata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,097 udiodata/pluck-pcm32.aiff /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/test/ab09fe018cac/lib/python2.7/test/audiodata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,097 4 ./Lib/test/audiodata/pluck-pcm8.aiff /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/test/audiodata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,097 udiodata/pluck-pcm32.wav /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/test/a9fe018cac/lib/python2.7/test/audiodata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,097 4 ./Lib/test/audiodata/pluck-pcm8.wav /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/test/audiodata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,097 udiodata/pluck-pcm8.au /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/test/ab09fe018cac/lib/python2.7/test/audiodata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,097 4 ./Lib/test/audiodata/pluck-ulaw.au /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/test/audiodata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,097 udiodata/pluck-ulaw.aifc /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/test/ccac/lib/python2.7/test/capath tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,097 4 ./Lib/test/capath/5ed36f99.0 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/test/capath tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,098 apath/4e1295a3.0 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/ccac/lib/python2.7/test/capath tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,098 apath/6e88d7b8.0 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018on/2.7/iuc/package_pythonhon2.7/test/capath tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,098 /usr/bin/install -c -m 644 ./Lib/test/capath/99d0fa06.0 /galaxydir/galaxy/database/dependencies/pyth_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Li18cac/lib/python2.7/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:18,106 b/test/data/README /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib/gs install_environment.STDOUT DEBUG 2017-11-18 17:03:18,110 b/test/cjkencodings/big5.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ncodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,119 gs/big5hkscs-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib/gs install_environment.STDOUT DEBUG 2017-11-18 17:03:18,122 b/test/cjkencodings/cp949-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt/cjkencodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,130 gs/cp949.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64uc/package_python_2_7/8b09fe018kencodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,133 b/test/cjkencodings/euc_jisx0213.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_est/cjkencodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,147 gs/euc_jp-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/test/c7/8b09fe018cac/lib/python2.7/test/cjkencodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,152 4 ./Lib/test/cjkencodings/euc_kr.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/test/cjkencodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,159 jkencodings/gb18030-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py install_environment.STDOUT DEBUG 2017-11-18 17:03:18,164 b/test/cjkencodings/gb2312-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pst/cjkencodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,170 gs/gb2312.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/ps install_environment.STDOUT DEBUG 2017-11-18 17:03:18,173 b/test/cjkencodings/gbk.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,193 gs/hz-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/cn_2_7/8b09fe018cac/lib/python2.7/test/cjkencodinncies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/test/cjkencodings/iso2022_kr-utf8.txt /galt/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,198 b/test/data/README /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib/gs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,199 b/test/cjkencodings/big5.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ncodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,199 4 ./Lib/test/cjkencodings/big5-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packapython2.7/test/cjkencodin/usr/bin/install -c -m 644 ./Li_7/8b09fe018cac/lib/python2.7/test/cjke/usr/bin/install -c -m 644 ./Lib/test/cjkencodinfe018cac/lib/python2.7/test/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,199 gs/big5hkscs-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib/gs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,200 b/test/cjkencodings/cp949-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,200 4 ./Lib/test/cjkencodings/big5hkscs.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packapython2.7/test/cjkencodin/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/cjkencodinlib/python2.7/test/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,200 gs/cp949.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64uc/package_python_2_7/8b09fe018kencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,200 b/test/cjkencodings/euc_jisx0213.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_est/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,200 4 ./Lib/test/cjkencodings/euc_jisx0213-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/icac/lib/python2.7/test/cj/usr/bin/install -c -m 644 ./Lipython_2_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/cjkencodin18cac/lib/python2.7/test/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,200 4 ./Lib/test/cjkencodings/euc_jp.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/test/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,200 gs/euc_jp-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/test/c7/8b09fe018cac/lib/python2.7/test/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,200 4 ./Lib/test/cjkencodings/euc_kr.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/test/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,200 jkencodings/euc_kr-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/test/c_7/8b09fe018cac/lib/python2.7/test/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,200 jkencodings/gb18030-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,200 b/test/cjkencodings/gb2312-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pst/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,201 4 ./Lib/test/cjkencodings/gb18030.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/test/cjkencodings/usr/bin/install -c -m 644 ./Liython_2_7/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/cjkencodin/lib/python2.7/test/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,201 gs/gb2312.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/ps tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,201 b/test/cjkencodings/gbk.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,202 4 ./Lib/test/cjkencodings/gbk-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/test/cjkencoding/usr/bin/install -c -m 644 ./Li7/8b09fe018cac/lib/python2.7/test/cjken/usr/bin/install -c -m 644 ./Lib/test/cjkencodinc/lib/python2.7/test/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,202 4 ./Lib/test/cjkencodings/hz.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/test/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,202 jkencodings/iso2022_jp-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythogs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,202 /usr/bin/install -c -m 644 ./Lib/test/cjkencodings/iso2022_jp.txt /galaxydir/galaxy/database/dependehon2.7/test/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,202 gs/hz-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/cn_2_7/8b09fe018cac/lib/python2.7/test/cjkencodinncies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/test/cjkencodings/iso2022_kr-utf8.txt /galt/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,202 axydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 64age_python_2_7/8b09fe018cac/libngs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,202 b/test/cjkencodings/johab-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/cjkencodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,205 4 ./Lib/test/cjkencodings/iso2022_kr.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack/python2.7/test/cjkencodi/usr/bin/install -c -m 644 ./Li/usr/bin/install -c -m 644 ./Lib/test/cfe018cac/lib/python2.7/test/cjkencodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,213 4 ./Lib/test/cjkencodings/shift_jis-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc//lib/python2.7/test/cjken/usr/bin/install -c -m 644 ./Lihon_2_7/8b09fe018cac/lib/python2.7/test/cjkencodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,232 4 ./Lib/test/cjkencodings/shift_jisx0213-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.718cac/lib/python2.7/test//usr/bin/install -c -m 644 ./Lie_python_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/decimaltes8cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,245 4 ./Lib/test/decimaltestdata/add.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack/python2.7/test/decimalte/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/decimaltes18cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,258 4 ./Lib/test/decimaltestdata/clamp.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/paib/python2.7/test/decimal/usr/bin/install -c -m 644 ./Lipython_2_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/decimaltesfe018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,266 4 ./Lib/test/decimaltestdata/comparetotal.decTest /galaxydir/galaxy/database/dependencies/python/2.718cac/lib/python2.7/test//usr/bin/install -c -m 644 ./Lipackage_python_2_7/8b09fe018cac/lib/pytta install_environment.STDOUT DEBUG 2017-11-18 17:03:18,269 b/test/decimaltestdata/copy.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pst/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,275 tdata/copyabs.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64uc/package_python_2_7/8b09fe018cimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,279 b/test/decimaltestdata/copysign.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,292 tdata/ddAbs.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64ckage_python_2_7/8b09fe018cac/ldencies/python/2.7/iuc/package_python_2n2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,296 b/test/decimaltestdata/ddBase.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagetest/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,305 tdata/ddCanonical.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64package_python_2_7/8b09fe018cacaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,306 4 ./Lib/test/cjkencodings/iso2022_kr.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack/python2.7/test/cjkencodi/usr/bin/install -c -m 644 ./Li/usr/bin/install -c -m 644 ./Lib/test/cfe018cac/lib/python2.7/test/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,307 jkencodings/johab.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64package_python_2_7/8b09fe018caccodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,307 4 ./Lib/test/cjkencodings/shift_jis-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc//lib/python2.7/test/cjken/usr/bin/install -c -m 644 ./Lihon_2_7/8b09fe018cac/lib/python2.7/test/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,307 b/test/cjkencodings/shift_jis.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt/usr/bin/install -c -m 64/iuc/package_python_2_7/8b09fe0cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,307 b/test/cjkencodings/shift_jisx0213.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packag/test/cjkencodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,307 4 ./Lib/test/cjkencodings/shift_jisx0213-utf8.txt /galaxydir/galaxy/database/dependencies/python/2.718cac/lib/python2.7/test//usr/bin/install -c -m 644 ./Lie_python_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/decimaltes8cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,307 tdata/abs.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64age_python_2_7/8b09fe018cac/libstdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,307 b/test/decimaltestdata/and.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,307 4 ./Lib/test/decimaltestdata/add.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack/python2.7/test/decimalte/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/decimaltes18cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,308 tdata/base.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64ckage_python_2_7/8b09fe018cac/ltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,308 b/test/decimaltestdata/class.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_est/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,308 4 ./Lib/test/decimaltestdata/clamp.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/paib/python2.7/test/decimal/usr/bin/install -c -m 644 ./Lipython_2_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/decimaltesfe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,308 tdata/compare.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64/iuc/package_python_2_7/8b09fe0decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,308 4 ./Lib/test/decimaltestdata/comparetotal.decTest /galaxydir/galaxy/database/dependencies/python/2.718cac/lib/python2.7/test//usr/bin/install -c -m 644 ./Lipackage_python_2_7/8b09fe018cac/lib/pytta tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,308 b/test/decimaltestdata/copy.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pst/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,308 b/test/decimaltestdata/comparetotmag.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/hon2.7/test/decimaltestda/usr/bin/install -c -m 644 ./Liython_2_7/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/decimaltesfe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,308 tdata/copyabs.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64uc/package_python_2_7/8b09fe018cimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,308 b/test/decimaltestdata/copysign.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,308 4 ./Lib/test/decimaltestdata/copynegate.decTest /galaxydir/galaxy/database/dependencies/python/2.7/icac/lib/python2.7/test/de/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/decimaltes018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,309 4 ./Lib/test/decimaltestdata/ddAdd.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/paib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,309 tdata/ddAbs.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64ckage_python_2_7/8b09fe018cac/ldencies/python/2.7/iuc/package_python_2n2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,309 b/test/decimaltestdata/ddBase.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagetest/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,309 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/ddAnd.decTest /galaxydir/galaxy/database/depen_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Li_python_2_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/decimaltes8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,309 tdata/ddCanonical.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64package_python_2_7/8b09fe018cacaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,311 b/test/decimaltestdata/ddCompare.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,326 tdata/ddCompareSig.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64.7/iuc/package_python_2_7/8b09ft/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,342 b/test/decimaltestdata/ddCompareTotalMag.decTest /galaxydir/galaxy/database/dependencies/python/2.7//python2.7/test/decimalte/usr/bin/install -c -m 644 ./Li_python_2_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/decimaltes09fe018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,359 4 ./Lib/test/decimaltestdata/ddCopyNegate.decTest /galaxydir/galaxy/database/dependencies/python/2.718cac/lib/python2.7/test//usr/bin/install -c -m 644 ./Likage_python_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/decimaltes9fe018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,373 4 ./Lib/test/decimaltestdata/ddDivideInt.decTest /galaxydir/galaxy/database/dependencies/python/2.7/8cac/lib/python2.7/test/d/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/decimaltes018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,383 4 ./Lib/test/decimaltestdata/ddInvert.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/test/deci/usr/bin/install -c -m 644 ./Li_python_2_7/8b09fe018cac/lib/python2.7/dencies/python/2.7/iuc/package_python_2_7/8b09fe/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,387 b/test/decimaltestdata/ddMaxMag.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,393 tdata/ddMin.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64/package_python_2_7/8b09fe018camaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,396 b/test/decimaltestdata/ddMinus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packag/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,404 tdata/ddMultiply.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64iuc/package_python_2_7/8b09fe01ecimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,408 b/test/decimaltestdata/ddNextPlus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pac2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,409 b/test/decimaltestdata/ddCompare.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,410 4 ./Lib/test/decimaltestdata/ddClass.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc//lib/python2.7/test/decim/usr/bin/install -c -m 644 ./Liage_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/decimaltes/8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,410 tdata/ddCompareSig.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64.7/iuc/package_python_2_7/8b09ft/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,410 4 ./Lib/test/decimaltestdata/ddCompareTotal.decTest /galaxydir/galaxy/database/dependencies/python/2e018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Liiuc/package_python_2_7/8b09fe018cac/libstdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,410 b/test/decimaltestdata/ddCopy.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagetest/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,410 b/test/decimaltestdata/ddCompareTotalMag.decTest /galaxydir/galaxy/database/dependencies/python/2.7//python2.7/test/decimalte/usr/bin/install -c -m 644 ./Li_python_2_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/decimaltes09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,410 tdata/ddCopyAbs.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64/iuc/package_python_2_7/8b09fe0decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,410 b/test/decimaltestdata/ddCopySign.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pac2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,410 4 ./Lib/test/decimaltestdata/ddCopyNegate.decTest /galaxydir/galaxy/database/dependencies/python/2.718cac/lib/python2.7/test//usr/bin/install -c -m 644 ./Likage_python_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/decimaltes9fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,410 tdata/ddDivide.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64iuc/package_python_2_7/8b09fe01ecimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,410 b/test/decimaltestdata/ddEncode.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,411 4 ./Lib/test/decimaltestdata/ddDivideInt.decTest /galaxydir/galaxy/database/dependencies/python/2.7/8cac/lib/python2.7/test/d/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/decimaltes018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,411 tdata/ddFMA.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64/package_python_2_7/8b09fe018camaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,411 b/test/decimaltestdata/ddLogB.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagetest/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,411 4 ./Lib/test/decimaltestdata/ddInvert.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/test/deci/usr/bin/install -c -m 644 ./Li_python_2_7/8b09fe018cac/lib/python2.7/dencies/python/2.7/iuc/package_python_2_7/8b09fe/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,411 b/test/decimaltestdata/ddMaxMag.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,411 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/ddMax.decTest /galaxydir/galaxy/database/depen018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/decimaltes018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,411 tdata/ddMin.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64/package_python_2_7/8b09fe018camaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,411 b/test/decimaltestdata/ddMinus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packag/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,411 4 ./Lib/test/decimaltestdata/ddMinMag.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/test/deci/usr/bin/install -c -m 644 ./Lie_python_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/decimaltesb09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,412 tdata/ddMultiply.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64iuc/package_python_2_7/8b09fe01ecimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,412 b/test/decimaltestdata/ddNextPlus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pac2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,425 tdata/ddNextToward.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7encies/python/2.7/iuc/pacndencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,457 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/ddQuantize.decTest /galaxydir/galaxy/database/uc/package_python_2_7/8b0pendencies/python/2.7/iuc/packa/dependencies/python/2.7/iuc/package_pybase/dependencies/python/2.7/iuc/package_python_pendencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/liestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,469 b/test/decimaltestdata/ddSameQuantum.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/hon2.7/test/decimaltestda/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/decimaltesfe018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,477 4 ./Lib/test/decimaltestdata/ddSubtract.decTest /galaxydir/galaxy/database/dependencies/python/2.7/icac/lib/python2.7/test/de/usr/bin/install -c -m 644 ./Liackage_python_2_7/8b09fe018cac/lib/pytha install_environment.STDOUT DEBUG 2017-11-18 17:03:18,481 b/test/decimaltestdata/ddXor.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_est/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,490 tdata/decDouble.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64package_python_2_7/8b09fe018cacaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,495 b/test/decimaltestdata/decSingle.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,505 tdata/divide.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64c/package_python_2_7/8b09fe018cimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,510 b/test/decimaltestdata/dqAbs.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_est/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,513 4 ./Lib/test/decimaltestdata/ddNextMinus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/8cac/lib/python2.7/test/d/usr/bin/install -c -m 644 ./Likage_python_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/decimaltes/8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,513 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/ddOr.decTest /galaxydir/galaxy/database/dependkage_python_2_7/8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,514 tdata/ddNextToward.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7encies/python/2.7/iuc/pacndencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,514 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/ddPlus.decTest /galaxydir/galaxy/database/depedependencies/python/2.7/i9fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,514 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/ddReduce.decTest /galaxydir/galaxy/database/dege_python_2_7/8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,514 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/ddRemainder.decTest /galaxydir/galaxy/databasethon_2_7/8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,514 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/ddRemainderNear.decTest /galaxydir/galaxy/data2_7/8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,514 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/ddQuantize.decTest /galaxydir/galaxy/database/uc/package_python_2_7/8b0pendencies/python/2.7/iuc/packa/dependencies/python/2.7/iuc/package_pybase/dependencies/python/2.7/iuc/package_python_pendencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/liestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,514 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/ddRotate.decTest /galaxydir/galaxy/database/deb/python2.7/test/decimalt/usr/bin/install -c -m 644 ./Lipackage_python_2_7/8b09fe018cac/lib/pytta tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,514 b/test/decimaltestdata/ddScaleB.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,515 b/test/decimaltestdata/ddSameQuantum.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/hon2.7/test/decimaltestda/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/decimaltesfe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,515 tdata/ddShift.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64uc/package_python_2_7/8b09fe018cimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,515 4 ./Lib/test/decimaltestdata/ddSubtract.decTest /galaxydir/galaxy/database/dependencies/python/2.7/icac/lib/python2.7/test/de/usr/bin/install -c -m 644 ./Liackage_python_2_7/8b09fe018cac/lib/pytha tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,515 b/test/decimaltestdata/ddXor.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_est/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,515 b/test/decimaltestdata/ddToIntegral.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pon2.7/test/decimaltestdat/usr/bin/install -c -m 644 ./Lipython_2_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/decimaltes09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,515 tdata/decDouble.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64package_python_2_7/8b09fe018cacaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,516 b/test/decimaltestdata/decSingle.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,516 4 ./Lib/test/decimaltestdata/decQuad.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc//lib/python2.7/test/decim/usr/bin/install -c -m 644 ./Liage_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/decimaltese018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,516 tdata/divide.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64c/package_python_2_7/8b09fe018cimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,516 b/test/decimaltestdata/dqAbs.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_est/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,516 4 ./Lib/test/decimaltestdata/divideint.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuac/lib/python2.7/test/dec/usr/bin/install -c -m 644 ./Lipython_2_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/decimaltes018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,531 tdata/dqAdd.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fedencies/python/2.7/iuc/pa8cac/lib/python2.7/test/decimal/usr/bin/install -c -m 644 ./Lib/test/d2_7/8b09fe018cac/lib/python2.7/test/decimaltestd/usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/dqCano/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,541 4 ./Lib/test/decimaltestdata/dqClass.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc//lib/python2.7/test/decim/usr/bin/install -c -m 644 ./Liage_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/decimaltes/8b09fe018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,549 4 ./Lib/test/decimaltestdata/dqCompareTotal.decTest /galaxydir/galaxy/database/dependencies/python/2e018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Liiuc/package_python_2_7/8b09fe018cac/libstdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,553 b/test/decimaltestdata/dqCopy.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagetest/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,561 tdata/dqCopyAbs.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64/iuc/package_python_2_7/8b09fe0decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,565 b/test/decimaltestdata/dqCopySign.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pac2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,573 tdata/dqDivide.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64iuc/package_python_2_7/8b09fe01ecimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,578 b/test/decimaltestdata/dqEncode.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,586 tdata/dqFMA.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64/package_python_2_7/8b09fe018camaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,589 b/test/decimaltestdata/dqLogB.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagetest/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,596 tdata/dqMax.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64/package_python_2_7/8b09fe018camaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,599 b/test/decimaltestdata/dqMin.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_est/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,604 tdata/dqMinMag.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64package_python_2_7/8b09fe018cacaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,607 b/test/decimaltestdata/dqMultiply.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pac2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,616 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/dqAnd.decTest /galaxydir/galaxy/database/depenckage_python_2_7/8b09fe01testdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,616 ecimaltestdata/dqBase.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_ata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,616 tdata/dqAdd.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fedencies/python/2.7/iuc/pa8cac/lib/python2.7/test/decimal/usr/bin/install -c -m 644 ./Lib/test/d2_7/8b09fe018cac/lib/python2.7/test/decimaltestd/usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/dqCano/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,617 nical.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64package_python_2_7/8b09fe018cacaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,617 b/test/decimaltestdata/dqCompare.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,617 4 ./Lib/test/decimaltestdata/dqClass.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc//lib/python2.7/test/decim/usr/bin/install -c -m 644 ./Liage_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/decimaltes/8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,617 tdata/dqCompareSig.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64.7/iuc/package_python_2_7/8b09ft/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,617 4 ./Lib/test/decimaltestdata/dqCompareTotal.decTest /galaxydir/galaxy/database/dependencies/python/2e018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Liiuc/package_python_2_7/8b09fe018cac/libstdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,617 b/test/decimaltestdata/dqCopy.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagetest/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,617 b/test/decimaltestdata/dqCompareTotalMag.decTest /galaxydir/galaxy/database/dependencies/python/2.7//python2.7/test/decimalte/usr/bin/install -c -m 644 ./Li_python_2_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/decimaltes09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,618 tdata/dqCopyAbs.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64/iuc/package_python_2_7/8b09fe0decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,618 b/test/decimaltestdata/dqCopySign.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pac2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,618 4 ./Lib/test/decimaltestdata/dqCopyNegate.decTest /galaxydir/galaxy/database/dependencies/python/2.718cac/lib/python2.7/test//usr/bin/install -c -m 644 ./Likage_python_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/decimaltes9fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,618 tdata/dqDivide.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64iuc/package_python_2_7/8b09fe01ecimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,618 b/test/decimaltestdata/dqEncode.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,618 4 ./Lib/test/decimaltestdata/dqDivideInt.decTest /galaxydir/galaxy/database/dependencies/python/2.7/8cac/lib/python2.7/test/d/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/decimaltes018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,618 tdata/dqFMA.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64/package_python_2_7/8b09fe018camaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,618 b/test/decimaltestdata/dqLogB.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagetest/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,618 4 ./Lib/test/decimaltestdata/dqInvert.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/test/deci/usr/bin/install -c -m 644 ./Li_python_2_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/decimaltes018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,618 tdata/dqMax.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64/package_python_2_7/8b09fe018camaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,618 b/test/decimaltestdata/dqMin.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_est/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,619 4 ./Lib/test/decimaltestdata/dqMaxMag.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/test/deci/usr/bin/install -c -m 644 ./Lipython_2_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/decimaltes9fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,619 tdata/dqMinMag.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64package_python_2_7/8b09fe018cacaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,619 b/test/decimaltestdata/dqMultiply.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pac2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,619 4 ./Lib/test/decimaltestdata/dqMinus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc//lib/python2.7/test/decim/usr/bin/install -c -m 644 ./Likage_python_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/test/decimaltes8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,619 4 ./Lib/test/decimaltestdata/dqNextPlus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/icac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,622 tdata/dqNextMinus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64uc/package_python_2_7/8b09fe018e/dependencies/python/2.7/iuc/package_pb/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,625 b/test/decimaltestdata/dqOr.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pst/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,632 tdata/dqPlus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64uc/package_python_2_7/8b09fe018cimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,645 b/test/decimaltestdata/dqReduce.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa/dependencies/python/2.7/09fe018cac/lib/python2.7/test/d/usr/bin/install -c -m 644 ./Lib/test/dpendencies/python/2.7/iuc/package_python_2_7/8b0est/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,655 b/test/decimaltestdata/dqSameQuantum.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/hon2.7/test/decimaltestda/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/decimaltesfe018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,663 4 ./Lib/test/decimaltestdata/dqSubtract.decTest /galaxydir/galaxy/database/dependencies/python/2.7/icac/lib/python2.7/test/de/usr/bin/install -c -m 644 ./Liackage_python_2_7/8b09fe018cac/lib/pytha install_environment.STDOUT DEBUG 2017-11-18 17:03:18,666 b/test/decimaltestdata/dqXor.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_est/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,673 tdata/dsBase.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64/package_python_2_7/8b09fe018camaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,677 b/test/decimaltestdata/exp.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,688 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/extra.decTest /galaxydir/galaxy/database/depen018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/decimaltesfe018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,698 4 ./Lib/test/decimaltestdata/invert.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/plib/python2.7/test/decima/usr/bin/install -c -m 644 ./Lihon_2_7/8b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/decimaltes018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,706 4 ./Lib/test/decimaltestdata/logb.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/test/decimalt/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/decimaltese018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,719 4 ./Lib/test/decimaltestdata/min.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack/python2.7/test/decimalte/usr/bin/install -c -m 644 ./Li_python_2_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/decimaltes018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,719 tdata/dqNextMinus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64uc/package_python_2_7/8b09fe018e/dependencies/python/2.7/iuc/package_pb/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,720 b/test/decimaltestdata/dqOr.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pst/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,720 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/dqNextToward.decTest /galaxydir/galaxy/databasython_2_7/8b09fe018cac/li/usr/bin/install -c -m 644 ./Liython_2_7/8b09fe018cac/lib/python2.7/te/usr/bin/install -c -m 644 ./Lib/test/decimaltese018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,720 tdata/dqPlus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64uc/package_python_2_7/8b09fe018cimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,720 4 ./Lib/test/decimaltestdata/dqQuantize.decTest /galaxydir/galaxy/database/dependencies/python/2.7/icac/lib/python2.7/test/de/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,720 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/dqRemainder.decTest /galaxydir/galaxy/databaseiuc/package_python_2_7/8becimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,720 ecimaltestdata/dqRemainderNear.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,720 b/test/decimaltestdata/dqReduce.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa/dependencies/python/2.7/09fe018cac/lib/python2.7/test/d/usr/bin/install -c -m 644 ./Lib/test/dpendencies/python/2.7/iuc/package_python_2_7/8b0est/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,720 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/dqRotate.decTest /galaxydir/galaxy/database/de9fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lipackage_python_2_7/8b09fe018cac/lib/pytta tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,721 b/test/decimaltestdata/dqScaleB.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,721 b/test/decimaltestdata/dqSameQuantum.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/hon2.7/test/decimaltestda/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/decimaltesfe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,721 tdata/dqShift.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64uc/package_python_2_7/8b09fe018cimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,721 4 ./Lib/test/decimaltestdata/dqSubtract.decTest /galaxydir/galaxy/database/dependencies/python/2.7/icac/lib/python2.7/test/de/usr/bin/install -c -m 644 ./Liackage_python_2_7/8b09fe018cac/lib/pytha tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,721 b/test/decimaltestdata/dqXor.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_est/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,721 b/test/decimaltestdata/dqToIntegral.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pon2.7/test/decimaltestdat/usr/bin/install -c -m 644 ./Lipython_2_7/8b09fe018cac/lib/python2.7/t/usr/bin/install -c -m 644 ./Lib/test/decimaltese018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,721 tdata/dsBase.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64/package_python_2_7/8b09fe018camaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,721 b/test/decimaltestdata/exp.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,721 4 ./Lib/test/decimaltestdata/dsEncode.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/test/deci/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/tesdencies/python/2.7/iuc/package_python_2_7/8b09fe/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,721 b/test/decimaltestdata/fma.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,722 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/extra.decTest /galaxydir/galaxy/database/depen018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/decimaltesfe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,722 tdata/inexact.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64ackage_python_2_7/8b09fe018cac/ltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,722 b/test/decimaltestdata/ln.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,722 4 ./Lib/test/decimaltestdata/invert.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/plib/python2.7/test/decima/usr/bin/install -c -m 644 ./Lihon_2_7/8b09fe018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lib/test/decimaltes018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,722 tdata/log10.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64kage_python_2_7/8b09fe018cac/liestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,722 b/test/decimaltestdata/max.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,722 4 ./Lib/test/decimaltestdata/logb.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/test/decimalt/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/decimaltese018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,722 tdata/maxmag.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64age_python_2_7/8b09fe018cac/libstdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,722 b/test/decimaltestdata/minmag.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagetest/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,722 4 ./Lib/test/decimaltestdata/min.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack/python2.7/test/decimalte/usr/bin/install -c -m 644 ./Li_python_2_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/decimaltes018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,732 4 ./Lib/test/decimaltestdata/multiply.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/test/deci/usr/bin/install -c -m 644 ./Liage_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/decimaltes9fe018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,741 4 ./Lib/test/decimaltestdata/nexttoward.decTest /galaxydir/galaxy/database/dependencies/python/2.7/icies/python/2.7/iuc/packac/lib/python2.7/test/decimaltes/usr/bin/install -c -m 644 ./Lib/test/d7/8b09fe018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,752 4 ./Lib/test/decimaltestdata/power.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/paib/python2.7/test/decimal/usr/bin/install -c -m 644 ./Liage_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/decimaltes9fe018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,764 4 ./Lib/test/decimaltestdata/randomBound32.decTest /galaxydir/galaxy/database/dependencies/python/2.018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lie_python_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/decimaltese018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,772 4 ./Lib/test/decimaltestdata/remainder.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuac/lib/python2.7/test/dec/usr/bin/install -c -m 644 ./Lipackage_python_2_7/8b09fe018cac/lib/pytta install_environment.STDOUT DEBUG 2017-11-18 17:03:18,775 b/test/decimaltestdata/rescale.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packag/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,784 tdata/rotate.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64/package_python_2_7/8b09fe018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,793 4 ./Lib/test/decimaltestdata/samequantum.decTest /galaxydir/galaxy/database/dependencies/python/2.7/8cac/lib/python2.7/test/d/usr/bin/install -c -m 644 ./Li_python_2_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/decimaltes018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,802 4 ./Lib/test/decimaltestdata/squareroot.decTest /galaxydir/galaxy/database/dependencies/python/2.7/icac/lib/python2.7/test/de/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/decimaltesfe018cac/lib/python2.7/test/decimaltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,808 4 ./Lib/test/decimaltestdata/tointegral.decTest /galaxydir/galaxy/database/dependencies/python/2.7/icac/lib/python2.7/test/de/usr/bin/install -c -m 644 ./Lickage_python_2_7/8b09fe018cac/lib/pytho install_environment.STDOUT DEBUG 2017-11-18 17:03:18,812 b/test/decimaltestdata/xor.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,825 tdata/minus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64/package_python_2_7/8b09fe018camaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,825 b/test/decimaltestdata/nextminus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,825 4 ./Lib/test/decimaltestdata/multiply.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/test/deci/usr/bin/install -c -m 644 ./Liage_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/decimaltes9fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,825 tdata/nextplus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64uc/package_python_2_7/8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,825 /usr/bin/install -c -m 644 ./Lib/test/decimaltestdata/or.decTest /galaxydir/galaxy/database/dependenge_python_2_7/8b09fe018catdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,826 4 ./Lib/test/decimaltestdata/nexttoward.decTest /galaxydir/galaxy/database/dependencies/python/2.7/icies/python/2.7/iuc/packac/lib/python2.7/test/decimaltes/usr/bin/install -c -m 644 ./Lib/test/d7/8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,826 ecimaltestdata/plus.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/usr/bin/install -c -m 64ckage_python_2_7/8b09fe018cac/ltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,827 b/test/decimaltestdata/powersqrt.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,827 4 ./Lib/test/decimaltestdata/power.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/paib/python2.7/test/decimal/usr/bin/install -c -m 644 ./Liage_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/test/decimaltes9fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,828 tdata/quantize.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 647/iuc/package_python_2_7/8b09fe/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,828 b/test/decimaltestdata/randoms.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packag/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,828 4 ./Lib/test/decimaltestdata/randomBound32.decTest /galaxydir/galaxy/database/dependencies/python/2.018cac/lib/python2.7/test/usr/bin/install -c -m 644 ./Lie_python_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/decimaltese018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,828 tdata/reduce.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64c/package_python_2_7/8b09fe018cimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,828 4 ./Lib/test/decimaltestdata/remainder.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuac/lib/python2.7/test/dec/usr/bin/install -c -m 644 ./Lipackage_python_2_7/8b09fe018cac/lib/pytta tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,828 b/test/decimaltestdata/rescale.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packag/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,828 b/test/decimaltestdata/remainderNear.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/hon2.7/test/decimaltestda/usr/bin/install -c -m 644 ./Lie_python_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/test/decimaltese018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,828 tdata/rotate.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64/package_python_2_7/8b09fe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,828 4 ./Lib/test/decimaltestdata/rounding.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/usr/bin/install -c -m 64iuc/package_python_2_7/8b09fe01ecimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,828 b/test/decimaltestdata/scaleb.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagetest/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,829 4 ./Lib/test/decimaltestdata/samequantum.decTest /galaxydir/galaxy/database/dependencies/python/2.7/8cac/lib/python2.7/test/d/usr/bin/install -c -m 644 ./Li_python_2_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/test/decimaltes018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,829 tdata/shift.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64uc/package_python_2_7/8b09fe018cimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,829 b/test/decimaltestdata/subtract.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,830 4 ./Lib/test/decimaltestdata/squareroot.decTest /galaxydir/galaxy/database/dependencies/python/2.7/icac/lib/python2.7/test/de/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/test/decimaltesfe018cac/lib/python2.7/test/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,830 tdata/testall.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64uc/package_python_2_7/8b09fe018cimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,830 4 ./Lib/test/decimaltestdata/tointegral.decTest /galaxydir/galaxy/database/dependencies/python/2.7/icac/lib/python2.7/test/de/usr/bin/install -c -m 644 ./Lickage_python_2_7/8b09fe018cac/lib/pytho tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,830 b/test/decimaltestdata/xor.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt/decimaltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,830 b/test/decimaltestdata/tointegralx.decTest /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pan2.7/test/decimaltestdata/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/tes/usr/bin/install -c -m 644 ./Lib/test/xmltestdatac/lib/python2.7/test/xmltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,830 4 ./Lib/test/xmltestdata/simple.xml /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/test/xmltestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,835 a/simple-ns.xml /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/test/xes/python/2.7/iuc/package_python_2_7/8b09fe018caestdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,842 b/test/imghdrdata/python.bmp /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2drdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,853 /python.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/test/ie018cac/lib/python2.7/test/imghdrdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,862 4 ./Lib/test/imghdrdata/python.pgm /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pypython/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/imghdrdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,871 /usr/bin/install -c -m 644 ./Lib/test/imghdrdata/python.ppm /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_py/python2.7/test/imghdrdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,874 b/test/imghdrdata/python.sgi /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2drdata install_environment.STDOUT DEBUG 2017-11-18 17:03:18,897 /python.tiff /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/test/son_2_7/8b09fe018cac/lib/python2.7/test/subproces/usr/bin/install -c -m 644 ./Lib/test/tracedmodules/__init__n2.7/test/tracedmodules install_environment.STDOUT DEBUG 2017-11-18 17:03:18,912 4 ./Lib/test/tracedmodules/testmod.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagen/2.7/iuc/package_python_on2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,922 b/encodings/aliases.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodi018cac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,928 /usr/bin/install -c -m 644 ./Lib/encodings/big5.py /galaxydir/galaxy/database/dependencies/python/2.8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib09fe018cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,930 mltestdata/test.xml /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/xmltestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,931 a/simple-ns.xml /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/test/xes/python/2.7/iuc/package_python_2_7/8b09fe018caestdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,931 b/test/imghdrdata/python.bmp /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2drdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,931 /usr/bin/install -c -m 644 ./Lib/test/xmltestdata/test.xml.out /galaxydir/galaxy/database/dependencic/lib/python2.7/test/xmlt/usr/bin/install -c -m 644 ./Li_7/8b09fe018cac/lib/python2.7/test/imgh/usr/bin/install -c -m 644 ./Lib/test/imghdrdataib/python2.7/test/imghdrdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,931 4 ./Lib/test/imghdrdata/python.jpg /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/test/imghdrdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,931 /python.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/test/ie018cac/lib/python2.7/test/imghdrdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,932 mghdrdata/python.pbm /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/python2.7/test/imghdrdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,932 4 ./Lib/test/imghdrdata/python.pgm /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pypython/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/imghdrdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,932 /usr/bin/install -c -m 644 ./Lib/test/imghdrdata/python.png /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/imghdrdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,932 /usr/bin/install -c -m 644 ./Lib/test/imghdrdata/python.ppm /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_py/python2.7/test/imghdrdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,932 b/test/imghdrdata/python.sgi /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2drdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,932 /usr/bin/install -c -m 644 ./Lib/test/imghdrdata/python.ras /galaxydir/galaxy/database/dependencies/thon_2_7/8b09fe018cac/lib/usr/bin/install -c -m 644 ./Li_7/8b09fe018cac/lib/python2.7/test/imgh/usr/bin/install -c -m 644 ./Lib/test/imghdrdatalib/python2.7/test/imghdrdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,933 4 ./Lib/test/imghdrdata/python.xbm /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/test/imghdrdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,933 ubprocessdata/sigchild_ignore.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythsdata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,933 /python.tiff /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/test/son_2_7/8b09fe018cac/lib/python2.7/test/subproces/usr/bin/install -c -m 644 ./Lib/test/tracedmodules/__init__n2.7/test/tracedmodules tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,933 .py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/python2.7/test/tracedmodules tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,933 4 ./Lib/test/tracedmodules/testmod.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagen/2.7/iuc/package_python_on2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,933 /usr/bin/install -c -m 644 ./Lib/encodings/__init__.py /galaxydir/galaxy/database/dependencies/pytho2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Li9fe018cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,933 4 ./Lib/encodings/ascii.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,933 b/encodings/aliases.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodi018cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,933 ngs/base64_codec.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe7/iuc/package_python_2_7/7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:18,934 /usr/bin/install -c -m 644 ./Lib/encodings/big5.py /galaxydir/galaxy/database/dependencies/python/2.8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib09fe018cac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,934 4 ./Lib/encodings/bz2_codec.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,943 ngs/charmap.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,946 4 ./Lib/encodings/cp1026.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,957 ngs/cp1140.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/en/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,961 4 ./Lib/encodings/cp1252.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,971 ngs/cp1253.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/en/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,974 4 ./Lib/encodings/cp1256.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,984 ngs/cp1257.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/en/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,987 4 ./Lib/encodings/cp437.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings install_environment.STDOUT DEBUG 2017-11-18 17:03:18,996 ngs/cp500.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,001 4 ./Lib/encodings/cp775.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,012 ngs/cp850.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,017 4 ./Lib/encodings/cp856.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,026 ngs/cp857.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,032 4 ./Lib/encodings/cp861.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,036 4 ./Lib/encodings/bz2_codec.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,036 b/encodings/big5hkscs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodic/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,036 4 ./Lib/encodings/cp037.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,036 ngs/charmap.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,036 4 ./Lib/encodings/cp1026.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,037 ngs/cp1006.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/en/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,037 4 ./Lib/encodings/cp1250.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,037 ngs/cp1140.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/en/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,037 4 ./Lib/encodings/cp1252.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,037 ngs/cp1251.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/en/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,037 4 ./Lib/encodings/cp1254.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,037 ngs/cp1253.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/en/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,037 4 ./Lib/encodings/cp1256.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,037 ngs/cp1255.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/en/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,037 4 ./Lib/encodings/cp1258.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,037 ngs/cp1257.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/en/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,037 4 ./Lib/encodings/cp437.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,038 ngs/cp424.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,038 4 ./Lib/encodings/cp720.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,038 ngs/cp500.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,038 4 ./Lib/encodings/cp775.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,038 ngs/cp737.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,038 4 ./Lib/encodings/cp852.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,038 ngs/cp850.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,038 4 ./Lib/encodings/cp856.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,038 ngs/cp855.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,038 4 ./Lib/encodings/cp858.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,038 ngs/cp857.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,038 4 ./Lib/encodings/cp861.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,038 ngs/cp860.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,040 ngs/cp862.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/.7/iuc/package_python_2_7.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,054 b/encodings/cp864.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,059 4 ./Lib/encodings/cp869.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,080 ngs/cp874.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,086 4 ./Lib/encodings/cp949.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,098 ngs/cp950.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/encodi018cac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,102 4 ./Lib/encodings/euc_jp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,111 ngs/euc_kr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/e/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,115 4 ./Lib/encodings/gbk.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8ings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,124 ngs/hex_codec.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodi/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,129 4 ./Lib/encodings/idna.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/dings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,140 ngs/iso2022_jp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/encodi018cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,144 ngs/cp862.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/.7/iuc/package_python_2_7.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,144 /usr/bin/install -c -m 644 ./Lib/encodings/cp863.py /galaxydir/galaxy/database/dependencies/python/2/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lie018cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,144 4 ./Lib/encodings/cp865.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,144 b/encodings/cp864.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,144 4 ./Lib/encodings/cp869.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,144 ngs/cp866.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,144 4 ./Lib/encodings/cp875.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,145 ngs/cp874.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,145 4 ./Lib/encodings/cp949.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,145 ngs/cp932.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,145 4 ./Lib/encodings/euc_jis_2004.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,145 ngs/cp950.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/encodi018cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,145 4 ./Lib/encodings/euc_jp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,145 ngs/euc_jisx0213.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/en/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,146 4 ./Lib/encodings/gb18030.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ncodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,146 ngs/euc_kr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/e/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,146 4 ./Lib/encodings/gbk.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8ings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,146 ngs/gb2312.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/encod/usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,146 4 ./Lib/encodings/hp_roman8.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,146 ngs/hex_codec.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodi/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,146 4 ./Lib/encodings/idna.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/dings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,146 ngs/hz.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/enco/usr/bin/install -c -m 644 ./Lib/encodi8cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,146 4 ./Lib/encodings/iso2022_jp_1.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,147 ngs/iso2022_jp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/encodi018cac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,147 4 ./Lib/encodings/iso2022_jp_2004.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,158 /usr/bin/install -c -m 644 ./Lib/encodings/iso2022_jp_3.py /galaxydir/galaxy/database/dependencies/p018cac/lib/python2.7/enco/usr/bin/install -c -m 644 ./Li2_7/8b09fe018cac/lib/python2.7/encoding/usr/bin/install -c -m 644 ./Lib/encodings/iso20python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,162 4 ./Lib/encodings/iso8859_1.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,175 ngs/iso8859_10.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/encodi8cac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,181 4 ./Lib/encodings/iso8859_14.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,191 ngs/iso8859_15.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,194 4 ./Lib/encodings/iso8859_3.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,204 ngs/iso8859_4.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,207 4 ./Lib/encodings/iso8859_7.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,220 ngs/iso8859_8.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,223 4 ./Lib/encodings/koi8_r.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,236 ngs/koi8_u.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/e/usr/bin/install -c -m 644 ./Lib/encodi8cac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,240 4 ./Lib/encodings/mac_centeuro.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,247 4 ./Lib/encodings/iso2022_jp_2004.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,247 ngs/iso2022_jp_2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pytython/2.7/iuc/package_python_2_7/8b09fedings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,247 b/encodings/iso2022_jp_ext.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_s tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,248 /usr/bin/install -c -m 644 ./Lib/encodings/iso2022_jp_3.py /galaxydir/galaxy/database/dependencies/p018cac/lib/python2.7/enco/usr/bin/install -c -m 644 ./Li2_7/8b09fe018cac/lib/python2.7/encoding/usr/bin/install -c -m 644 ./Lib/encodings/iso20python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,248 4 ./Lib/encodings/iso8859_1.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,248 22_kr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodi8cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,248 4 ./Lib/encodings/iso8859_11.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,249 ngs/iso8859_10.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/encodi8cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,249 4 ./Lib/encodings/iso8859_14.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,249 ngs/iso8859_13.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/encodi8cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,249 4 ./Lib/encodings/iso8859_16.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,249 ngs/iso8859_15.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,249 4 ./Lib/encodings/iso8859_3.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,250 ngs/iso8859_2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,250 4 ./Lib/encodings/iso8859_5.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,250 ngs/iso8859_4.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,250 4 ./Lib/encodings/iso8859_7.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,250 ngs/iso8859_6.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,250 4 ./Lib/encodings/iso8859_9.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,250 ngs/iso8859_8.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,250 4 ./Lib/encodings/koi8_r.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,251 ngs/johab.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/en/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,251 4 ./Lib/encodings/latin_1.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ncodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,251 ngs/koi8_u.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/e/usr/bin/install -c -m 644 ./Lib/encodi8cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,251 4 ./Lib/encodings/mac_centeuro.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,251 ngs/mac_arabic.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/encodi018cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,251 4 ./Lib/encodings/mac_cyrillic.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,252 ngs/mac_croatian.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,255 4 ./Lib/encodings/mac_greek.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,266 ngs/mac_iceland.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,272 4 ./Lib/encodings/mac_romanian.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,290 ngs/mac_turkish.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/enco/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,294 4 ./Lib/encodings/ptcp154.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ncodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,306 ngs/punycode.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/encodi8b09fe018cac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,312 /encodings/rot_13.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f install_environment.STDOUT DEBUG 2017-11-18 17:03:19,325 ngs/shift_jis.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/encodife018cac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,333 4 ./Lib/encodings/string_escape.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,351 ngs/tis_620.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodife018cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,352 ngs/mac_croatian.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,352 4 ./Lib/encodings/mac_greek.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,352 ngs/mac_farsi.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodi18cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,352 4 ./Lib/encodings/mac_latin2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,353 ngs/mac_iceland.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,353 4 ./Lib/encodings/mac_romanian.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,353 ngs/mac_roman.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/encodi18cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,353 4 ./Lib/encodings/mbcs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/dings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,353 ngs/mac_turkish.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/enco/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,353 4 ./Lib/encodings/ptcp154.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ncodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,353 ngs/palmos.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/e/usr/bin/install -c -m 644 ./Lib/encodiac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,354 4 ./Lib/encodings/quopri_codec.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,354 ngs/punycode.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/encodi8b09fe018cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,354 /encodings/rot_13.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,354 ngs/raw_unicode_escape.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c ./Libe018cac/lib/python2.7/encodings/usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,354 4 ./Lib/encodings/shift_jis_2004.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,354 ngs/shift_jis.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/encodife018cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,354 4 ./Lib/encodings/string_escape.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,355 ngs/shift_jisx0213.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/encodic/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,355 4 ./Lib/encodings/undefined.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,355 ngs/tis_620.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodife018cac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,358 4 ./Lib/encodings/unicode_internal.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,370 ngs/utf_16.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,374 4 ./Lib/encodings/utf_32.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,384 ngs/utf_32_be.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,388 4 ./Lib/encodings/utf_8.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,399 ngs/utf_8_sig.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/encodi8cac/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,408 4 ./Lib/compiler/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ompiler install_environment.STDOUT DEBUG 2017-11-18 17:03:19,419 er/ast.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/com/usr/bin/install -c -m 644 ./Lib/compillib/python2.7/compiler install_environment.STDOUT DEBUG 2017-11-18 17:03:19,422 4 ./Lib/compiler/misc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8ler install_environment.STDOUT DEBUG 2017-11-18 17:03:19,431 er/pyassem.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/compil/lib/python2.7/compiler install_environment.STDOUT DEBUG 2017-11-18 17:03:19,436 4 ./Lib/compiler/syntax.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7piler tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,457 4 ./Lib/encodings/unicode_internal.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,462 ngs/unicode_escape.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/encodi/lib/python2.7/encodings install_environment.STDOUT DEBUG 2017-11-18 17:03:19,462 er/transformer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/co/usr/bin/install -c -m 644 ./Lib/hotsho/lib/python2.7/hotshot install_environment.STDOUT DEBUG 2017-11-18 17:03:19,466 4 ./Lib/hotshot/log.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hotshot tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,466 4 ./Lib/encodings/utf_16_be.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,477 ngs/utf_16.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,477 4 ./Lib/encodings/utf_32.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_codings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,477 ngs/utf_16_le.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/en/usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,477 4 ./Lib/encodings/utf_32_le.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,482 ngs/utf_32_be.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/encodilib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,483 4 ./Lib/encodings/utf_8.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7odings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,483 ngs/utf_7.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/enc/usr/bin/install -c -m 644 ./Lib/encodicac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,483 4 ./Lib/encodings/uu_codec.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,483 ngs/utf_8_sig.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/encodi8cac/lib/python2.7/encodings tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,483 4 ./Lib/compiler/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ompiler tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,483 ngs/zlib_codec.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/c/usr/bin/install -c -m 644 ./Lib/compil/python2.7/compiler tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,483 4 ./Lib/compiler/consts.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7piler tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,485 er/ast.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/com/usr/bin/install -c -m 644 ./Lib/compillib/python2.7/compiler tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,485 4 ./Lib/compiler/misc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8ler tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,485 er/future.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64b09fe018cac/lib/python2.7/compi/usr/bin/install -c -m 644 ./Lib/compil/lib/python2.7/compiler tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,485 4 ./Lib/compiler/pycodegen.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_compiler tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,491 er/pyassem.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/compil/lib/python2.7/compiler tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,491 4 ./Lib/compiler/syntax.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7piler tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,491 er/symbols.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/com/usr/bin/install -c -m 644 ./Lib/compil8cac/lib/python2.7/compiler tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,491 4 ./Lib/compiler/visitor.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_mpiler install_environment.STDOUT DEBUG 2017-11-18 17:03:19,491 /usr/bin/install -c -m 644 ./Lib/hotshot/stats.py /galaxydir/galaxy/database/dependencies/python/2.7/usr/bin/install -c -m 647/iuc/package_python_2_7/8b09fel tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,492 er/transformer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/co/usr/bin/install -c -m 644 ./Lib/hotsho/lib/python2.7/hotshot tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,492 4 ./Lib/hotshot/log.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hotshot tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,492 t/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hotshot tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,492 4 ./Lib/hotshot/stones.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hotshot tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,492 /usr/bin/install -c -m 644 ./Lib/hotshot/stats.py /galaxydir/galaxy/database/dependencies/python/2.7/usr/bin/install -c -m 647/iuc/package_python_2_7/8b09fel install_environment.STDOUT DEBUG 2017-11-18 17:03:19,508 b/email/_parseaddr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/em/usr/bin/install -c -m 644 ./Lib/email/b/python2.7/email install_environment.STDOUT DEBUG 2017-11-18 17:03:19,512 4 ./Lib/email/encoders.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/l install_environment.STDOUT DEBUG 2017-11-18 17:03:19,523 errors.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/em/usr/bin/install -c -m 644 ./Lib/email/lib/python2.7/email install_environment.STDOUT DEBUG 2017-11-18 17:03:19,535 4 ./Lib/email/header.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/ema/usr/bin/install -c -m 644 ./Lib/email/b/python2.7/email install_environment.STDOUT DEBUG 2017-11-18 17:03:19,565 4 ./Lib/email/parser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/em/usr/bin/install -c -m 644 ./Lib/email/on/2.7/iuc/package_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/email/mime/application.py /email/mime install_environment.STDOUT DEBUG 2017-11-18 17:03:19,570 4 ./Lib/email/mime/audio.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_ail/mime install_environment.STDOUT DEBUG 2017-11-18 17:03:19,589 mime/base.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/em/usr/bin/install -c -m 644 ./Lib/email/ac/lib/python2.7/email/mime install_environment.STDOUT DEBUG 2017-11-18 17:03:19,593 4 ./Lib/email/mime/multipart.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/email/mime tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,597 /usr/bin/install -c -m 644 ./Lib/email/__init__.py /galaxydir/galaxy/database/dependencies/python/2.018cac/lib/python2.7/emai/usr/bin/install -c -m 644 ./Life018cac/lib/python2.7/email tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,597 4 ./Lib/email/base64mime.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_ail tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,597 b/email/_parseaddr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/em/usr/bin/install -c -m 644 ./Lib/email/b/python2.7/email tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,597 4 ./Lib/email/encoders.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/l tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,597 charset.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/emai/usr/bin/install -c -m 644 ./Lib/email//python2.7/email tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,597 4 ./Lib/email/feedparser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_ail tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,598 errors.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/em/usr/bin/install -c -m 644 ./Lib/email/lib/python2.7/email install_environment.STDOUT DEBUG 2017-11-18 17:03:19,598 mime/nonmultipart.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/email/mime tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,598 generator.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 6409fe018cac/lib/python2.7/email tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,598 4 ./Lib/email/iterators.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7il tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,598 4 ./Lib/email/header.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/ema/usr/bin/install -c -m 644 ./Lib/email/b/python2.7/email tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,598 message.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 6409fe018cac/lib/python2.7/email tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,598 4 ./Lib/email/quoprimime.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_ail tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,598 utils.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/email tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,598 /usr/bin/install -c -m 644 ./Lib/email/mime/__init__.py /galaxydir/galaxy/database/dependencies/pythython2.7/email/mime tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,598 4 ./Lib/email/parser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/em/usr/bin/install -c -m 644 ./Lib/email/on/2.7/iuc/package_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/email/mime/application.py /email/mime tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,599 4 ./Lib/email/mime/audio.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_ail/mime tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,599 galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/em/usr/bin/install -c -m 644 ./Lib/email/lib/python2.7/email/mime tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,599 4 ./Lib/email/mime/image.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_ail/mime tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,599 mime/base.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/em/usr/bin/install -c -m 644 ./Lib/email/ac/lib/python2.7/email/mime tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,599 4 ./Lib/email/mime/multipart.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/email/mime tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,599 mime/nonmultipart.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/email/mime install_environment.STDOUT DEBUG 2017-11-18 17:03:19,616 .py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/email/18cac/lib/python2.7/email/test install_environment.STDOUT DEBUG 2017-11-18 17:03:19,620 4 ./Lib/email/test/test_email_codecs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packapython2.7/email/test install_environment.STDOUT DEBUG 2017-11-18 17:03:19,629 test/test_email_codecs_renamed.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt/usr/bin/install -c -m 64age_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 644 ./Lib/email//8b09fe018cac/lib/python2.7/email/test install_environment.STDOUT DEBUG 2017-11-18 17:03:19,654 4 ./Lib/email/test/data/PyBanner048.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packapython2.7/email/test/data/usr/bin/install -c -m 644 ./Li_2_7/8b09fe018cac/lib/python2.7/email/t/usr/bin/install -c -m 644 ./Lib/email/test/datapython/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/email/test/data/msg_03.txt /galaxydir/galaa install_environment.STDOUT DEBUG 2017-11-18 17:03:19,658 4 ./Lib/email/test/data/msg_04.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,669 test/data/msg_05.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,672 4 ./Lib/email/test/data/msg_08.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,681 test/data/msg_09.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,684 4 ./Lib/email/test/data/msg_12.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,692 test/data/msg_12a.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/python2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,703 /usr/bin/install -c -m 644 ./Lib/email/test/data/msg_14.txt /galaxydir/galaxy/database/dependencies/thon_2_7/8b09fe018cac/lib/usr/bin/install -c -m 644 ./Li_7/8b09fe018cac/lib/python2.7/email/tespython/2.7/iuc/package_python_2_7/8b09fe018cac/lata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,704 mime/message.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/email//usr/bin/install -c -m 644 ./Lib/email/mime/textn2.7/email/mime tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,704 4 ./Lib/email/test/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/email/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,705 .py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/email/18cac/lib/python2.7/email/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,705 4 ./Lib/email/test/test_email_codecs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packapython2.7/email/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,705 test/test_email.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 644 ./Lib/email/hon_2_7/8b09fe018cac/lib/python2.7/email/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,705 4 ./Lib/email/test/test_email_renamed.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack/python2.7/email/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,705 test/test_email_codecs_renamed.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt/usr/bin/install -c -m 64age_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 644 ./Lib/email//8b09fe018cac/lib/python2.7/email/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,706 test/test_email_torture.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,706 b/email/test/data/audiotest.au /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythonest/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,706 /msg_01.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,706 /usr/bin/install -c -m 644 ./Lib/email/test/data/msg_02.txt /galaxydir/galaxy/database/dependencies//email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,706 4 ./Lib/email/test/data/PyBanner048.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packapython2.7/email/test/data/usr/bin/install -c -m 644 ./Li_2_7/8b09fe018cac/lib/python2.7/email/t/usr/bin/install -c -m 644 ./Lib/email/test/datapython/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/email/test/data/msg_03.txt /galaxydir/galaa tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,706 4 ./Lib/email/test/data/msg_04.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,706 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/email/test/dat/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,706 4 ./Lib/email/test/data/msg_06.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,706 test/data/msg_05.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,706 4 ./Lib/email/test/data/msg_08.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,706 test/data/msg_07.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,707 4 ./Lib/email/test/data/msg_10.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,707 test/data/msg_09.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,707 4 ./Lib/email/test/data/msg_12.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,707 test/data/msg_11.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/fe018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,707 test/data/msg_12a.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,707 4 ./Lib/email/test/data/msg_13.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pypython/2.7/iuc/package_py/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,707 b/email/test/data/msg_15.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2t/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,707 /usr/bin/install -c -m 644 ./Lib/email/test/data/msg_14.txt /galaxydir/galaxy/database/dependencies/thon_2_7/8b09fe018cac/lib/usr/bin/install -c -m 644 ./Li_7/8b09fe018cac/lib/python2.7/email/tespython/2.7/iuc/package_python_2_7/8b09fe018cac/lata tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,707 /usr/bin/install -c -m 644 ./Lib/email/test/data/msg_16.txt /galaxydir/galaxy/database/dependencies/ib/python2.7/email/test/d/usr/bin/install -c -m 644 ./Li_7/8b09fe018cac/lib/python2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,715 b/email/test/data/msg_17.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,719 4 ./Lib/email/test/data/msg_20.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,729 test/data/msg_21.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,733 4 ./Lib/email/test/data/msg_24.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,745 test/data/msg_25.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,749 4 ./Lib/email/test/data/msg_28.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,759 test/data/msg_29.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,763 4 ./Lib/email/test/data/msg_32.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,773 test/data/msg_33.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,777 4 ./Lib/email/test/data/msg_36.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,788 test/data/msg_37.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,791 4 ./Lib/email/test/data/msg_40.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,800 test/data/msg_41.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,803 4 ./Lib/email/test/data/msg_44.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,808 4 ./Lib/email/test/data/msg_18.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,809 b/email/test/data/msg_17.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,809 4 ./Lib/email/test/data/msg_20.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,809 test/data/msg_19.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,809 4 ./Lib/email/test/data/msg_22.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,809 test/data/msg_21.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,809 4 ./Lib/email/test/data/msg_24.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,809 test/data/msg_23.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,809 4 ./Lib/email/test/data/msg_26.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,810 test/data/msg_25.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,810 4 ./Lib/email/test/data/msg_28.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,810 test/data/msg_27.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,810 4 ./Lib/email/test/data/msg_30.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,810 test/data/msg_29.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,810 4 ./Lib/email/test/data/msg_32.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,810 test/data/msg_31.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,810 4 ./Lib/email/test/data/msg_34.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,811 test/data/msg_33.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,811 4 ./Lib/email/test/data/msg_36.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,811 test/data/msg_35.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,811 4 ./Lib/email/test/data/msg_38.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,811 test/data/msg_37.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,811 4 ./Lib/email/test/data/msg_40.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,811 test/data/msg_39.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,811 4 ./Lib/email/test/data/msg_42.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,812 test/data/msg_41.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,812 4 ./Lib/email/test/data/msg_44.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,812 test/data/msg_43.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/email/e018cac/lib/python2.7/email/test/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,812 4 ./Lib/email/test/data/msg_46.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/email/test/data install_environment.STDOUT DEBUG 2017-11-18 17:03:19,820 test/data/msg_45.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64n/2.7/iuc/package_python_2_7/8bensurepip install_environment.STDOUT DEBUG 2017-11-18 17:03:19,842 b/ensurepip/__main__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/ensureackage_python_2_7/8b09fe018cac/lib/python2.7/ens/usr/bin/install -c -m 644 ./Lib/ensurepip/_bundled/setuptoo_7/8b09fe018cac/lib/python2.7/ensurepip/_bundled install_environment.STDOUT DEBUG 2017-11-18 17:03:19,859 4 ./Lib/json/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 6409fe018cac/lib/python2.7/json install_environment.STDOUT DEBUG 2017-11-18 17:03:19,866 4 ./Lib/json/encoder.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 6409fe018cac/lib/python2.7/json install_environment.STDOUT DEBUG 2017-11-18 17:03:19,891 4 ./Lib/json/tool.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/json/tython/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 644 ./Lib/json/tests/test_default.py /json/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:19,894 4 ./Lib/json/tests/test_dump.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/json/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:19,900 ests/test_encode_basestring_ascii.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_ install_environment.STDOUT DEBUG 2017-11-18 17:03:19,911 laxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/js/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/json/t018cac/lib/python2.7/json/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:19,913 4 ./Lib/json/tests/test_pass1.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,914 test/data/msg_45.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64n/2.7/iuc/package_python_2_7/8bensurepip tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,914 /usr/bin/install -c -m 644 ./Lib/ensurepip/__init__.py /galaxydir/galaxy/database/dependencies/pytho09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Li09fe018cac/lib/python2.7/ensurepip tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,914 4 ./Lib/ensurepip/_uninstall.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/ensurepip tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,914 pip/_bundled/pip-6.1.1-py2.py3-none-any.whl /galaxydir/galaxy/database/dependencies/python/2.7/iuc/purepip/_bundled tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,914 b/ensurepip/__main__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/ensureackage_python_2_7/8b09fe018cac/lib/python2.7/ens/usr/bin/install -c -m 644 ./Lib/ensurepip/_bundled/setuptoo_7/8b09fe018cac/lib/python2.7/ensurepip/_bundled tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,914 ls-15.2-py2.py3-none-any.whl /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/json tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,914 4 ./Lib/json/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 6409fe018cac/lib/python2.7/json tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,914 4 ./Lib/json/decoder.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 6409fe018cac/lib/python2.7/json tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,914 4 ./Lib/json/encoder.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 6409fe018cac/lib/python2.7/json tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,914 4 ./Lib/json/scanner.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64e018cac/lib/python2.7/json tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,914 4 ./Lib/json/tests/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,914 ests/test_check_circular.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,914 /usr/bin/install -c -m 644 ./Lib/json/tests/test_decode.py /galaxydir/galaxy/database/dependencies/pb/python2.7/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,915 4 ./Lib/json/tool.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/json/tython/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 644 ./Lib/json/tests/test_default.py /json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,915 4 ./Lib/json/tests/test_dump.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,915 ests/test_encode_basestring_ascii.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,915 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/json/tpython_2_7/8b09fe018cac/lib/python2.7/json/tests/usr/bin/install -c -m 644 ./Lib/json/tests/test_fail.py /gaon/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,915 4 ./Lib/json/tests/test_float.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,915 laxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/js/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/json/t018cac/lib/python2.7/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:19,915 4 ./Lib/json/tests/test_pass1.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/json/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:19,922 ests/test_pass2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0thon/2.7/iuc/package_pythython2.7/json/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:19,925 b/json/tests/test_recursion.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythonsts install_environment.STDOUT DEBUG 2017-11-18 17:03:19,934 _scanstring.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/json/tfe018cac/lib/python2.7/json/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:19,937 4 ./Lib/json/tests/test_tool.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/json/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:19,954 ests/test_unicode.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/sq/usr/bin/install -c -m 644 ./Lib/sqliteib/python2.7/sqlite3 install_environment.STDOUT DEBUG 2017-11-18 17:03:19,958 4 ./Lib/sqlite3/dump.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b3 install_environment.STDOUT DEBUG 2017-11-18 17:03:19,973 3/test/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/sqlitec/lib/python2.7/sqlite3/test install_environment.STDOUT DEBUG 2017-11-18 17:03:19,976 4 ./Lib/sqlite3/test/factory.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/sqlite3/test install_environment.STDOUT DEBUG 2017-11-18 17:03:19,986 3/test/hooks.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/sqlitee018cac/lib/python2.7/sqlite3/test install_environment.STDOUT DEBUG 2017-11-18 17:03:19,989 4 ./Lib/sqlite3/test/transactions.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/sqlite3/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,007 3/test/types.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/loggin/lib/python2.7/logging install_environment.STDOUT DEBUG 2017-11-18 17:03:20,011 4 ./Lib/logging/config.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,017 ests/test_indent.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/json/t18cac/lib/python2.7/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,017 ests/test_pass2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0thon/2.7/iuc/package_pythython2.7/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,017 b/json/tests/test_recursion.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythonsts tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,018 /usr/bin/install -c -m 644 ./Lib/json/tests/test_pass3.py /galaxydir/galaxy/database/dependencies/pyon_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Li_2_7/8b09fe018cac/lib/python2.7/json/te/usr/bin/install -c -m 644 ./Lib/json/tests/testc/lib/python2.7/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,018 4 ./Lib/json/tests/test_separators.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,018 _scanstring.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/json/tfe018cac/lib/python2.7/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,018 4 ./Lib/json/tests/test_tool.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,018 ests/test_speedups.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/json/te018cac/lib/python2.7/json/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,019 4 ./Lib/sqlite3/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_lite3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,019 ests/test_unicode.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/sq/usr/bin/install -c -m 644 ./Lib/sqliteib/python2.7/sqlite3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,019 4 ./Lib/sqlite3/dump.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,019 3/dbapi2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 6409fe018cac/lib/python2.7/sqlite/usr/bin/install -c -m 644 ./Lib/sqlite18cac/lib/python2.7/sqlite3/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,019 4 ./Lib/sqlite3/test/dbapi.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_sqlite3/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,019 3/test/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/sqlitec/lib/python2.7/sqlite3/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,019 4 ./Lib/sqlite3/test/factory.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/sqlite3/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,020 3/test/dump.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/sqliteac/lib/python2.7/sqlite3/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,020 4 ./Lib/sqlite3/test/py25tests.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/sqlite3/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,020 3/test/hooks.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/sqlitee018cac/lib/python2.7/sqlite3/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,020 4 ./Lib/sqlite3/test/transactions.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/sqlite3/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,020 3/test/regression.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/sqliteac/lib/python2.7/sqlite3/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,020 4 ./Lib/sqlite3/test/userfunctions.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/sqlite3/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,020 3/test/types.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/loggin/lib/python2.7/logging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,020 4 ./Lib/logging/config.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/ing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,020 g/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/logg/usr/bin/install -c -m 644 ./Lib/loggin/lib/python2.7/logging install_environment.STDOUT DEBUG 2017-11-18 17:03:20,027 g/handlers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/bsdd/usr/bin/install -c -m 644 ./Lib/bsddb/hon2.7/bsddb install_environment.STDOUT DEBUG 2017-11-18 17:03:20,037 4 ./Lib/bsddb/dbobj.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/bsddb/usr/bin/install -c -m 644 ./Lib/bsddb/ib/python2.7/bsddb install_environment.STDOUT DEBUG 2017-11-18 17:03:20,041 4 ./Lib/bsddb/dbtables.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/b install_environment.STDOUT DEBUG 2017-11-18 17:03:20,062 dbutils.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/bsddb/cac/lib/python2.7/bsddb/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,065 4 ./Lib/bsddb/test/test_associate.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/bsddb/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,076 test/test_basics.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/bsddb/018cac/lib/python2.7/bsddb/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,079 4 ./Lib/bsddb/test/test_cursor_pget_bug.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/paib/python2.7/bsddb/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,092 test/test_db.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/bsddb/18cac/lib/python2.7/bsddb/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,097 4 ./Lib/bsddb/test/test_dbshelve.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/bsddb/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,109 test/test_dbtables.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64.7/iuc/package_python_2_7/8b09fdb/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,113 b/bsddb/test/test_early_close.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,123 4 ./Lib/bsddb/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/b tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,123 g/handlers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/bsdd/usr/bin/install -c -m 644 ./Lib/bsddb/hon2.7/bsddb tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,123 db.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 649fe018cac/lib/python2.7/bsddb tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,123 4 ./Lib/bsddb/dbrecio.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,123 4 ./Lib/bsddb/dbobj.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/bsddb/usr/bin/install -c -m 644 ./Lib/bsddb/ib/python2.7/bsddb tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,123 4 ./Lib/bsddb/dbtables.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/b tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,123 dbshelve.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/bsdd/usr/bin/install -c -m 644 ./Lib/bsddb/b/python2.7/bsddb tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,123 4 ./Lib/bsddb/test/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,124 dbutils.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/bsddb/cac/lib/python2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,124 4 ./Lib/bsddb/test/test_associate.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,124 test/test_all.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/bsddb/018cac/lib/python2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,124 4 ./Lib/bsddb/test/test_compare.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,124 test/test_basics.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/bsddb/018cac/lib/python2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,124 4 ./Lib/bsddb/test/test_cursor_pget_bug.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/paib/python2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,124 test/test_compat.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64ckage_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 644 ./Lib/bsddb/ac/lib/python2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,124 4 ./Lib/bsddb/test/test_dbenv.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,124 test/test_db.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/bsddb/18cac/lib/python2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,124 4 ./Lib/bsddb/test/test_dbshelve.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,125 test/test_dbobj.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/bsddb/fe018cac/lib/python2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,125 test/test_dbtables.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64.7/iuc/package_python_2_7/8b09fdb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,125 b/bsddb/test/test_early_close.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,125 4 ./Lib/bsddb/test/test_distributed_transactions.py /galaxydir/galaxy/database/dependencies/python/2e018cac/lib/python2.7/bsd/usr/bin/install -c -m 644 ./Lion_2_7/8b09fe018cac/lib/python2.7/bsddb/usr/bin/install -c -m 644 ./Lib/bsddb/test/testb/python2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,125 4 ./Lib/bsddb/test/test_get_none.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,129 _fileid.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64hon/2.7/iuc/package_python_2_7/7/bsddb/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,142 b/bsddb/test/test_lock.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/bsddb/018cac/lib/python2.7/bsddb/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,145 4 ./Lib/bsddb/test/test_queue.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/bsddb/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,154 test/test_recno.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0ies/python/2.7/iuc/packag/lib/python2.7/bsddb/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,157 b/bsddb/test/test_sequence.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_st install_environment.STDOUT DEBUG 2017-11-18 17:03:20,179 _thread.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/wsgire/lib/python2.7/wsgiref install_environment.STDOUT DEBUG 2017-11-18 17:03:20,183 4 ./Lib/wsgiref/handlers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_giref install_environment.STDOUT DEBUG 2017-11-18 17:03:20,195 f/headers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/wsgire/python2.7/wsgiref install_environment.STDOUT DEBUG 2017-11-18 17:03:20,198 4 ./Lib/wsgiref/validate.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_giref install_environment.STDOUT DEBUG 2017-11-18 17:03:20,215 3/Grammar.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/lib2to/lib/python2.7/lib2to3 install_environment.STDOUT DEBUG 2017-11-18 17:03:20,219 4 ./Lib/lib2to3/__main__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b2to3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,227 _fileid.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64hon/2.7/iuc/package_python_2_7/7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,227 /usr/bin/install -c -m 644 ./Lib/bsddb/test/test_join.py /galaxydir/galaxy/database/dependencies/pyt8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Li8b09fe018cac/lib/python2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,227 4 ./Lib/bsddb/test/test_misc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,227 b/bsddb/test/test_lock.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/bsddb/018cac/lib/python2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,228 4 ./Lib/bsddb/test/test_queue.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,228 test/test_pickle.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/bsddb/18cac/lib/python2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,228 test/test_recno.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0ies/python/2.7/iuc/packag/lib/python2.7/bsddb/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,228 3/btm_matcher.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,228 b/bsddb/test/test_sequence.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,228 /usr/bin/install -c -m 644 ./Lib/bsddb/test/test_replication.py /galaxydir/galaxy/database/dependence_python_2_7/8b09fe018cac/usr/bin/install -c -m 644 ./Li2_7/8b09fe018cac/lib/python2.7/bsddb/te/usr/bin/install -c -m 644 ./Lib/bsddb/test/testb/python2.7/bsddb/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,228 4 ./Lib/importlib/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_importlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,228 _thread.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/wsgire/lib/python2.7/wsgiref tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,228 4 ./Lib/wsgiref/handlers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_giref tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,229 f/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/ws/usr/bin/install -c -m 644 ./Lib/wsgirelib/python2.7/wsgiref tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,229 4 ./Lib/wsgiref/simple_server.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/wsgiref tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,229 f/headers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/wsgire/python2.7/wsgiref tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,229 4 ./Lib/wsgiref/validate.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_giref tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,229 f/util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/ws/usr/bin/install -c -m 644 ./Lib/lib2to/lib/python2.7/lib2to3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,229 4 ./Lib/lib2to3/PatternGrammar.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/lib2to3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,229 3/Grammar.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/lib2to/lib/python2.7/lib2to3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,229 4 ./Lib/lib2to3/__main__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b2to3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,229 3/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/li/usr/bin/install -c -m 644 ./Lib/lib2tocac/lib/python2.7/lib2to3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,229 3/btm_matcher.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3 install_environment.STDOUT DEBUG 2017-11-18 17:03:20,234 4 ./Lib/lib2to3/fixer_base.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_lib2to3 install_environment.STDOUT DEBUG 2017-11-18 17:03:20,246 3/fixer_util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 6409fe018cac/lib/python2.7/lib2to/usr/bin/install -c -m 644 ./Lib/lib2tolib/python2.7/lib2to3 install_environment.STDOUT DEBUG 2017-11-18 17:03:20,251 4 ./Lib/lib2to3/pygram.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/to3 install_environment.STDOUT DEBUG 2017-11-18 17:03:20,273 3/pytree.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/li/usr/bin/install -c -m 644 ./Lib/lib2to018cac/lib/python2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,277 4 ./Lib/lib2to3/fixes/fix_apply.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,292 3/fixes/fix_asserts.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 644 ./Lib/lib2tofe018cac/lib/python2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,301 4 ./Lib/lib2to3/fixes/fix_callable.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,312 3/fixes/fix_dict.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64ython/2.7/iuc/package_python_2_2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,315 b/lib2to3/fixes/fix_execfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,326 ix_exitfunc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/lib2tob09fe018cac/lib/python2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,329 4 ./Lib/lib2to3/fixes/fix_future.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,333 4 ./Lib/lib2to3/fixer_base.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_lib2to3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,333 /usr/bin/install -c -m 644 ./Lib/lib2to3/btm_utils.py /galaxydir/galaxy/database/dependencies/python/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/lib2toac/lib/python2.7/lib2to3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,333 4 ./Lib/lib2to3/main.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,333 3/fixer_util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 6409fe018cac/lib/python2.7/lib2to/usr/bin/install -c -m 644 ./Lib/lib2tolib/python2.7/lib2to3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,334 4 ./Lib/lib2to3/pygram.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/to3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,334 3/patcomp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 648b09fe018cac/lib/python2.7/lib2/usr/bin/install -c -m 644 ./Lib/lib2toib/python2.7/lib2to3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,334 4 ./Lib/lib2to3/refactor.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b2to3 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,334 3/pytree.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/li/usr/bin/install -c -m 644 ./Lib/lib2to018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,335 4 ./Lib/lib2to3/fixes/fix_apply.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,335 3/fixes/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/lib2to9fe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,335 4 ./Lib/lib2to3/fixes/fix_basestring.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packapython2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,336 3/fixes/fix_asserts.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 644 ./Lib/lib2tofe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,336 4 ./Lib/lib2to3/fixes/fix_callable.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,336 3/fixes/fix_buffer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/lib2to018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,336 4 ./Lib/lib2to3/fixes/fix_except.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,336 3/fixes/fix_dict.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64ython/2.7/iuc/package_python_2_2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,336 b/lib2to3/fixes/fix_execfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,336 /usr/bin/install -c -m 644 ./Lib/lib2to3/fixes/fix_exec.py /galaxydir/galaxy/database/dependencies/p7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lin_2_7/8b09fe018cac/lib/python2.7/lib2to/usr/bin/install -c -m 644 ./Lib/lib2to3/fixes/fc/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,336 4 ./Lib/lib2to3/fixes/fix_filter.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,336 ix_exitfunc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/lib2tob09fe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,336 4 ./Lib/lib2to3/fixes/fix_future.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,337 3/fixes/fix_funcattrs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/lib2to9fe018cac/lib/python2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,341 3/fixes/fix_getcwdu.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/lib2tofe018cac/lib/python2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,346 4 ./Lib/lib2to3/fixes/fix_import.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,358 3/fixes/fix_imports.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/lib2toe018cac/lib/python2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,362 4 ./Lib/lib2to3/fixes/fix_intern.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,374 3/fixes/fix_isinstance.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/lib2toon_2_7/8b09fe018cac/lib/python2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,378 4 ./Lib/lib2to3/fixes/fix_long.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,390 3/fixes/fix_map.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/lib2to/8b09fe018cac/lib/python2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,393 4 ./Lib/lib2to3/fixes/fix_ne.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,407 3/fixes/fix_next.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/lib2to/8b09fe018cac/lib/python2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,412 4 ./Lib/lib2to3/fixes/fix_operator.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,426 3/fixes/fix_paren.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/lib2toe018cac/lib/python2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,430 4 ./Lib/lib2to3/fixes/fix_raw_input.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,437 4 ./Lib/lib2to3/fixes/fix_has_key.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,437 3/fixes/fix_getcwdu.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/lib2tofe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,437 4 ./Lib/lib2to3/fixes/fix_import.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,437 3/fixes/fix_idioms.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/lib2to9fe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,438 4 ./Lib/lib2to3/fixes/fix_imports2.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,438 3/fixes/fix_imports.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/lib2toe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,438 4 ./Lib/lib2to3/fixes/fix_intern.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,438 3/fixes/fix_input.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/lib2to8b09fe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,438 4 ./Lib/lib2to3/fixes/fix_itertools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,438 3/fixes/fix_isinstance.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/lib2toon_2_7/8b09fe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,439 4 ./Lib/lib2to3/fixes/fix_long.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,439 3/fixes/fix_itertools_imports.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/lib2to18cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,439 4 ./Lib/lib2to3/fixes/fix_metaclass.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,439 3/fixes/fix_map.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/lib2to/8b09fe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,439 4 ./Lib/lib2to3/fixes/fix_ne.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,440 3/fixes/fix_methodattrs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/lib2to018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,440 4 ./Lib/lib2to3/fixes/fix_nonzero.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,440 3/fixes/fix_next.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/lib2to/8b09fe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,440 4 ./Lib/lib2to3/fixes/fix_operator.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,440 3/fixes/fix_numliterals.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/lib2toe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,440 4 ./Lib/lib2to3/fixes/fix_print.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,440 3/fixes/fix_paren.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/lib2toe018cac/lib/python2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,440 3/fixes/fix_reduce.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,441 4 ./Lib/lib2to3/fixes/fix_raw_input.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,441 3/fixes/fix_raise.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/lib2tofe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,441 3/fixes/fix_reduce.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/python2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,445 4 ./Lib/lib2to3/fixes/fix_repr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,455 3/fixes/fix_set_literal.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64ckage_python_2_7/8b09fe018cac/ls install_environment.STDOUT DEBUG 2017-11-18 17:03:20,460 b/lib2to3/fixes/fix_sys_exc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,466 ix_throw.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64kage_python_2_7/8b09fe018cac/li install_environment.STDOUT DEBUG 2017-11-18 17:03:20,471 b/lib2to3/fixes/fix_types.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,483 ix_unicode.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64es/python/2.7/iuc/package_pythothon2.7/lib2to3/fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,488 b/lib2to3/fixes/fix_xrange.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_fixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,532 ix_xreadlines.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/lib2to/usr/bin/install -c -m 644 ./Lib/lib2to3/pgen2/chon/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/li/usr/bin/install -c -m 644 ./Lib/lib2to3/pgen2/grammar.py /galaxydir/galaxy/usr/bin/install -c -m 644 ./Lib/lib2to3/pgen2/literals.py /galaxydir/galaxy/database/dependenon/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/pgen2 install_environment.STDOUT DEBUG 2017-11-18 17:03:20,536 4 ./Lib/lib2to3/pgen2/pgen.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_lib2to3/pgen2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,543 4 ./Lib/lib2to3/fixes/fix_repr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,543 4 ./Lib/lib2to3/fixes/fix_renames.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/lib2to/8b09fe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,543 3/fixes/fix_set_literal.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64ckage_python_2_7/8b09fe018cac/ls tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,543 b/lib2to3/fixes/fix_sys_exc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,543 4 ./Lib/lib2to3/fixes/fix_standarderror.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/paib/python2.7/lib2to3/fixe/usr/bin/install -c -m 644 ./Li_2_7/8b09fe018cac/lib/python2.7/lib2to3/usr/bin/install -c -m 644 ./Lib/lib2to3/fixes/fib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,543 ix_throw.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64kage_python_2_7/8b09fe018cac/li tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,543 b/lib2to3/fixes/fix_types.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,544 4 ./Lib/lib2to3/fixes/fix_tuple_params.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/lib2to3/fixes/usr/bin/install -c -m 644 ./Li_7/8b09fe018cac/lib/python2.7/lib2to3/f/usr/bin/install -c -m 644 ./Lib/lib2to3/fixes/f/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,544 4 ./Lib/lib2to3/fixes/fix_urllib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,544 ix_unicode.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64es/python/2.7/iuc/package_pythothon2.7/lib2to3/fixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,544 b/lib2to3/fixes/fix_xrange.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_fixes 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64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/lib2to/usr/bin/install -c -m 644 ./Lib/lib2to3/pgen2/chon/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/li/usr/bin/install -c -m 644 ./Lib/lib2to3/pgen2/grammar.py /galaxydir/galaxy/usr/bin/install -c -m 644 ./Lib/lib2to3/pgen2/literals.py /galaxydir/galaxy/database/dependenon/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/pgen2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,545 4 ./Lib/lib2to3/pgen2/pgen.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_lib2to3/pgen2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,545 /usr/bin/install -c -m 644 ./Lib/lib2to3/pgen2/parse.py /galaxydir/galaxy/database/dependencies/pyth/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c ./Lib/lib2to3/pgen2/python2.7/lib2to3/pgen2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,545 4 ./Lib/lib2to3/pgen2/tokenize.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/pgen2 install_environment.STDOUT DEBUG 2017-11-18 17:03:20,552 /token.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 64ython/2.7/iuc/package_python_2_2.7/lib2to3/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:20,556 o3/tests/pytree_idempotency.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:20,565 upport.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 64age_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 644 ./Lib/lib2to9fe018cac/lib/python2.7/lib2to3/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:20,569 4 ./Lib/lib2to3/tests/test_main.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/lib2to3/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:20,580 3/tests/test_parser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/lib2tob09fe018cac/lib/python2.7/lib2to3/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:20,584 4 ./Lib/lib2to3/tests/test_util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/lib2to3/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:20,603 3/tests/data/README /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/lib2toe018cac/lib/python2.7/lib2to3/tests/data install_environment.STDOUT DEBUG 2017-11-18 17:03:20,614 /lib2to3/tests/data/different_encoding.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/lib2to3/tests/usr/bin/install -c ./Lib/lib2tn_2_7/8b09fe018cac/lib/python2.7/lib2to/usr/bin/install -c -m 644 ./Lib/lib2to3/tests/d8b09fe018cac/lib/python2.7/lib2to3/tests/data install_environment.STDOUT DEBUG 2017-11-18 17:03:20,629 4 ./Lib/lib2to3/tests/data/py2_test_grammar.py /galaxydir/galaxy/database/dependencies/python/2.7/iuac/lib/python2.7/lib2to3//usr/bin/install -c -m 644 ./Liage_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/lib2to3/tests/d09fe018cac/lib/python2.7/lib2to3/tests/data/fixers install_environment.STDOUT DEBUG 2017-11-18 17:03:20,636 4 ./Lib/lib2to3/tests/data/fixers/no_fixer_cls.py /galaxydir/galaxy/database/dependencies/python/2.718cac/lib/python2.7/lib2t/usr/bin/install -c -m 644 ./Li/package_python_2_7/8b09fe018cac/lib/pya/fixers tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,646 /token.py 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,647 upport.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 64age_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 644 ./Lib/lib2to9fe018cac/lib/python2.7/lib2to3/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,647 4 ./Lib/lib2to3/tests/test_main.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/lib2to3/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,647 3/tests/test_fixers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/lib2to9fe018cac/lib/python2.7/lib2to3/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,647 4 ./Lib/lib2to3/tests/test_pytree.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/lib2to3/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,647 3/tests/test_parser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/lib2tob09fe018cac/lib/python2.7/lib2to3/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,647 4 ./Lib/lib2to3/tests/test_util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/lib2to3/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,647 3/tests/test_refactor.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 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o3/tests/data/false_encoding.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho3/tests/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,648 /lib2to3/tests/data/different_encoding.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/lib2to3/tests/usr/bin/install -c ./Lib/lib2tn_2_7/8b09fe018cac/lib/python2.7/lib2to/usr/bin/install -c -m 644 ./Lib/lib2to3/tests/d8b09fe018cac/lib/python2.7/lib2to3/tests/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,648 ata/infinite_recursion.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64c/package_python_2_7/8b09fe018ctests/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,648 b/lib2to3/tests/data/py3_test_grammar.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack.7/lib2to3/tests/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,648 4 ./Lib/lib2to3/tests/data/py2_test_grammar.py /galaxydir/galaxy/database/dependencies/python/2.7/iuac/lib/python2.7/lib2to3//usr/bin/install -c -m 644 ./Liage_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/lib2to3/tests/d09fe018cac/lib/python2.7/lib2to3/tests/data/fixers tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,648 ata/fixers/bad_order.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64/iuc/package_python_2_7/8b09fe0o3/tests/data/fixers tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,648 4 ./Lib/lib2to3/tests/data/fixers/no_fixer_cls.py /galaxydir/galaxy/database/dependencies/python/2.718cac/lib/python2.7/lib2t/usr/bin/install -c -m 644 ./Li/package_python_2_7/8b09fe018cac/lib/pya/fixers tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,648 b/lib2to3/tests/data/fixers/parrot_example.py /galaxydir/galaxy/database/dependencies/python/2.7/iucthon2.7/lib2to3/tests/dat/usr/bin/install -c -m 644 ./Liuc/package_python_2_7/8b09fe018cac/lib/ata/fixers/myfixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,648 b/lib2to3/tests/data/fixers/myfixes/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/ipython2.7/lib2to3/tests/d/usr/bin/install -c -m 644 ./Li.7/iuc/package_python_2_7/8b09fe018cac/ts/data/fixers/myfixes install_environment.STDOUT DEBUG 2017-11-18 17:03:20,657 b/lib2to3/tests/data/fixers/myfixes/fix_first.py /galaxydir/galaxy/database/dependencies/python/2.7//python2.7/lib2to3/tests//usr/bin/install -c -m 644 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install_environment.STDOUT DEBUG 2017-11-18 17:03:20,708 4 ./Lib/ctypes/test/test_array_in_pointer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc//lib/python2.7/ctypes/tes/usr/bin/install -c -m 644 ./Li_7/8b09fe018cac/lib/python2.7/ctypes/te/usr/bin/install -c -m 644 ./Lib/ctypes/test/tes8cac/lib/python2.7/ctypes/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,712 4 ./Lib/ctypes/test/test_bitfields.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/ctypes/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,723 /test/test_buffers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/ctypes09fe018cac/lib/python2.7/ctypes/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,726 4 ./Lib/ctypes/test/test_cast.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/ctypes/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,735 /test/test_cfuncs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 644 ./Lib/ctypesfe018cac/lib/python2.7/ctypes/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,740 4 ./Lib/ctypes/test/test_errno.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,749 b/lib2to3/tests/data/fixers/myfixes/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/ipython2.7/lib2to3/tests/d/usr/bin/install -c -m 644 ./Li.7/iuc/package_python_2_7/8b09fe018cac/ts/data/fixers/myfixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,749 b/lib2to3/tests/data/fixers/myfixes/fix_explicit.py /galaxydir/galaxy/database/dependencies/python/2lib/python2.7/lib2to3/tes/usr/bin/install -c -m 644 ./Liiuc/package_python_2_7/8b09fe018cac/libdata/fixers/myfixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,749 b/lib2to3/tests/data/fixers/myfixes/fix_first.py /galaxydir/galaxy/database/dependencies/python/2.7//python2.7/lib2to3/tests//usr/bin/install -c -m 644 ./Liuc/package_python_2_7/8b09fe018cac/lib/ata/fixers/myfixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,749 b/lib2to3/tests/data/fixers/myfixes/fix_last.py /galaxydir/galaxy/database/dependencies/python/2.7/ipython2.7/lib2to3/tests/d/usr/bin/install -c -m 644 ./Li/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/tests/data/fixers/myfixes tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,749 b/lib2to3/tests/data/fixers/myfixes/fix_parrot.py 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64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/ctypes18cac/lib/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,750 /test/test_anon.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64package_python_2_7/8b09fe018cact tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,750 b/ctypes/test/test_arrays.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2st tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,750 4 ./Lib/ctypes/test/test_array_in_pointer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc//lib/python2.7/ctypes/tes/usr/bin/install -c -m 644 ./Li_7/8b09fe018cac/lib/python2.7/ctypes/te/usr/bin/install -c -m 644 ./Lib/ctypes/test/tes8cac/lib/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,750 4 ./Lib/ctypes/test/test_bitfields.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,751 t_as_parameter.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/ctypesfe018cac/lib/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,751 4 ./Lib/ctypes/test/test_byteswap.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,752 /test/test_buffers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/ctypes09fe018cac/lib/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,752 4 ./Lib/ctypes/test/test_cast.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,752 /test/test_callbacks.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/ctypese018cac/lib/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,752 4 ./Lib/ctypes/test/test_checkretval.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packapython2.7/ctypes/test 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4 ./Lib/ctypes/test/test_frombuffer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,753 /test/test_funcptr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ctypes/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,754 /test/test_find.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/ctypeses/python/2.7/iuc/package_python_2_7/8b09fe018cast install_environment.STDOUT DEBUG 2017-11-18 17:03:20,757 b/ctypes/test/test_incomplete.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyths/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,766 t_init.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/ctypes9fe018cac/lib/python2.7/ctypes/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,771 4 ./Lib/ctypes/test/test_libc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/ctypes/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,781 /test/test_loading.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/ctypes/8b09fe018cac/lib/python2.7/ctypes/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,786 4 ./Lib/ctypes/test/test_numbers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/ctypes/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,796 /test/test_objects.py 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-m 644 ./Lib/ctypeses/python/2.7/iuc/package_python_2_7/8b09fe018cast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,856 b/ctypes/test/test_incomplete.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyths/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,856 /usr/bin/install -c -m 644 ./Lib/ctypes/test/test_functions.py /galaxydir/galaxy/database/dependencic/lib/python2.7/ctypes/te/usr/bin/install -c -m 644 ./Lion_2_7/8b09fe018cac/lib/python2.7/ctype/usr/bin/install -c -m 644 ./Lib/ctypes/test/tes/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,856 4 ./Lib/ctypes/test/test_internals.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,856 t_init.py 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/galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,858 t_python_api.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64kage_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 644 ./Lib/ctypes09fe018cac/lib/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,858 4 ./Lib/ctypes/test/test_repr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,858 /test/test_refcounts.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/ctypes_7/8b09fe018cac/lib/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,858 /test/test_returnfuncptrs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/usr/bin/install -c -m 64package_python_2_7/8b09fe018cact tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,858 b/ctypes/test/test_sizes.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_t tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,858 4 ./Lib/ctypes/test/test_simplesubclasses.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc//lib/python2.7/ctypes/tes/usr/bin/install -c -m 644 ./Li7/8b09fe018cac/lib/python2.7/ctypes/tes/usr/bin/install -c -m 644 ./Lib/ctypes/test/teslib/python2.7/ctypes/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,858 /test/test_strings.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64kage_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 644 ./Lib/ctypes/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,859 4 ./Lib/ctypes/test/test_stringptr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,859 t_slicing.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/ctypesfe018cac/lib/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,859 4 ./Lib/ctypes/test/test_struct_fields.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,859 /test/test_structures.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,859 /test/test_strings.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64kage_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 644 ./Lib/ctypes/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ctypes/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,863 4 ./Lib/ctypes/test/test_unicode.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/ctypes/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,874 /test/test_values.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64ckage_python_2_7/8b09fe018cac/lython/2.7/iuc/package_python_2_7/8b09fees/test install_environment.STDOUT DEBUG 2017-11-18 17:03:20,877 b/ctypes/test/test_wintypes.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythontest install_environment.STDOUT DEBUG 2017-11-18 17:03:20,890 /README.ctypes /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/python2.7/ctypes/macholib install_environment.STDOUT DEBUG 2017-11-18 17:03:20,893 /usr/bin/install -c -m 644 ./Lib/ctypes/macholib/dyld.py /galaxydir/galaxy/database/dependencies/pytn_2_7/8b09fe018cac/lib/python2.7/ctypes/macholib install_environment.STDOUT DEBUG 2017-11-18 17:03:20,896 /usr/bin/install -c -m 644 ./Lib/ctypes/macholib/dylib.py /galaxydir/galaxy/database/dependencies/py/8b09fe018cac/lib/python2.7/ctypes/macholib install_environment.STDOUT DEBUG 2017-11-18 17:03:20,907 /usr/bin/install -c ./Lib/ctypes/macholib/fetch_macholib /galaxydir/galaxy/database/dependencies/pyt8cac/lib/python2.7/ctypes/usr/bin/install -c -m 644 ./Lipython_2_7/8b09fe018cac/lib/python2.7/c/usr/bin/install -c -m 644 ./Lib/ctypes/macholib/lib/python2.7/ctypes/macholib install_environment.STDOUT DEBUG 2017-11-18 17:03:20,919 4 ./Lib/idlelib/AutoComplete.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:20,924 /usr/bin/install -c -m 644 ./Lib/idlelib/AutoCompleteWindow.py /galaxydir/galaxy/database/dependenci09fe018cac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:20,929 and.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:20,932 4 ./Lib/idlelib/CREDITS.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_lelib install_environment.STDOUT DEBUG 2017-11-18 17:03:20,941 b/CallTipWindow.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/id/usr/bin/install -c -m 644 ./Lib/idleliib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:20,948 /usr/bin/install -c -m 644 ./Lib/idlelib/ClassBrowser.py /galaxydir/galaxy/database/dependencies/pytn_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib09fe018cac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:20,952 4 ./Lib/idlelib/ColorDelegator.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:20,962 b/Debugger.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/i/usr/bin/install -c -m 644 ./Lib/idleli8cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,964 4 ./Lib/ctypes/test/test_unicode.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,964 /usr/bin/install -c -m 644 ./Lib/ctypes/test/test_unaligned_structures.py /galaxydir/galaxy/database/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/ctypese018cac/lib/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,964 4 ./Lib/ctypes/test/test_varsize_struct.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/paib/python2.7/ctypes/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,964 /test/test_values.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64ckage_python_2_7/8b09fe018cac/lython/2.7/iuc/package_python_2_7/8b09fees/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,964 b/ctypes/test/test_wintypes.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythontest tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,964 /usr/bin/install -c -m 644 ./Lib/ctypes/test/test_win32.py /galaxydir/galaxy/database/dependencies/p018cac/lib/python2.7/ctyp/usr/bin/install -c -m 644 ./Li_2_7/8b09fe018cac/lib/python2.7/ctypes//usr/bin/install -c -m 644 ./Lib/ctypes/macholibc/lib/python2.7/ctypes/macholib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,964 /README.ctypes /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/python2.7/ctypes/macholib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,965 /usr/bin/install -c -m 644 ./Lib/ctypes/macholib/dyld.py /galaxydir/galaxy/database/dependencies/pytn_2_7/8b09fe018cac/lib/python2.7/ctypes/macholib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,965 /usr/bin/install -c -m 644 ./Lib/ctypes/macholib/dylib.py /galaxydir/galaxy/database/dependencies/py/8b09fe018cac/lib/python2.7/ctypes/macholib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,965 4 ./Lib/ctypes/macholib/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_phon/2.7/iuc/package_pythothon/2.7/iuc/package_python_2_7hon/2.7/iuc/package_python_2_7/8b09fe01/macholib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,965 b/ctypes/macholib/fetch_macholib.bat /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_types/macholib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,965 /usr/bin/install -c ./Lib/ctypes/macholib/fetch_macholib /galaxydir/galaxy/database/dependencies/pyt8cac/lib/python2.7/ctypes/usr/bin/install -c -m 644 ./Lipython_2_7/8b09fe018cac/lib/python2.7/c/usr/bin/install -c -m 644 ./Lib/ctypes/macholib/lib/python2.7/ctypes/macholib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,965 4 ./Lib/idlelib/AutoComplete.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,965 /usr/bin/install -c -m 644 ./Lib/idlelib/AutoCompleteWindow.py /galaxydir/galaxy/database/dependenci09fe018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,965 /framework.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2.es/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 644 ./Lib/idlelib/AutoExpthon2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,965 and.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,966 4 ./Lib/idlelib/CREDITS.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_lelib install_environment.STDOUT DEBUG 2017-11-18 17:03:20,966 4 ./Lib/idlelib/FileList.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,966 4 ./Lib/idlelib/Bindings.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/id/usr/bin/install -c -m 644 ./Lib/idleli18cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,966 4 ./Lib/idlelib/CallTips.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_lelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,966 b/CallTipWindow.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/id/usr/bin/install -c -m 644 ./Lib/idleliib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,966 b/ChangeLog /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lhon/2.7/iuc/package_pythothon2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,966 /usr/bin/install -c -m 644 ./Lib/idlelib/ClassBrowser.py /galaxydir/galaxy/database/dependencies/pytn_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib09fe018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,966 4 ./Lib/idlelib/ColorDelegator.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,966 b/idlelib/CodeContext.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/idleli/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,966 4 ./Lib/idlelib/Delegator.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2dlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,966 b/Debugger.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/i/usr/bin/install -c -m 644 ./Lib/idleli8cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:20,967 4 ./Lib/idlelib/FileList.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:20,975 /usr/bin/install -c -m 644 ./Lib/idlelib/FormatParagraph.py /galaxydir/galaxy/database/dependencies/_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Li09fe018cac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:20,988 4 ./Lib/idlelib/HISTORY.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_on/2.7/iuc/package_python/2.7/iuc/package_python_2_7/8b0on/2.7/iuc/package_python_2_7/8b09fe018 install_environment.STDOUT DEBUG 2017-11-18 17:03:20,999 b/idlelib/MultiCall.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/idlelib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,004 4 ./Lib/idlelib/ObjectBrowser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,016 b/OutputWindow.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/idlelicac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,020 4 ./Lib/idlelib/Percolator.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,026 b/PyParse.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c ./Lib018cac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,030 4 ./Lib/idlelib/README.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7elib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,043 b/RemoteDebugger.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/idleli18cac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,047 4 ./Lib/idlelib/RstripExtension.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,058 b/ScriptBinding.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2.hon/2.7/iuc/package_python_2_7/8b09fe01b install_environment.STDOUT DEBUG 2017-11-18 17:03:21,067 b/idlelib/SearchDialogBase.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/idlelicac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,067 b/EditorWindow.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64python/2.7/iuc/package_python_2n2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,067 /usr/bin/install -c -m 644 ./Lib/idlelib/FormatParagraph.py /galaxydir/galaxy/database/dependencies/_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Li09fe018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,067 b/idlelib/GrepDialog.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,067 /usr/bin/install -c -m 644 ./Lib/idlelib/HyperParser.py /galaxydir/galaxy/database/dependencies/pyth_2_7/8b09fe018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,067 /usr/bin/install -c -m 644 ./Lib/idlelib/IOBinding.py /galaxydir/galaxy/database/dependencies/python9fe018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,068 4 ./Lib/idlelib/HISTORY.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_on/2.7/iuc/package_python/2.7/iuc/package_python_2_7/8b0on/2.7/iuc/package_python_2_7/8b09fe018 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,068 /usr/bin/install -c -m 644 ./Lib/idlelib/IdleHistory.py /galaxydir/galaxy/database/dependencies/pythcac/lib/python2.7/idlelib/usr/bin/install -c -m 644 ./Li9fe018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,068 4 ./Lib/idlelib/MultiStatusBar.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,068 b/idlelib/MultiCall.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/idlelib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,068 4 ./Lib/idlelib/ObjectBrowser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,068 b/NEWS.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/idleli8cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,068 4 ./Lib/idlelib/ParenMatch.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,068 b/OutputWindow.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/idlelicac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,069 4 ./Lib/idlelib/Percolator.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,069 b/PathBrowser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/idlelilib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,069 b/PyParse.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c ./Lib018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,069 4 ./Lib/idlelib/README.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7elib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,069 /idlelib/PyShell.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/idl/usr/bin/install -c -m 644 ./Lib/idleli018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,069 4 ./Lib/idlelib/RemoteObjectBrowser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,069 b/RemoteDebugger.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/idleli18cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,069 4 ./Lib/idlelib/RstripExtension.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,069 b/ReplaceDialog.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/idleli18cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,069 4 ./Lib/idlelib/ScrolledList.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,069 b/ScriptBinding.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2.hon/2.7/iuc/package_python_2_7/8b09fe01b tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,070 /usr/bin/install -c -m 644 ./Lib/idlelib/SearchDialog.py /galaxydir/galaxy/database/dependencies/pyt8cac/lib/python2.7/idleli/usr/bin/install -c -m 644 ./Li2_7/8b09fe018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,070 4 ./Lib/idlelib/SearchEngine.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,070 b/idlelib/SearchDialogBase.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/idlelicac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,071 4 ./Lib/idlelib/TODO.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8ib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,087 b/ToolTip.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/idleli18cac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,092 4 ./Lib/idlelib/WidgetRedirector.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,117 b/WindowList.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c2.7/iuc/package_python_2_on/2.7/iuc/package_python_2_7/8/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,126 b/idlelib/config-extensions.def /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythob install_environment.STDOUT DEBUG 2017-11-18 17:03:21,137 highlight.def /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cachon/2.7/iuc/package_pythothon2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,148 b/idlelib/config-main.def /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64thon/2.7/iuc/package_python_2_7.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,152 b/idlelib/configHelpSourceEdit.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytlib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,165 ectionNameDialog.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/idlelilib/python2.7/idlelib 127.0.0.1 - - [18/Nov/2017:17:03:21 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,174 4 ./Lib/idlelib/TODO.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8ib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,174 b/StackViewer.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/idlel/usr/bin/install -c -m 644 ./Lib/idlelilib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,174 4 ./Lib/idlelib/TreeWidget.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,174 b/ToolTip.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/idleli18cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,175 4 ./Lib/idlelib/WidgetRedirector.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,175 b/UndoDelegator.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/idleliac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,175 /usr/bin/install -c -m 644 ./Lib/idlelib/ZoomHeight.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,175 /usr/bin/install -c -m 644 ./Lib/idlelib/help.txt /galaxydir/galaxy/database/dependencies/python/2.7b09fe018cac/lib/python2.7ckage_python_2_7/8b09fe018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,175 /usr/bin/install -c -m 644 ./Lib/idlelib/__init__.py /galaxydir/galaxy/database/dependencies/python/7/8b09fe018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,176 b/WindowList.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c2.7/iuc/package_python_2_on/2.7/iuc/package_python_2_7/8/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,176 b/idlelib/config-extensions.def /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythob tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,176 /usr/bin/install -c -m 644 ./Lib/idlelib/aboutDialog.py /galaxydir/galaxy/database/dependencies/pythb09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lin_2_7/8b09fe018cac/lib/python2.7/idleli/usr/bin/install -c -m 644 ./Lib/idlelib/config-/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,176 highlight.def /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cachon/2.7/iuc/package_pythothon2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,176 /usr/bin/install -c -m 644 ./Lib/idlelib/config-keys.def /galaxydir/galaxy/database/dependencies/pytn_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Li8b09fe018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,176 4 ./Lib/idlelib/configDialog.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,176 b/idlelib/config-main.def /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64thon/2.7/iuc/package_python_2_7.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,176 b/idlelib/configHelpSourceEdit.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,176 /usr/bin/install -c -m 644 ./Lib/idlelib/configHandler.py /galaxydir/galaxy/database/dependencies/py/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lihon_2_7/8b09fe018cac/lib/python2.7/idle/usr/bin/install -c -m 644 ./Lib/idlelib/configS018cac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,176 4 ./Lib/idlelib/dynOptionMenuWidget.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,176 ectionNameDialog.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/idlelilib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,177 b/extend.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//iuc/package_python_2_7/8/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,177 /usr/bin/install -c -m 644 ./Lib/idlelib/help.txt /galaxydir/galaxy/database/dependencies/python/2.7b09fe018cac/lib/python2.7ckage_python_2_7/8b09fe018cac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,181 4 ./Lib/idlelib/idle.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8bb install_environment.STDOUT DEBUG 2017-11-18 17:03:21,194 b/idle.pyw /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/idl/usr/bin/install -c -m 644 ./Lib/idlelife018cac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,197 4 ./Lib/idlelib/macosxSupport.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,207 b/rpc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 649fe018cac/lib/python2.7/idlelib/usr/bin/install -c -m 644 ./Lib/idlelicac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,211 4 ./Lib/idlelib/textView.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_lelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,235 b/Icons/folder.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/idlelicac/lib/python2.7/idlelib/Icons install_environment.STDOUT DEBUG 2017-11-18 17:03:21,239 4 ./Lib/idlelib/Icons/idle_16.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/idlelib/Icons install_environment.STDOUT DEBUG 2017-11-18 17:03:21,249 b/Icons/idle_16.png /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/idleli018cac/lib/python2.7/idlelib/Icons install_environment.STDOUT DEBUG 2017-11-18 17:03:21,252 4 ./Lib/idlelib/Icons/idle_48.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/idlelib/Icons install_environment.STDOUT DEBUG 2017-11-18 17:03:21,261 b/Icons/idle_48.png /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/idleli9fe018cac/lib/python2.7/idlelib/Icons install_environment.STDOUT DEBUG 2017-11-18 17:03:21,264 4 ./Lib/idlelib/Icons/plusnode.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/idlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,281 4 ./Lib/idlelib/idle.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8bb tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,281 /usr/bin/install -c ./Lib/idlelib/idle.bat /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pa/usr/bin/install -c -m 6409fe018cac/lib/python2.7/idleli/usr/bin/install -c -m 644 ./Lib/idlelib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,281 4 ./Lib/idlelib/idlever.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7elib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,281 b/idle.pyw /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/idl/usr/bin/install -c -m 644 ./Lib/idlelife018cac/lib/python2.7/idlelib install_environment.STDOUT DEBUG 2017-11-18 17:03:21,284 b/Icons/python.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/i/usr/bin/install -c -m 644 ./Lib/idleli9fe018cac/lib/python2.7/idlelib/idle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,284 4 ./Lib/idlelib/macosxSupport.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,284 b/keybindingDialog.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/idlelipython2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,284 4 ./Lib/idlelib/run.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,285 b/rpc.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 649fe018cac/lib/python2.7/idlelib/usr/bin/install -c -m 644 ./Lib/idlelicac/lib/python2.7/idlelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,285 4 ./Lib/idlelib/textView.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_lelib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,285 b/tabbedpages.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/id/usr/bin/install -c -m 644 ./Lib/idleli18cac/lib/python2.7/idlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,285 4 ./Lib/idlelib/Icons/idle.icns /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/idlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,289 b/Icons/folder.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/idlelicac/lib/python2.7/idlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,289 4 ./Lib/idlelib/Icons/idle_16.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/idlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,289 b/Icons/idle.ico /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/idleli018cac/lib/python2.7/idlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,289 4 ./Lib/idlelib/Icons/idle_32.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/idlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,289 b/Icons/idle_16.png /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/idleli018cac/lib/python2.7/idlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,289 4 ./Lib/idlelib/Icons/idle_48.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/idlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,289 b/Icons/idle_32.png /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/idleli018cac/lib/python2.7/idlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,289 4 ./Lib/idlelib/Icons/minusnode.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/idlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,290 b/Icons/idle_48.png /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/idleli9fe018cac/lib/python2.7/idlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,290 4 ./Lib/idlelib/Icons/plusnode.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/idlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,290 b/Icons/openfolder.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/idleli18cac/lib/python2.7/idlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,290 4 ./Lib/idlelib/Icons/tk.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2dlelib/Icons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,290 b/Icons/python.gif /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/i/usr/bin/install -c -m 644 ./Lib/idleli9fe018cac/lib/python2.7/idlelib/idle_test install_environment.STDOUT DEBUG 2017-11-18 17:03:21,297 4 ./Lib/idlelib/idle_test/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/idlelib/idle_test/usr/bin/install -c -m 644 ./Li_7/8b09fe018cac/lib/python2.7/idlelib/i/usr/bin/install -c -m 644 ./Lib/idlelib/idle_teac/lib/python2.7/idlelib/idle_test install_environment.STDOUT DEBUG 2017-11-18 17:03:21,300 4 ./Lib/idlelib/idle_test/mock_tk.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/idlelib/idle_test install_environment.STDOUT DEBUG 2017-11-18 17:03:21,311 b/idle_test/test_autocomplete.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythendencies/python/2.7/iuc/018cac/lib/python2.7/idlelib/id/usr/bin/install -c -m 644 ./Lib/idleli_7/8b09fe018cac/lib/python2.7/idlelib/idle_test install_environment.STDOUT DEBUG 2017-11-18 17:03:21,324 4 ./Lib/idlelib/idle_test/test_config_name.py /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/idlelib/i/usr/bin/install -c -m 644 ./Liage_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/idlelib/idle_tee018cac/lib/python2.7/idlelib/idle_test install_environment.STDOUT DEBUG 2017-11-18 17:03:21,339 4 ./Lib/idlelib/idle_test/test_formatparagraph.py /galaxydir/galaxy/database/dependencies/python/2.718cac/lib/python2.7/idlel/usr/bin/install -c -m 644 ./Lion_2_7/8b09fe018cac/lib/python2.7/idlel/usr/bin/install -c -m 644 ./Lib/idlelib/idle_te9fe018cac/lib/python2.7/idlelib/idle_test install_environment.STDOUT DEBUG 2017-11-18 17:03:21,349 4 ./Lib/idlelib/idle_test/test_idlehistory.py /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/idlelib/i/usr/bin/install -c -m 644 ./Li_2_7/8b09fe018cac/lib/python2.7/idlelib/usr/bin/install -c -m 644 ./Lib/idlelib/idle_tefe018cac/lib/python2.7/idlelib/idle_test install_environment.STDOUT DEBUG 2017-11-18 17:03:21,360 4 ./Lib/idlelib/idle_test/test_pathbrowser.py /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/idlelib/i/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/idl/usr/bin/install -c -m 644 ./Lib/idlelib/idle_te7/8b09fe018cac/lib/python2.7/idlelib/idle_test install_environment.STDOUT DEBUG 2017-11-18 17:03:21,370 4 ./Lib/idlelib/idle_test/test_searchengine.py /galaxydir/galaxy/database/dependencies/python/2.7/iuac/lib/python2.7/idlelib//usr/bin/install -c -m 644 ./Lion_2_7/8b09fe018cac/lib/python2.7/idlel/usr/bin/install -c -m 644 ./Lib/idlelib/idle_te018cac/lib/python2.7/idlelib/idle_test install_environment.STDOUT DEBUG 2017-11-18 17:03:21,374 4 ./Lib/idlelib/idle_test/test_warning.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/idlelib/idle_test install_environment.STDOUT DEBUG 2017-11-18 17:03:21,379 b/idle_test/test_widgetredir.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythost tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,391 b/idle_test/README.txt /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,391 b/idlelib/idle_test/htest.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2dle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,391 4 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./Lib/idlelib/idle_test/test_autoexpand.py /galaxydir/galaxy/database/deppackage_python_2_7/8b09fele_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,392 b/idle_test/test_autocomplete.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythendencies/python/2.7/iuc/018cac/lib/python2.7/idlelib/id/usr/bin/install -c -m 644 ./Lib/idleli_7/8b09fe018cac/lib/python2.7/idlelib/idle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,392 b/idle_test/test_calltips.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/usr/bin/install -c -m 64/package_python_2_7/8b09fe018cadle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,392 b/idlelib/idle_test/test_configdialog.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack.7/idlelib/idle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,392 4 ./Lib/idlelib/idle_test/test_config_name.py /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/idlelib/i/usr/bin/install -c -m 644 ./Liage_python_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/idlelib/idle_tee018cac/lib/python2.7/idlelib/idle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,392 st/test_delegator.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64/iuc/package_python_2_7/8b09fe0ib/idle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,392 b/idlelib/idle_test/test_grep.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythib/idle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,392 4 ./Lib/idlelib/idle_test/test_formatparagraph.py /galaxydir/galaxy/database/dependencies/python/2.718cac/lib/python2.7/idlel/usr/bin/install -c -m 644 ./Lion_2_7/8b09fe018cac/lib/python2.7/idlel/usr/bin/install -c -m 644 ./Lib/idlelib/idle_te9fe018cac/lib/python2.7/idlelib/idle_test install_environment.STDOUT DEBUG 2017-11-18 17:03:21,392 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,392 st/test_hyperparser.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64/package_python_2_7/8b09fe018cadle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,393 b/idlelib/idle_test/test_io.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/idle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,393 4 ./Lib/idlelib/idle_test/test_idlehistory.py /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/idlelib/i/usr/bin/install -c -m 644 ./Li_2_7/8b09fe018cac/lib/python2.7/idlelib/usr/bin/install -c -m 644 ./Lib/idlelib/idle_tefe018cac/lib/python2.7/idlelib/idle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,393 st/test_parenmatch.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64/package_python_2_7/8b09fe018cadle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,393 b/idlelib/idle_test/test_rstrip.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyelib/idle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,393 4 ./Lib/idlelib/idle_test/test_pathbrowser.py /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/idlelib/i/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/idl/usr/bin/install -c -m 644 ./Lib/idlelib/idle_te7/8b09fe018cac/lib/python2.7/idlelib/idle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,393 st/test_searchdialogbase.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/usr/bin/install -c -m 64c/package_python_2_7/8b09fe018cidle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,393 b/idlelib/idle_test/test_text.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythib/idle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,393 4 ./Lib/idlelib/idle_test/test_searchengine.py /galaxydir/galaxy/database/dependencies/python/2.7/iuac/lib/python2.7/idlelib//usr/bin/install -c -m 644 ./Lion_2_7/8b09fe018cac/lib/python2.7/idlel/usr/bin/install -c -m 644 ./Lib/idlelib/idle_te018cac/lib/python2.7/idlelib/idle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,393 4 ./Lib/idlelib/idle_test/test_warning.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/idlelib/idle_test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,394 b/idle_test/test_widgetredir.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythost tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,394 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,397 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,400 cies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,403 age_python_2_7/8b09fe018cac/lib/python2.7/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,407 python2.7/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,425 /usr/bin/install -c -m 644 ./Lib/distutils/config.py /galaxydir/galaxy/database/dependencies/python//usr/bin/install -c -m 648b09fe018cac/lib/python2.7/dist/usr/bin/install -c -m 644 ./Lib/distut9fe018cac/lib/python2.7/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,430 4 ./Lib/distutils/debug.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7tutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,441 ils/dep_util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/distutib/python2.7/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,445 4 ./Lib/distutils/emxccompiler.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,457 ils/errors.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/distut018cac/lib/python2.7/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,460 4 ./Lib/distutils/file_util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,475 ils/filelist.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/distu/usr/bin/install -c -m 644 ./Lib/distute018cac/lib/python2.7/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,481 4 ./Lib/distutils/msvccompiler.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,500 tabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,500 cies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,500 age_python_2_7/8b09fe018cac/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,500 python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,500 st/test_textview.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64kage_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 644 ./Lib/idlelin_2_7/8b09fe018cac/lib/python2.7/idlelib/idle_te/usr/bin/install -c -m 644 ./Lib/distutils/README /galaxydir/usr/bin/install -c -m 644 ./Lib/distutils/__init__.py /galaxydir/galaxy/da/usr/bin/install -c -m 644 ./Lib/distutils/archive_util.py /galaxydir/galaxy/database/dependen/usr/bin/install -c -m 644 ./Lib/distutils/bcppcompiler.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack/usr/bin/install -c -m 644 ./Lib/distutils/ccompiler.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 644 ./Lib/distutils/cmd.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,501 2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,501 4 ./Lib/distutils/core.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/utils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,502 /usr/bin/install -c -m 644 ./Lib/distutils/config.py /galaxydir/galaxy/database/dependencies/python//usr/bin/install -c -m 648b09fe018cac/lib/python2.7/dist/usr/bin/install -c -m 644 ./Lib/distut9fe018cac/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,502 4 ./Lib/distutils/debug.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7tutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,502 ils/cygwinccompiler.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/dis/usr/bin/install -c -m 644 ./Lib/distutac/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,502 4 ./Lib/distutils/dir_util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,506 ils/dep_util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/distutib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,506 4 ./Lib/distutils/emxccompiler.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,506 ils/dist.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/distut/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,506 4 ./Lib/distutils/extension.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,507 ils/errors.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/distut018cac/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,507 4 ./Lib/distutils/file_util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,507 ils/fancy_getopt.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/distutac/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,507 4 ./Lib/distutils/log.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8tils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,507 ils/filelist.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/distu/usr/bin/install -c -m 644 ./Lib/distute018cac/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,508 4 ./Lib/distutils/msvccompiler.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,508 ils/msvc9compiler.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/distutlib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,508 4 ./Lib/distutils/sysconfig.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,508 ils/spawn.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/distutcac/lib/python2.7/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,511 4 ./Lib/distutils/unixccompiler.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,522 ils/util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/d/usr/bin/install -c -m 644 ./Lib/distut09fe018cac/lib/python2.7/distutils install_environment.STDOUT DEBUG 2017-11-18 17:03:21,536 4 ./Lib/distutils/command/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/distutils/command/usr/bin/install -c -m 644 ./Li_7/8b09fe018cac/lib/python2.7/distutils/usr/bin/install -c -m 644 ./Lib/distutils/commacac/lib/python2.7/distutils/command install_environment.STDOUT DEBUG 2017-11-18 17:03:21,553 4 ./Lib/distutils/command/bdist_msi.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/distutils/comman/usr/bin/install -c -m 644 ./Lipython/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/command install_environment.STDOUT DEBUG 2017-11-18 17:03:21,557 ies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/command install_environment.STDOUT DEBUG 2017-11-18 17:03:21,564 4 ./Lib/distutils/command/build_py.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/distutils/command/usr/bin/install -c -m 644 ./Lipython_2_7/8b09fe018cac/lib/python2.7/distutils/command install_environment.STDOUT DEBUG 2017-11-18 17:03:21,573 /usr/bin/install -c -m 644 ./Lib/distutils/command/check.py /galaxydir/galaxy/database/dependencies/thon_2_7/8b09fe018cac/lib/usr/bin/install -c -m 644 ./Li_7/8b09fe018cac/lib/python2.7/distutils/usr/bin/install -c -m 644 ./Lib/distutils/comma018cac/lib/python2.7/distutils/command install_environment.STDOUT DEBUG 2017-11-18 17:03:21,577 4 ./Lib/distutils/command/config.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/distutils/command install_environment.STDOUT DEBUG 2017-11-18 17:03:21,585 ils/command/install.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64kage_python_2_7/8b09fe018cac/limand install_environment.STDOUT DEBUG 2017-11-18 17:03:21,589 b/distutils/command/install_egg_info.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/distutils/command install_environment.STDOUT DEBUG 2017-11-18 17:03:21,597 nd/install_headers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64age_python_2_7/8b09fe018cac/liband install_environment.STDOUT DEBUG 2017-11-18 17:03:21,600 b/distutils/command/install_scripts.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packag/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,608 ils/spawn.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/distutcac/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,608 4 ./Lib/distutils/unixccompiler.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,608 ils/text_file.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/distutib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,608 4 ./Lib/distutils/version.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2istutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,608 ils/util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/d/usr/bin/install -c -m 644 ./Lib/distut09fe018cac/lib/python2.7/distutils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,609 ils/versionpredicate.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,609 b/distutils/command/bdist.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,609 4 ./Lib/distutils/command/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/distutils/command/usr/bin/install -c -m 644 ./Li_7/8b09fe018cac/lib/python2.7/distutils/usr/bin/install -c -m 644 ./Lib/distutils/commacac/lib/python2.7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,609 nd/bdist_dumb.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/pd tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,609 b/distutils/command/bdist_rpm.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,609 /usr/bin/install -c -m 644 ./Lib/distutils/command/bdist_wininst.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,609 /usr/bin/install -c -m 644 ./Lib/distutils/command/build.py /galaxydir/galaxy/database/dependencies//usr/bin/install -c -m 644 ./Lib/distutils/command/build_clib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,609 4 ./Lib/distutils/command/bdist_msi.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/distutils/comman/usr/bin/install -c -m 644 ./Lipython/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,609 ies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,609 /usr/bin/install -c -m 644 ./Lib/distutils/command/build_ext.py /galaxydir/galaxy/database/dependenc/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,609 4 ./Lib/distutils/command/build_py.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/distutils/command/usr/bin/install -c -m 644 ./Lipython_2_7/8b09fe018cac/lib/python2.7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,610 b/distutils/command/build_scripts.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/2.7/iuc/package_py/python2.7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,610 b/distutils/command/clean.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,610 /usr/bin/install -c -m 644 ./Lib/distutils/command/check.py /galaxydir/galaxy/database/dependencies/thon_2_7/8b09fe018cac/lib/usr/bin/install -c -m 644 ./Li_7/8b09fe018cac/lib/python2.7/distutils/usr/bin/install -c -m 644 ./Lib/distutils/comma018cac/lib/python2.7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,610 4 ./Lib/distutils/command/config.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,610 nd/command_template /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/distut9fe018cac/lib/python2.7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,610 ils/command/install.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64kage_python_2_7/8b09fe018cac/limand tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,610 b/distutils/command/install_egg_info.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packa7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,610 4 ./Lib/distutils/command/install_data.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/distutils/com/usr/bin/install -c -m 644 ./Lige_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/distutils/commafe018cac/lib/python2.7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,610 nd/install_headers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64age_python_2_7/8b09fe018cac/liband tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,610 b/distutils/command/install_scripts.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packag/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,610 4 ./Lib/distutils/command/install_lib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack/python2.7/distutils/comm/usr/bin/install -c -m 644 ./Lie_python_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/distutils/commac/lib/python2.7/distutils/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,610 4 ./Lib/distutils/command/sdist.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/distutils/command install_environment.STDOUT DEBUG 2017-11-18 17:03:21,612 nd/register.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/distutfe018cac/lib/python2.7/distutils/command install_environment.STDOUT DEBUG 2017-11-18 17:03:21,624 4 ./Lib/distutils/command/wininst-6.0.exe /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/distutils/com/usr/bin/install -c -m 644 ./Liython_2_7/8b09fe018cac/lib/python2.7/di/usr/bin/install -c -m 644 ./Lib/distutils/comma18cac/lib/python2.7/distutils/command install_environment.STDOUT DEBUG 2017-11-18 17:03:21,645 4 ./Lib/distutils/command/wininst-9.0-amd64.exe /galaxydir/galaxy/database/dependencies/python/2.7/icac/lib/python2.7/distuti/usr/bin/install -c -m 644 ./Liython_2_7/8b09fe018cac/lib/python2.7/di/usr/bin/install -c -m 644 ./Lib/distutils/tests/lib/python2.7/distutils/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:21,649 4 ./Lib/distutils/tests/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/distutils/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:21,653 ils/tests/setuptools_build_ext.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytts install_environment.STDOUT DEBUG 2017-11-18 17:03:21,664 extension.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/distut_2_7/8b09fe018cac/lib/python2.7/distutils/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:21,667 4 ./Lib/distutils/tests/test_bdist.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/distutils/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:21,675 ils/tests/test_bdist_dumb.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/usr/bin/install -c -m 64kage_python_2_7/8b09fe018cac/lits install_environment.STDOUT DEBUG 2017-11-18 17:03:21,678 b/distutils/tests/test_bdist_rpm.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pstutils/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:21,687 /test_bdist_wininst.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/distut_7/8b09fe018cac/lib/python2.7/distutils/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:21,698 4 ./Lib/distutils/tests/test_build_ext.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/distutils/tes/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/dis/usr/bin/install -c -m 644 ./Lib/distutils/tests9fe018cac/lib/python2.7/distutils/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:21,710 4 ./Lib/distutils/tests/test_ccompiler.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/distutils/tes/usr/bin/install -c -m 644 ./Lin_2_7/8b09fe018cac/lib/python2.7/distut/usr/bin/install -c -m 644 ./Lib/distutils/testsc/lib/python2.7/distutils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,711 nd/register.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,713 ils/tests/test_bdist_dumb.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/usr/bin/install -c -m 64kage_python_2_7/8b09fe018cac/lits tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,713 b/distutils/tests/test_bdist_rpm.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pstutils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,713 4 ./Lib/distutils/tests/test_bdist_msi.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/distutils/tes/usr/bin/install -c -m 644 ./Liython_2_7/8b09fe018cac/lib/python2.7/di/usr/bin/install -c -m 644 ./Lib/distutils/tests9fe018cac/lib/python2.7/distutils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,713 4 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,713 4 ./Lib/distutils/tests/test_build_ext.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pacb/python2.7/distutils/tes/usr/bin/install -c -m 644 ./Lithon_2_7/8b09fe018cac/lib/python2.7/dis/usr/bin/install -c -m 644 ./Lib/distutils/tests9fe018cac/lib/python2.7/distutils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,713 /test_build_scripts.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64kage_python_2_7/8b09fe018cac/lits tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,713 b/distutils/tests/test_check.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythoils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,713 4 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/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64age_python_2_7/8b09fe018cac/libs install_environment.STDOUT DEBUG 2017-11-18 17:03:21,735 b/distutils/tests/test_dist.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythonls/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:21,741 /test_file_util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64age_python_2_7/8b09fe018cac/libs install_environment.STDOUT DEBUG 2017-11-18 17:03:21,744 b/distutils/tests/test_install.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytutils/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:21,751 /test_install_data.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64uc/package_python_2_7/8b09fe018ls/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:21,754 b/distutils/tests/test_install_lib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagedistutils/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:21,764 /test_install_scripts.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64/package_python_2_7/8b09fe018cancies/python/2.7/iuc/package_python_2_7.7/distutils/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:21,767 b/distutils/tests/test_sdist.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythoils/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:21,775 /test_spawn.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64kage_python_2_7/8b09fe018cac/lits install_environment.STDOUT DEBUG 2017-11-18 17:03:21,778 b/distutils/tests/test_text_file.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pstutils/tests install_environment.STDOUT DEBUG 2017-11-18 17:03:21,791 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64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/distutb09fe018cac/lib/python2.7/distutils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,814 ils/tests/test_config.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64ckage_python_2_7/8b09fe018cac/lsts tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,814 b/distutils/tests/test_core.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythonls/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,814 4 ./Lib/distutils/tests/test_config_cmd.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/paib/python2.7/distutils/te/usr/bin/install -c -m 644 ./Li_2_7/8b09fe018cac/lib/python2.7/distuti/usr/bin/install -c -m 644 ./Lib/distutils/tests8cac/lib/python2.7/distutils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,814 /test_dep_util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64age_python_2_7/8b09fe018cac/libs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,815 b/distutils/tests/test_dist.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythonls/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,815 4 ./Lib/distutils/tests/test_dir_util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pack/python2.7/distutils/test/usr/bin/install -c -m 644 ./Li_2_7/8b09fe018cac/lib/python2.7/distuti/usr/bin/install -c -m 644 ./Lib/distutils/tests18cac/lib/python2.7/distutils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,815 /test_file_util.py 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64uc/package_python_2_7/8b09fe018ls/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,815 b/distutils/tests/test_install_lib.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagedistutils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,815 4 ./Lib/distutils/tests/test_install_headers.py /galaxydir/galaxy/database/dependencies/python/2.7/icac/lib/python2.7/distuti/usr/bin/install -c -m 644 ./Li_python_2_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/distutils/testsb09fe018cac/lib/python2.7/distutils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,815 4 ./Lib/distutils/tests/test_msvc9compiler.py /galaxydir/galaxy/database/dependencies/python/2.7/iucc/lib/python2.7/distutils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,817 4 ./Lib/distutils/tests/test_upload.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/distutils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,817 /test_unixccompiler.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/distut9fe018cac/lib/python2.7/distutils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,817 ils/tests/test_util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,818 b/distutils/tests/test_versionpredicate.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pan2.7/distutils/tests tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,818 4 ./Lib/distutils/tests/test_version.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packapython2.7/distutils/tests/usr/bin/install -c -m 644 ./Lickage_python_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/xml/__init__.py7/xml tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,818 4 ./Lib/xml/dom/NodeFilter.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/dom install_environment.STDOUT DEBUG 2017-11-18 17:03:21,828 b/xml/dom/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/xml//usr/bin/install -c -m 644 ./Lib/xml/do8cac/lib/python2.7/xml/dom install_environment.STDOUT DEBUG 2017-11-18 17:03:21,832 4 ./Lib/xml/dom/minicompat.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_xml/dom install_environment.STDOUT DEBUG 2017-11-18 17:03:21,841 m/minidom.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/xml/dom install_environment.STDOUT DEBUG 2017-11-18 17:03:21,853 4 ./Lib/xml/dom/xmlbuilder.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_/python/2.7/iuc/package_pb/python2.7/xml/etree install_environment.STDOUT DEBUG 2017-11-18 17:03:21,863 b/xml/etree/ElementPath.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/xml/etac/lib/python2.7/xml/etree install_environment.STDOUT DEBUG 2017-11-18 17:03:21,867 4 ./Lib/xml/etree/cElementTree.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/xml/etree install_environment.STDOUT DEBUG 2017-11-18 17:03:21,889 rsers/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/x/usr/bin/install -c -m 644 ./Lib/xml/sa/lib/python2.7/xml/sax install_environment.STDOUT DEBUG 2017-11-18 17:03:21,893 4 ./Lib/xml/sax/_exceptions.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/xml/sax install_environment.STDOUT DEBUG 2017-11-18 17:03:21,907 x/expatreader.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/sax install_environment.STDOUT DEBUG 2017-11-18 17:03:21,916 4 ./Lib/xml/sax/saxutils.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/2.7/iuc/package_python_2n2.7/xml/sax tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,918 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 64/usr/bin/install -c -m 644 ./Life018cac/lib/python2.7/xml/dom tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,919 4 ./Lib/xml/dom/domreg.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/dom tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,919 b/xml/dom/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/xml//usr/bin/install -c -m 644 ./Lib/xml/do8cac/lib/python2.7/xml/dom tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,919 4 ./Lib/xml/dom/minicompat.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_xml/dom tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,919 m/expatbuilder.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/xml/dolib/python2.7/xml/dom tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,919 m/minidom.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/xml/dom tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,919 4 ./Lib/xml/dom/pulldom.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7/xml/dom tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,919 4 ./Lib/xml/dom/xmlbuilder.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_/python/2.7/iuc/package_pb/python2.7/xml/etree tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,920 /usr/bin/install -c -m 644 ./Lib/xml/etree/ElementInclude.py /galaxydir/galaxy/database/dependenciesython_2_7/8b09fe018cac/li/usr/bin/install -c -m 644 ./Li/8b09fe018cac/lib/python2.7/xml/etree tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,920 4 ./Lib/xml/etree/ElementTree.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/xml/etree tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,920 b/xml/etree/ElementPath.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/xml/etac/lib/python2.7/xml/etree tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,920 4 ./Lib/xml/etree/cElementTree.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/xml/etree tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,921 ree/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/xml/pa8cac/lib/python2.7/xml/parsers tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,921 4 ./Lib/xml/parsers/expat.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ml/parsers tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,921 rsers/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/x/usr/bin/install -c -m 644 ./Lib/xml/sa/lib/python2.7/xml/sax tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,921 4 ./Lib/xml/sax/_exceptions.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/xml/sax tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,922 x/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/xml/sacac/lib/python2.7/xml/sax tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,922 x/expatreader.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/sax tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,922 /usr/bin/install -c -m 644 ./Lib/xml/sax/handler.py /galaxydir/galaxy/database/dependencies/python/2/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/xml/sax tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:21,922 4 ./Lib/xml/sax/saxutils.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/2.7/iuc/package_python_2n2.7/xml/sax install_environment.STDOUT DEBUG 2017-11-18 17:03:21,927 b/multiprocessing/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_cessing install_environment.STDOUT DEBUG 2017-11-18 17:03:21,936 /connection.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/multip8cac/lib/python2.7/multiprocessing install_environment.STDOUT DEBUG 2017-11-18 17:03:21,940 4 ./Lib/multiprocessing/managers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/multiprocessing install_environment.STDOUT DEBUG 2017-11-18 17:03:21,949 rocessing/pool.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/multip018cac/lib/python2.7/multiprocessing install_environment.STDOUT DEBUG 2017-11-18 17:03:21,959 4 ./Lib/multiprocessing/reduction.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_cies/python/2.7/iuc/packac/lib/python2.7/multiprocessing/usr/bin/install -c -m 644 ./Lib/multipb09fe018cac/lib/python2.7/multiprocessing install_environment.STDOUT DEBUG 2017-11-18 17:03:21,962 4 ./Lib/multiprocessing/util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/multiprocessing install_environment.STDOUT DEBUG 2017-11-18 17:03:21,971 rocessing/dummy/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_my install_environment.STDOUT DEBUG 2017-11-18 17:03:21,986 ction.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/u/usr/bin/install -c -m 644 ./Lib/unittec/lib/python2.7/unittest install_environment.STDOUT DEBUG 2017-11-18 17:03:21,993 /usr/bin/install -c -m 644 ./Lib/unittest/case.py /galaxydir/galaxy/database/dependencies/python/2.7b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lie018cac/lib/python2.7/unittest install_environment.STDOUT DEBUG 2017-11-18 17:03:21,996 4 ./Lib/unittest/main.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8est install_environment.STDOUT DEBUG 2017-11-18 17:03:22,008 st/result.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/uni/usr/bin/install -c -m 644 ./Lib/unitte/lib/python2.7/unittest install_environment.STDOUT DEBUG 2017-11-18 17:03:22,012 4 ./Lib/unittest/suite.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,024 b/multiprocessing/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_cessing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,024 /usr/bin/install -c -m 644 ./Lib/xml/sax/xmlreader.py /galaxydir/galaxy/database/dependencies/python_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Li2_7/8b09fe018cac/lib/python2.7/multipro/usr/bin/install -c -m 644 ./Lib/multiprocessingc/lib/python2.7/multiprocessing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,024 4 ./Lib/multiprocessing/forking.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/multiprocessing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,025 /connection.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/multip8cac/lib/python2.7/multiprocessing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,025 4 ./Lib/multiprocessing/managers.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/multiprocessing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,025 rocessing/heap.py 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/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/python2.7/multiprocessing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,025 /usr/bin/install -c -m 644 ./Lib/multiprocessing/sharedctypes.py /galaxydir/galaxy/database/dependenge_python_2_7/8b09fe018ca tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,025 4 ./Lib/multiprocessing/reduction.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_cies/python/2.7/iuc/packac/lib/python2.7/multiprocessing/usr/bin/install -c -m 644 ./Lib/multipb09fe018cac/lib/python2.7/multiprocessing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,025 4 ./Lib/multiprocessing/util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/multiprocessing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,025 rocessing/dummy/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_my tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,025 rocessing/synchronize.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/multip7/8b09fe018cac/lib/python2.7/multiprocessing/dum/usr/bin/install -c -m 644 ./Lib/multiprocessing/dummy/connepython2.7/multiprocessing/dummy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,026 4 ./Lib/unittest/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2nittest tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,026 ction.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/u/usr/bin/install -c -m 644 ./Lib/unittec/lib/python2.7/unittest tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,026 st/__main__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/iuc/package_python_2_7/8/unittest tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,026 /usr/bin/install -c -m 644 ./Lib/unittest/case.py /galaxydir/galaxy/database/dependencies/python/2.7b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lie018cac/lib/python2.7/unittest tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,026 4 ./Lib/unittest/main.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8est tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,026 b/unittest/loader.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64b09fe018cac/lib/python2.7/unitt/usr/bin/install -c -m 644 ./Lib/unittelib/python2.7/unittest tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,026 4 ./Lib/unittest/runner.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7ttest tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,031 st/result.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/uni/usr/bin/install -c -m 644 ./Lib/unitte/lib/python2.7/unittest tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,031 4 ./Lib/unittest/suite.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,031 st/signals.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/unit/usr/bin/install -c -m 644 ./Lib/unitteb/python2.7/unittest install_environment.STDOUT DEBUG 2017-11-18 17:03:22,048 st/util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/unittecac/lib/python2.7/unittest/test install_environment.STDOUT DEBUG 2017-11-18 17:03:22,053 4 ./Lib/unittest/test/support.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/unittest/test install_environment.STDOUT DEBUG 2017-11-18 17:03:22,066 st/test/test_assertions.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/unittee018cac/lib/python2.7/unittest/test install_environment.STDOUT DEBUG 2017-11-18 17:03:22,073 4 ./Lib/unittest/test/test_discovery.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packapython2.7/unittest/test install_environment.STDOUT DEBUG 2017-11-18 17:03:22,084 st/test/test_functiontestcase.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/unitte09fe018cac/lib/python2.7/unittest/test install_environment.STDOUT DEBUG 2017-11-18 17:03:22,088 4 ./Lib/unittest/test/test_result.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/unittest/test install_environment.STDOUT DEBUG 2017-11-18 17:03:22,099 st/test/test_runner.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/unitteb09fe018cac/lib/python2.7/unittest/test install_environment.STDOUT DEBUG 2017-11-18 17:03:22,102 4 ./Lib/unittest/test/test_suite.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/unittest/test install_environment.STDOUT DEBUG 2017-11-18 17:03:22,122 /__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 6409fe018cac/lib/python2.7/curses/usr/bin/install -c -m 644 ./Lib/cursesib/python2.7/curses install_environment.STDOUT DEBUG 2017-11-18 17:03:22,126 4 ./Lib/curses/panel.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,132 4 ./Lib/unittest/test/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,132 st/util.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/unittecac/lib/python2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,132 4 ./Lib/unittest/test/support.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,132 st/test/dummy.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/unitte/8b09fe018cac/lib/python2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,132 4 ./Lib/unittest/test/test_break.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,132 st/test/test_assertions.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/unittee018cac/lib/python2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,132 4 ./Lib/unittest/test/test_discovery.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packapython2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,132 st/test/test_case.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 644 ./Lib/unitteon_2_7/8b09fe018cac/lib/python2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,132 4 ./Lib/unittest/test/test_loader.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,132 st/test/test_functiontestcase.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/unitte09fe018cac/lib/python2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,133 4 ./Lib/unittest/test/test_result.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,133 st/test/test_program.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/unitte9fe018cac/lib/python2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,133 4 ./Lib/unittest/test/test_setups.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,133 st/test/test_runner.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/unitteb09fe018cac/lib/python2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,133 4 ./Lib/unittest/test/test_suite.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/unittest/test tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,133 st/test/test_skipping.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/curseslib/python2.7/curses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,133 4 ./Lib/curses/ascii.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,133 /__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 6409fe018cac/lib/python2.7/curses/usr/bin/install -c -m 644 ./Lib/cursesib/python2.7/curses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,133 4 ./Lib/curses/panel.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b install_environment.STDOUT DEBUG 2017-11-18 17:03:22,148 /textpad.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/curs/usr/bin/install -c -m 644 ./Lib/pydoc_cac/lib/python2.7/pydoc_data install_environment.STDOUT DEBUG 2017-11-18 17:03:22,151 4 ./Lib/pydoc_data/topics.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ydoc_data install_environment.STDOUT DEBUG 2017-11-18 17:03:22,172 arwin/IN.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c ./Lib18cac/lib/python2.7/plat-darwin/usr/bin/install -c -m 644 ./Lib/plat-mac/lib/python2.7/plat-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,176 4 ./Lib/plat-mac/EasyDialogs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/plat-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,189 ac/FrameWork.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/plat-m018cac/lib/python2.7/plat-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,194 4 ./Lib/plat-mac/aepack.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,210 ac/aetools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/pl/usr/bin/install -c -m 644 ./Lib/plat-m8cac/lib/python2.7/plat-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,214 4 ./Lib/plat-mac/appletrawmain.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/plat-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,224 etrunner.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,234 /has_key.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 6409fe018cac/lib/python2.7/curses/usr/bin/install -c -m 644 ./Lib/cursesib/python2.7/curses tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,234 4 ./Lib/curses/wrapper.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/es tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,234 /textpad.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 648b09fe018cac/lib/python2.7/curs/usr/bin/install -c -m 644 ./Lib/pydoc_cac/lib/python2.7/pydoc_data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,234 4 ./Lib/pydoc_data/topics.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ydoc_data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,234 data/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64_7/8b09fe018cac/lib/python2.7/p/usr/bin/install -c -m 644 ./Lib/plat-dib/python2.7/plat-darwin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,234 /plat-darwin/regen /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,234 arwin/IN.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c ./Lib18cac/lib/python2.7/plat-darwin/usr/bin/install -c -m 644 ./Lib/plat-mac/lib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,234 4 ./Lib/plat-mac/EasyDialogs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,234 ac/Audio_mac.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/plat-mac/lib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,234 4 ./Lib/plat-mac/MiniAEFrame.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,235 ac/FrameWork.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/plat-m018cac/lib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,235 4 ./Lib/plat-mac/aepack.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,235 ac/PixMapWrapper.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64/8b09fe018cac/lib/python2.7/pla/usr/bin/install -c -m 644 ./Lib/plat-m/lib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,235 4 ./Lib/plat-mac/aetypes.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_at-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,235 ac/aetools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 647/8b09fe018cac/lib/python2.7/pl/usr/bin/install -c -m 644 ./Lib/plat-m8cac/lib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,235 4 ./Lib/plat-mac/appletrawmain.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,235 ac/applesingle.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c ./Lib/plat-mac/applib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,235 etrunner.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,235 4 ./Lib/plat-mac/argvemulator.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythython/2.7/iuc/package_pytpython2.7/plat-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,236 /usr/bin/install -c -m 644 ./Lib/plat-mac/bgenlocations.py /galaxydir/galaxy/database/dependencies/phon_2_7/8b09fe018cac/lib//usr/bin/install -c -m 644 ./Lib09fe018cac/lib/python2.7/plat-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,244 /plat-mac/bundlebuilder.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,254 ac/cfmfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/plat-mc/lib/python2.7/plat-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,259 4 ./Lib/plat-mac/findertools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/plat-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,268 ac/gensuitemodule.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 649fe018cac/lib/python2.7/plat-ma/usr/bin/install -c -m 644 ./Lib/plat-mlib/python2.7/plat-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,271 4 ./Lib/plat-mac/macerrors.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_plat-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,282 ac/macostools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/plat-mb/python2.7/plat-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,286 4 ./Lib/plat-mac/terminalcommand.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/plat-mac install_environment.STDOUT DEBUG 2017-11-18 17:03:22,304 ac/videoreader.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/plat-mac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,309 4 ./Lib/plat-mac/Carbon/Alias.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,319 ac/Carbon/Aliases.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/plat-m09fe018cac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,322 4 ./Lib/plat-mac/Carbon/AppleEvents.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,336 /usr/bin/install -c -m 644 ./Lib/plat-mac/bgenlocations.py /galaxydir/galaxy/database/dependencies/phon_2_7/8b09fe018cac/lib//usr/bin/install -c -m 644 ./Lib09fe018cac/lib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,337 /plat-mac/bundlebuilder.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7t-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,337 b/plat-mac/buildtools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c ./Lib/8b09fe018cac/lib/python2.7/pla/usr/bin/install -c -m 644 ./Lib/plat-m/lib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,337 4 ./Lib/plat-mac/dialogs.rsrc /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,337 ac/cfmfile.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/plat-mc/lib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,337 4 ./Lib/plat-mac/findertools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,337 ac/errors.rsrc /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/plat-me018cac/lib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,337 4 ./Lib/plat-mac/ic.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,337 ac/gensuitemodule.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 649fe018cac/lib/python2.7/plat-ma/usr/bin/install -c -m 644 ./Lib/plat-mlib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,338 4 ./Lib/plat-mac/macerrors.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,338 ac/icopen.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/plat-mcac/lib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,338 4 ./Lib/plat-mac/macresource.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,338 ac/macostools.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/plat-mb/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,338 4 ./Lib/plat-mac/terminalcommand.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,338 ac/pimp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/plat-m8cac/lib/python2.7/plat-mac tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,338 4 ./Lib/plat-mac/Carbon/AE.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,338 ac/videoreader.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/plat-mac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,338 4 ./Lib/plat-mac/Carbon/Alias.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,338 ac/Carbon/AH.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/plat-me018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,339 4 ./Lib/plat-mac/Carbon/App.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,339 ac/Carbon/Aliases.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/plat-m09fe018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,340 4 ./Lib/plat-mac/Carbon/AppleEvents.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,340 ac/Carbon/Appearance.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/plat-m9fe018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,340 4 ./Lib/plat-mac/Carbon/CF.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,340 ac/Carbon/CG.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,343 ac/Carbon/AppleHelp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/plat-mcies/python/2.7/iuc/package_python_2_7/8b09fe018c/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,349 b/plat-mac/Carbon/CarbonEvt.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythonc/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,363 /Cm.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/plat-m_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,366 4 ./Lib/plat-mac/Carbon/Controls.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,373 ac/Carbon/CoreFoundation.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib/ install_environment.STDOUT DEBUG 2017-11-18 17:03:22,376 b/plat-mac/Carbon/Ctl.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8on install_environment.STDOUT DEBUG 2017-11-18 17:03:22,386 /Dialogs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/plat-m8cac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,394 4 ./Lib/plat-mac/Carbon/Dragconst.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,403 ac/Carbon/Events.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/plat-m8cac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,406 4 ./Lib/plat-mac/Carbon/Files.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,418 ac/Carbon/Fm.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/plat-me018cac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,422 4 ./Lib/plat-mac/Carbon/Fonts.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,434 ac/Carbon/Help.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/plat-m_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,439 4 ./Lib/plat-mac/Carbon/Icn.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,445 ac/Carbon/AppleHelp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 642_7/8b09fe018cac/lib/python2.7//usr/bin/install -c -m 644 ./Lib/plat-mcies/python/2.7/iuc/package_python_2_7/8b09fe018c/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,445 b/plat-mac/Carbon/CarbonEvt.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythonc/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,445 /usr/bin/install -c -m 644 ./Lib/plat-mac/Carbon/CarbonEvents.py /galaxydir/galaxy/database/dependencac/lib/python2.7/plat-ma/usr/bin/install -c -m 644 ./Li_2_7/8b09fe018cac/lib/python2.7/plat-ma/usr/bin/install -c -m 644 ./Lib/plat-mac/Carbonthon2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,445 4 ./Lib/plat-mac/Carbon/Components.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,445 /Cm.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/plat-m_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,445 4 ./Lib/plat-mac/Carbon/Controls.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,445 ac/Carbon/ControlAccessor.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/plat-m7/8b09fe018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,446 ac/Carbon/CoreFoundation.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/usr/bin/install -c -m 64ge_python_2_7/8b09fe018cac/lib/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,446 b/plat-mac/Carbon/Ctl.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8on tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,446 4 ./Lib/plat-mac/Carbon/CoreGraphics.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packapython2.7/plat-mac/Carbon/usr/bin/install -c -m 644 ./Lib09fe018cac/lib/python2.7/plat-mac/Carb/usr/bin/install -c -m 644 ./Lib/plat-mac/Carbonib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,446 4 ./Lib/plat-mac/Carbon/Dlg.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,446 /Dialogs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/plat-m8cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,446 4 ./Lib/plat-mac/Carbon/Dragconst.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,446 ac/Carbon/Drag.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/plat-m018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,446 4 ./Lib/plat-mac/Carbon/Evt.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,446 ac/Carbon/Events.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/plat-m8cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,446 4 ./Lib/plat-mac/Carbon/Files.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,446 ac/Carbon/File.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/plat-mac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,447 4 ./Lib/plat-mac/Carbon/Folder.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,447 ac/Carbon/Fm.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/plat-me018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,447 4 ./Lib/plat-mac/Carbon/Fonts.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,447 ac/Carbon/Folders.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/plat-m8cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,447 4 ./Lib/plat-mac/Carbon/IBCarbon.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,447 ac/Carbon/Help.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/plat-m_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,447 4 ./Lib/plat-mac/Carbon/Icn.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,457 ac/Carbon/Icons.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/plat-m7/8b09fe018cac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,461 4 ./Lib/plat-mac/Carbon/List.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,470 ac/Carbon/Lists.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/plat-m/8b09fe018cac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,473 4 ./Lib/plat-mac/Carbon/MediaDescr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,484 ac/Carbon/Menu.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/plat-m8cac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,488 4 ./Lib/plat-mac/Carbon/OSA.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,500 ac/Carbon/OSAconst.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/plat-mac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,503 4 ./Lib/plat-mac/Carbon/Qdoffs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,516 ac/Carbon/Qt.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/plat-m9fe018cac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,519 4 ./Lib/plat-mac/Carbon/Res.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,526 ac/Carbon/Resources.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,529 4 ./Lib/plat-mac/Carbon/Snd.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,542 ac/Carbon/Sndihooks.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/plat-mac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,545 4 ./Lib/plat-mac/Carbon/TextEdit.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,547 ac/Carbon/IBCarbonRuntime.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/plat-m18cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,548 4 ./Lib/plat-mac/Carbon/Launch.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,548 ac/Carbon/Icons.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/plat-m7/8b09fe018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,548 4 ./Lib/plat-mac/Carbon/List.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,548 ac/Carbon/LaunchServices.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_/usr/bin/install -c -m 64n_2_7/8b09fe018cac/lib/python2./usr/bin/install -c -m 644 ./Lib/plat-m18cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,548 4 ./Lib/plat-mac/Carbon/MacHelp.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,548 ac/Carbon/Lists.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64thon_2_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lib/plat-m/8b09fe018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,548 4 ./Lib/plat-mac/Carbon/MediaDescr.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,548 ac/Carbon/MacTextEditor.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/usr/bin/install -c -m 64_python_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lib/plat-m8cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,548 4 ./Lib/plat-mac/Carbon/Menus.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,548 ac/Carbon/Menu.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/plat-m8cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,549 4 ./Lib/plat-mac/Carbon/OSA.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,549 ac/Carbon/Mlte.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/plat-mfe018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,549 4 ./Lib/plat-mac/Carbon/QDOffscreen.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,549 ac/Carbon/OSAconst.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64e_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c -m 644 ./Lib/plat-mac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,549 4 ./Lib/plat-mac/Carbon/Qdoffs.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,549 ac/Carbon/Qd.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64hon_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 644 ./Lib/plat-mac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,550 4 ./Lib/plat-mac/Carbon/QuickDraw.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,550 ac/Carbon/Qt.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64python_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lib/plat-m9fe018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,550 4 ./Lib/plat-mac/Carbon/Res.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,550 ac/Carbon/QuickTime.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/plat-m9fe018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,550 ac/Carbon/Resources.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,550 4 ./Lib/plat-mac/Carbon/Snd.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,550 4 ./Lib/plat-mac/Carbon/Scrap.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth/usr/bin/install -c -m 64_2_7/8b09fe018cac/lib/python2.7/usr/bin/install -c -m 644 ./Lib/plat-m9fe018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,550 4 ./Lib/plat-mac/Carbon/Sound.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,550 ac/Carbon/Sndihooks.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64on_2_7/8b09fe018cac/lib/python2/usr/bin/install -c -m 644 ./Lib/plat-mac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,551 4 ./Lib/plat-mac/Carbon/TextEdit.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,550 ac/Carbon/Win.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon install_environment.STDOUT DEBUG 2017-11-18 17:03:22,578 /Windows.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/plat-miuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/_builtinSuites install_environment.STDOUT DEBUG 2017-11-18 17:03:22,583 /usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/_builtinSuites/builtin_Suite.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/_builtinSuites install_environment.STDOUT DEBUG 2017-11-18 17:03:22,598 /usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/CodeWarrior/CodeWarrior_suite.py /galaxgalaxydir/galaxy/databaseiuc/package_python_2_7/8b09fe01-scriptpackages/CodeWarrior install_environment.STDOUT DEBUG 2017-11-18 17:03:22,608 ac/lib-scriptpackages/CodeWarrior/Required.py /galaxydir/galaxy/database/dependencies/python/2.7/iuclat-mac/lib-scriptpackage/usr/bin/install -c -m 644 ./Lipython/2.7/iuc/package_python_2_7/8b09ft-mac/lib-scriptpackages/CodeWarrior install_environment.STDOUT DEBUG 2017-11-18 17:03:22,622 b/plat-mac/lib-scriptpackages/CodeWarrior/__init__.py /galaxydir/galaxy/database/dependencies/pythonc/lib/python2.7/plat-mac//usr/bin/install -c -m 644 ./Liendencies/python/2.7/iuc/package_pythonhon2.7/plat-mac/lib-scriptpackages/Explorer install_environment.STDOUT DEBUG 2017-11-18 17:03:22,630 b/plat-mac/lib-scriptpackages/Explorer/Netscape_Suite.py /galaxydir/galaxy/database/dependencies/pyt8cac/lib/python2.7/plat-m/usr/bin/install -c -m 644 ./Lihon/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer install_environment.STDOUT DEBUG 2017-11-18 17:03:22,636 /usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/Explorer/Standard_Suite.py /galaxydir/ges/python/2.7/iuc/packagethon2.7/plat-mac/lib-scriptpack/usr/bin/install -c -m 644 ./Lib/plat-mackage_python_2_7/8b09fe018cac/lib/python2.7/plaExplorer install_environment.STDOUT DEBUG 2017-11-18 17:03:22,643 b/plat-mac/lib-scriptpackages/Explorer/Web_Browser_Suite.py /galaxydir/galaxy/database/dependencies/e018cac/lib/python2.7/pla/usr/bin/install -c -m 644 ./Li7/iuc/package_python_2_7/8b09fe018cac/l-scriptpackages/Explorer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,651 ac/Carbon/Win.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,651 ac/Carbon/TE.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/plat-m/usr/bin/install -c -m 644 ./Lib/plat-mac/Carbonib/python2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,651 4 ./Lib/plat-mac/Carbon/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pon2.7/plat-mac/Carbon tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,651 /Windows.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/l/usr/bin/install -c -m 64ython_2_7/8b09fe018cac/lib/pyth/usr/bin/install -c -m 644 ./Lib/plat-miuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/_builtinSuites tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,651 /usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/_builtinSuites/builtin_Suite.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/_builtinSuites tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,651 ac/lib-scriptpackages/_builtinSuites/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,652 /usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/CodeWarrior/CodeWarrior_suite.py /galaxgalaxydir/galaxy/databaseiuc/package_python_2_7/8b09fe01-scriptpackages/CodeWarrior tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,652 /usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/CodeWarrior/Metrowerks_Shell_Suite.py //dependencies/python/2.7/8cac/lib/python2.7/plat-mac/lib/usr/bin/install -c -m 644 ./Lib/plat-m/package_python_2_7/8b09fe018cac/lib/python2.7/ps/CodeWarrior tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,652 ac/lib-scriptpackages/CodeWarrior/Required.py /galaxydir/galaxy/database/dependencies/python/2.7/iuclat-mac/lib-scriptpackage/usr/bin/install -c -m 644 ./Lipython/2.7/iuc/package_python_2_7/8b09ft-mac/lib-scriptpackages/CodeWarrior tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,652 b/plat-mac/lib-scriptpackages/CodeWarrior/Standard_Suite.py /galaxydir/galaxy/database/dependencies/e018cac/lib/python2.7/pla/usr/bin/install -c -m 644 ./Li/2.7/iuc/package_python_2_7/8b09fe018calib-scriptpackages/CodeWarrior tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,652 b/plat-mac/lib-scriptpackages/CodeWarrior/__init__.py /galaxydir/galaxy/database/dependencies/pythonc/lib/python2.7/plat-mac//usr/bin/install -c -m 644 ./Liendencies/python/2.7/iuc/package_pythonhon2.7/plat-mac/lib-scriptpackages/Explorer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,652 b/plat-mac/lib-scriptpackages/Explorer/Microsoft_Internet_Explorer.py /galaxydir/galaxy/database/dep_2_7/8b09fe018cac/lib/pyt/usr/bin/install -c -m 644 ./Lihon/2.7/iuc/package_python_2_7/8b09fe01ac/lib-scriptpackages/Explorer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,652 b/plat-mac/lib-scriptpackages/Explorer/Netscape_Suite.py /galaxydir/galaxy/database/dependencies/pyt8cac/lib/python2.7/plat-m/usr/bin/install -c -m 644 ./Lihon/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,652 b/plat-mac/lib-scriptpackages/Explorer/Required_Suite.py /galaxydir/galaxy/database/dependencies/pytalaxy/database/dependenci_python_2_7/8b09fe018cac/lib/pyages/Explorer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,652 /usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/Explorer/Standard_Suite.py /galaxydir/ges/python/2.7/iuc/packagethon2.7/plat-mac/lib-scriptpack/usr/bin/install -c -m 644 ./Lib/plat-mackage_python_2_7/8b09fe018cac/lib/python2.7/plaExplorer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,652 ac/lib-scriptpackages/Explorer/URL_Suite.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/pt-mac/lib-scriptpackages//usr/bin/install -c -m 644 ./Lipython/2.7/iuc/package_python_2_7/8b09ft-mac/lib-scriptpackages/Explorer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,652 b/plat-mac/lib-scriptpackages/Explorer/Web_Browser_Suite.py /galaxydir/galaxy/database/dependencies/e018cac/lib/python2.7/pla/usr/bin/install -c -m 644 ./Li7/iuc/package_python_2_7/8b09fe018cac/l-scriptpackages/Explorer install_environment.STDOUT DEBUG 2017-11-18 17:03:22,656 b/plat-mac/lib-scriptpackages/Finder/Containers_and_folders.py /galaxydir/galaxy/database/dependenciy/database/dependencies/phon_2_7/8b09fe018cac/lib/python/Finder install_environment.STDOUT DEBUG 2017-11-18 17:03:22,664 ac/lib-scriptpackages/Finder/Files.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagelib-scriptpackages/Finder/usr/bin/install -c -m 644 ./Li/2.7/iuc/package_python_2_7/8b09fe018calib-scriptpackages/Finder install_environment.STDOUT DEBUG 2017-11-18 17:03:22,671 b/plat-mac/lib-scriptpackages/Finder/Finder_items.py /galaxydir/galaxy/database/dependencies/python//lib/python2.7/plat-mac/l/usr/bin/install -c -m 644 ./Li2.7/iuc/package_python_2_7/8b09fe018cacib-scriptpackages/Finder install_environment.STDOUT DEBUG 2017-11-18 17:03:22,679 b/plat-mac/lib-scriptpackages/Finder/Standard_Suite.py /galaxydir/galaxy/database/dependencies/pythoac/lib/python2.7/plat-mac/usr/bin/install -c -m 644 ./Lihon/2.7/iuc/package_python_2_7/8b09fe01ac/lib-scriptpackages/Finder install_environment.STDOUT DEBUG 2017-11-18 17:03:22,685 b/plat-mac/lib-scriptpackages/Finder/Window_classes.py /galaxydir/galaxy/database/dependencies/pythotabase/dependencies/pytho2_7/8b09fe018cac/lib/python2.7/der install_environment.STDOUT DEBUG 2017-11-18 17:03:22,700 ac/lib-scriptpackages/Netscape/Mozilla_suite.py /galaxydir/galaxy/database/dependencies/python/2.7/i/plat-mac/lib-scriptpacka/usr/bin/install -c -m 644 ./Li2.7/iuc/package_python_2_7/8b09fe018cacib-scriptpackages/Netscape install_environment.STDOUT DEBUG 2017-11-18 17:03:22,715 b/plat-mac/lib-scriptpackages/Netscape/Required_suite.py /galaxydir/galaxy/database/dependencies/pyt8cac/lib/python2.7/plat-m/usr/bin/install -c -m 644 ./Lihon/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scackage_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-sc/usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/Netscape/Text.2.7/plat-mac/lib-scriptpackages/Netscape install_environment.STDOUT DEBUG 2017-11-18 17:03:22,721 4 ./Lib/plat-mac/lib-scriptpackages/Netscape/WorldWideWeb_suite.py /galaxydir/galaxy/database/dependdatabase/dependencies/pytn_2_7/8b09fe018cac/lib/python2.etscape install_environment.STDOUT DEBUG 2017-11-18 17:03:22,732 ac/lib-scriptpackages/StdSuites/AppleScript_Suite.py /galaxydir/galaxy/database/dependencies/python/on2.7/plat-mac/lib-script/usr/bin/install -c -m 644 ./Lipendencies/python/2.7/iuc/package_pythothon2.7/plat-mac/lib-scriptpackages/StdSuites install_environment.STDOUT DEBUG 2017-11-18 17:03:22,741 b/plat-mac/lib-scriptpackages/StdSuites/QuickDraw_Graphics_Suite.py /galaxydir/galaxy/database/depen_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lipendencies/python/2.7/iuc/package_pythothon2.7/plat-mac/lib-scriptpackages/StdSuites install_environment.STDOUT DEBUG 2017-11-18 17:03:22,749 b/plat-mac/lib-scriptpackages/StdSuites/Required_Suite.py /galaxydir/galaxy/database/dependencies/py18cac/lib/python2.7/plat-/usr/bin/install -c -m 644 ./Lithon/2.7/iuc/package_python_2_7/8b09fe0mac/lib-scriptpackages/StdSuites tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,753 b/plat-mac/lib-scriptpackages/Explorer/__init__.py /galaxydir/galaxy/database/dependencies/python/2.ib/python2.7/plat-mac/lib/usr/bin/install -c -m 644 ./Lies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,753 b/plat-mac/lib-scriptpackages/Finder/Containers_and_folders.py /galaxydir/galaxy/database/dependenciy/database/dependencies/phon_2_7/8b09fe018cac/lib/python/Finder tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,754 /usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/Finder/Enumerations.py /galaxydir/galaxython/2.7/iuc/package_pyt2.7/plat-mac/lib-scriptpackages/usr/bin/install -c -m 644 ./Lib/plat-m_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,754 ac/lib-scriptpackages/Finder/Files.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagelib-scriptpackages/Finder/usr/bin/install -c -m 644 ./Li/2.7/iuc/package_python_2_7/8b09fe018calib-scriptpackages/Finder tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,754 b/plat-mac/lib-scriptpackages/Finder/Finder_Basics.py /galaxydir/galaxy/database/dependencies/pythonc/lib/python2.7/plat-mac//usr/bin/install -c -m 644 ./Li2.7/iuc/package_python_2_7/8b09fe018cacib-scriptpackages/Finder tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,754 b/plat-mac/lib-scriptpackages/Finder/Finder_items.py /galaxydir/galaxy/database/dependencies/python//lib/python2.7/plat-mac/l/usr/bin/install -c -m 644 ./Li2.7/iuc/package_python_2_7/8b09fe018cacib-scriptpackages/Finder tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,754 b/plat-mac/lib-scriptpackages/Finder/Legacy_suite.py /galaxydir/galaxy/database/dependencies/python//lib/python2.7/plat-mac/l/usr/bin/install -c -m 644 ./Lin/2.7/iuc/package_python_2_7/8b09fe018c/lib-scriptpackages/Finder tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,754 b/plat-mac/lib-scriptpackages/Finder/Standard_Suite.py /galaxydir/galaxy/database/dependencies/pythoac/lib/python2.7/plat-mac/usr/bin/install -c -m 644 ./Lihon/2.7/iuc/package_python_2_7/8b09fe01ac/lib-scriptpackages/Finder tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,754 b/plat-mac/lib-scriptpackages/Finder/Type_Definitions.py /galaxydir/galaxy/database/dependencies/pyt8cac/lib/python2.7/plat-m/usr/bin/install -c -m 644 ./Lin/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,754 b/plat-mac/lib-scriptpackages/Finder/Window_classes.py /galaxydir/galaxy/database/dependencies/pythotabase/dependencies/pytho2_7/8b09fe018cac/lib/python2.7/der tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,754 /usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/Finder/__init__.py /galaxydir/galaxy/dan/2.7/iuc/package_python_plat-mac/lib-scriptpackages/Fin/usr/bin/install -c -m 644 ./Lib/plat-muc/package_python_2_7/8b09fe018cac/lib/python2.7ges/Netscape tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,754 ac/lib-scriptpackages/Netscape/Mozilla_suite.py /galaxydir/galaxy/database/dependencies/python/2.7/i/plat-mac/lib-scriptpacka/usr/bin/install -c -m 644 ./Li2.7/iuc/package_python_2_7/8b09fe018cacib-scriptpackages/Netscape tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,755 b/plat-mac/lib-scriptpackages/Netscape/PowerPlant.py /galaxydir/galaxy/database/dependencies/python//lib/python2.7/plat-mac/l/usr/bin/install -c -m 644 ./Lihon/2.7/iuc/package_python_2_7/8b09fe01ac/lib-scriptpackages/Netscape tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,755 b/plat-mac/lib-scriptpackages/Netscape/Standard_Suite.py /galaxydir/galaxy/database/dependencies/pyt8cac/lib/python2.7/plat-mac/lib-scriptpackages/Netscape tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,755 riptpackages/Netscape/Standard_URL_suite.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/priptpackages/Netscape tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,755 b/plat-mac/lib-scriptpackages/Netscape/Required_suite.py /galaxydir/galaxy/database/dependencies/pyt8cac/lib/python2.7/plat-m/usr/bin/install -c -m 644 ./Lihon/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scackage_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-sc/usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/Netscape/Text.2.7/plat-mac/lib-scriptpackages/Netscape tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,755 py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python/usr/bin/install -c -m 64encies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Netscape tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,755 4 ./Lib/plat-mac/lib-scriptpackages/Netscape/WorldWideWeb_suite.py /galaxydir/galaxy/database/dependdatabase/dependencies/pytn_2_7/8b09fe018cac/lib/python2.etscape tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,755 /usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/Netscape/__init__.py /galaxydir/galaxy/hon/2.7/iuc/package_pytho7/plat-mac/lib-scriptpackages/N/usr/bin/install -c -m 644 ./Lib/plat-m2.7/iuc/package_python_2_7/8b09fe018cac/lib/pythpackages/StdSuites tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,755 ac/lib-scriptpackages/StdSuites/AppleScript_Suite.py /galaxydir/galaxy/database/dependencies/python/on2.7/plat-mac/lib-script/usr/bin/install -c -m 644 ./Lipendencies/python/2.7/iuc/package_pythothon2.7/plat-mac/lib-scriptpackages/StdSuites tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,755 b/plat-mac/lib-scriptpackages/StdSuites/Macintosh_Connectivity_Clas.py /galaxydir/galaxy/database/den_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lidencies/python/2.7/iuc/package_python_2n2.7/plat-mac/lib-scriptpackages/StdSuites tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,755 b/plat-mac/lib-scriptpackages/StdSuites/QuickDraw_Graphics_Suite.py /galaxydir/galaxy/database/depen_7/8b09fe018cac/lib/pytho/usr/bin/install -c -m 644 ./Lipendencies/python/2.7/iuc/package_pythothon2.7/plat-mac/lib-scriptpackages/StdSuites tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,755 b/plat-mac/lib-scriptpackages/StdSuites/QuickDraw_Graphics_Suppleme.py /galaxydir/galaxy/database/den_2_7/8b09fe018cac/lib/py/usr/bin/install -c -m 644 ./Lithon/2.7/iuc/package_python_2_7/8b09fe0mac/lib-scriptpackages/StdSuites tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,756 b/plat-mac/lib-scriptpackages/StdSuites/Required_Suite.py /galaxydir/galaxy/database/dependencies/py18cac/lib/python2.7/plat-/usr/bin/install -c -m 644 ./Lithon/2.7/iuc/package_python_2_7/8b09fe0mac/lib-scriptpackages/StdSuites tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,756 b/plat-mac/lib-scriptpackages/StdSuites/Standard_Suite.py /galaxydir/galaxy/database/dependencies/py18cac/lib/python2.7/plat-/usr/bin/install -c -m 644 ./Lin/2.7/iuc/package_python_2_7/8b09fe018c/lib-scriptpackages/StdSuites install_environment.STDOUT DEBUG 2017-11-18 17:03:22,761 b/plat-mac/lib-scriptpackages/StdSuites/Table_Suite.py /galaxydir/galaxy/database/dependencies/pythoac/lib/python2.7/plat-mac/usr/bin/install -c -m 644 ./Li/2.7/iuc/package_python_2_7/8b09fe018calib-scriptpackages/StdSuites install_environment.STDOUT DEBUG 2017-11-18 17:03:22,766 b/plat-mac/lib-scriptpackages/StdSuites/Type_Names_Suite.py /galaxydir/galaxy/database/dependencies/e018cac/lib/python2.7/pla/usr/bin/install -c -m 644 ./Li.7/iuc/package_python_2_7/8b09fe018cac/b-scriptpackages/StdSuites install_environment.STDOUT DEBUG 2017-11-18 17:03:22,775 b/plat-mac/lib-scriptpackages/SystemEvents/Disk_Folder_File_Suite.py /galaxydir/galaxy/database/depe2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/SystemEvents install_environment.STDOUT DEBUG 2017-11-18 17:03:22,778 /usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/SystemEvents/Folder_Actions_Suite.py /g/iuc/package_python_2_7/8Events install_environment.STDOUT DEBUG 2017-11-18 17:03:22,790 idden_Suite.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64endencies/python/2.7/iuc/packag/lib/python2.7/plat-mac/lib-scriptpacka/usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scage_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scrip/usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/SystemEvents/P8cac/lib/python2.7/plat-mac/lib-scriptpackages/SystemEvents install_environment.STDOUT DEBUG 2017-11-18 17:03:22,793 4 ./Lib/plat-mac/lib-scriptpackages/SystemEvents/Standard_Suite.py /galaxydir/galaxy/database/dependython_2_7/8b09fe018cac/li/SystemEvents install_environment.STDOUT DEBUG 2017-11-18 17:03:22,800 riptpackages/SystemEvents/System_Events_Suite.py /galaxydir/galaxy/database/dependencies/python/2.7/ib-scriptpackages/SystemE/usr/bin/install -c -m 644 ./Lihon/2.7/iuc/package_python_2_7/8b09fe01ac/lib-scriptpackages/SystemEvents install_environment.STDOUT DEBUG 2017-11-18 17:03:22,812 b/plat-mac/lib-scriptpackages/SystemEvents/__init__.py /galaxydir/galaxy/database/dependencies/pythoac/lib/python2.7/plat-mac/usr/bin/install -c -m 644 ./Lihon/2.7/iuc/package_python_2_7/8b09fe01ac/lib-scriptpackages/Terminal install_environment.STDOUT DEBUG 2017-11-18 17:03:22,830 b/plat-mac/lib-scriptpackages/Terminal/Terminal_Suite.py /galaxydir/galaxy/database/dependencies/pyt8cac/lib/python2.7/plat-my/database/dependencies/python/7/8b09fe018cac/lib/python2.7/plat-mac/l/usr/bin/install -c -m 644 ./Lib/plat-mac/lib-schon_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackag/usr/bin/install -c -m 644 ./LICENSE /galaxydir/galaxy/database/dependencieif test -d /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018 /usr/bin/install -c -m 644 ./Modules/xxmodule.c \ install_environment.STDOUT DEBUG 2017-11-18 17:03:22,836 b/python2.7 DYLD_LIBRARY_PATH=/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 \ ./python.exe -E -Wi -tt -d /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 -f \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,860 b/plat-mac/lib-scriptpackages/StdSuites/Table_Suite.py /galaxydir/galaxy/database/dependencies/pythoac/lib/python2.7/plat-mac/usr/bin/install -c -m 644 ./Li/2.7/iuc/package_python_2_7/8b09fe018calib-scriptpackages/StdSuites tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,860 b/plat-mac/lib-scriptpackages/StdSuites/Text_Suite.py /galaxydir/galaxy/database/dependencies/pythonc/lib/python2.7/plat-mac//usr/bin/install -c -m 644 ./Lipython/2.7/iuc/package_python_2_7/8b09ft-mac/lib-scriptpackages/StdSuites tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,860 b/plat-mac/lib-scriptpackages/StdSuites/Type_Names_Suite.py /galaxydir/galaxy/database/dependencies/e018cac/lib/python2.7/pla/usr/bin/install -c -m 644 ./Li.7/iuc/package_python_2_7/8b09fe018cac/b-scriptpackages/StdSuites tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,860 b/plat-mac/lib-scriptpackages/SystemEvents/Disk_Folder_File_Suite.py /galaxydir/galaxy/database/depe2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/SystemEvents tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,861 /usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/SystemEvents/Folder_Actions_Suite.py /g/iuc/package_python_2_7/8Events tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,862 b/plat-mac/lib-scriptpackages/StdSuites/__init__.py /galaxydir/galaxy/database/dependencies/python/2lib/python2.7/plat-mac/li/usr/bin/install -c -m 644 ./Lindencies/python/2.7/iuc/package_python_alaxydir/galaxy/database/dependencies/python/2.7b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/System/usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/SystemEvents/Hc/lib/python2.7/plat-mac/lib-scriptpackages/SystemEvents tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,864 4 ./Lib/plat-mac/lib-scriptpackages/SystemEvents/Login_Items_Suite.py /galaxydir/galaxy/database/depe_python_2_7/8b09fe018cacges/SystemEvents tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,864 riptpackages/SystemEvents/Power_Suite.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packtpackages/SystemEvents tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,864 idden_Suite.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 64endencies/python/2.7/iuc/packag/lib/python2.7/plat-mac/lib-scriptpacka/usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scage_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scrip/usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/SystemEvents/P8cac/lib/python2.7/plat-mac/lib-scriptpackages/SystemEvents tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,864 4 ./Lib/plat-mac/lib-scriptpackages/SystemEvents/Standard_Suite.py /galaxydir/galaxy/database/dependython_2_7/8b09fe018cac/li/SystemEvents tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,864 rocesses_Suite.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64encies/python/2.7/iuc/package_pb/python2.7/plat-mac/lib-scriptpackages/usr/bin/install -c -m 644 ./Lib/plat-mac/lib-sciuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lvents tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,864 riptpackages/SystemEvents/System_Events_Suite.py /galaxydir/galaxy/database/dependencies/python/2.7/ib-scriptpackages/SystemE/usr/bin/install -c -m 644 ./Lihon/2.7/iuc/package_python_2_7/8b09fe01ac/lib-scriptpackages/SystemEvents tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,864 b/plat-mac/lib-scriptpackages/SystemEvents/Text_Suite.py /galaxydir/galaxy/database/dependencies/pyt8cac/lib/python2.7/plat-m/usr/bin/install -c -m 644 ./Lin/2.7/iuc/package_python_2_7/8b09fe018c/lib-scriptpackages/SystemEvents tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,864 b/plat-mac/lib-scriptpackages/SystemEvents/__init__.py /galaxydir/galaxy/database/dependencies/pythoac/lib/python2.7/plat-mac/usr/bin/install -c -m 644 ./Lihon/2.7/iuc/package_python_2_7/8b09fe01ac/lib-scriptpackages/Terminal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,865 b/plat-mac/lib-scriptpackages/Terminal/Standard_Suite.py /galaxydir/galaxy/database/dependencies/pyt8cac/lib/python2.7/plat-m/usr/bin/install -c -m 644 ./Lihon/2.7/iuc/package_python_2_7/8b09fe01ac/lib-scriptpackages/Terminal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,865 /usr/bin/install -c -m 644 ./Lib/plat-mac/lib-scriptpackages/Terminal/Text_Suite.py /galaxydir/galax2.7/iuc/package_python_2_ib-scriptpackages/Terminal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,865 riptpackages/Terminal/__init__.py /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytes/Terminal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,865 s/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/LICENSE.txt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,865 cac/lib/python2.7/distutils/tests; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,865 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/tests ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,865 fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,865 b/plat-mac/lib-scriptpackages/Terminal/Terminal_Suite.py /galaxydir/galaxy/database/dependencies/pyt8cac/lib/python2.7/plat-my/database/dependencies/python/7/8b09fe018cac/lib/python2.7/plat-mac/l/usr/bin/install -c -m 644 ./Lib/plat-mac/lib-schon_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackag/usr/bin/install -c -m 644 ./LICENSE /galaxydir/galaxy/database/dependencieif test -d /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018 /usr/bin/install -c -m 644 ./Modules/xxmodule.c \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,865 PYTHONPATH=/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,865 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/compileall.py \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,865 -x 'bad_coding|badsyntax|site-packages|lib2to3/tests/data' \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,865 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:22,866 b/python2.7 DYLD_LIBRARY_PATH=/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 \ ./python.exe -E -Wi -tt -d /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 -f \ install_environment.STDOUT DEBUG 2017-11-18 17:03:23,364 ython2.7 ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,364 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/BaseHTTPServer.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,364 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/Bastion.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,365 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/CGIHTTPServer.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,365 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ConfigParser.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,365 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/Cookie.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,365 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/DocXMLRPCServer.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,366 /python2.7/_pyio.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,367 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/_strptime.py .Compiling /galaxydir/gala.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,367 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/_threading_local.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,367 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/_weakrefset.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,367 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/abc.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,367 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/aifc.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,367 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/antigravity.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,367 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/anydbm.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,368 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/argparse.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,368 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ast.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,368 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/asynchat.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,368 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/asyncore.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,368 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/atexit.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,368 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/audiodev.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,368 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/base64.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,368 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bdb.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,368 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/binhex.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,369 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bisect.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,369 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,369 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/__init__.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,369 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/db.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,369 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/dbobj.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,369 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/dbrecio.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,369 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/dbshelve.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,369 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/dbtables.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,369 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/dbutils.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,370 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,370 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/__init__.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,370 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_all.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,370 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_associate.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,370 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_basics.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,370 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_compare.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,371 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_compat.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,371 abase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_cursor_pget_bug.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,371 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_db.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,371 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_dbenv.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,371 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_dbobj.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,372 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_dbshelve.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,372 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_dbtables.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,372 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_distributed_transactions.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,372 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_early_close.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,372 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_fileid.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,372 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_get_none.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,372 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_join.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,372 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_lock.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,372 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_misc.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,372 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_pickle.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,373 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_queue.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,373 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_recno.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,373 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_replication.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,373 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_sequence.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,373 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/bsddb/test/test_thread.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,373 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/cProfile.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,373 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/calendar.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,373 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/cgi.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,373 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/cgitb.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,374 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/chunk.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,374 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/cmd.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,374 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/code.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,374 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/codecs.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,374 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/codeop.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,374 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/collections.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,374 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/colorsys.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,375 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/commands.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,375 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/compileall.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,375 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/compiler ... install_environment.STDOUT DEBUG 2017-11-18 17:03:23,375 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/compiler/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,375 ython2.7 ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,376 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/BaseHTTPServer.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,376 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/Bastion.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,376 Compiling 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,380 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/MimeWriter.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,380 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/Queue.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,381 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/SimpleHTTPServer.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,381 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/SimpleXMLRPCServer.py ... 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,382 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/__phello__.foo.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,382 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/_abcoll.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,382 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/_osx_support.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,382 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/DocXMLRPCServer.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,382 /python2.7/_pyio.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,382 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/gala.. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,382 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/_strptime.py .Compiling /galaxydir/gala.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,382 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/_threading_local.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:23,382 Compiling 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17:03:23,822 /python2.7/distutils/msvc9compiler.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,165 /python2.7/distutils/tests/test_bdist_wininst.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,165 /python2.7/distutils/tests/test_check.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,165 /python2.7/distutils/tests/test_config.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,166 /python2.7/distutils/tests/test_dir_util.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,166 /python2.7/distutils/tests/test_filelist.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,166 ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,166 /python2.7/distutils/tests/test_install_lib.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,166 ipts.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,166 /python2.7/distutils/tests/test_register.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,167 Compiling 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DEBUG 2017-11-18 17:03:24,231 /python2.7/distutils/tests/test_config.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,232 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/tests/test_dist.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,232 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/tests/test_file_util.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,232 /python2.7/distutils/tests/test_dir_util.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,232 /python2.7/distutils/tests/test_filelist.py ... 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/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/genericpath.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,554 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ftplib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,554 /python2.7/getopt.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,554 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/gettext.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,554 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/glob.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,554 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/gzip.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,554 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/getpass.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,554 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/heapq.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,554 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hmac.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,554 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hotshot ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,554 /python2.7/hashlib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,554 /python2.7/hotshot/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,555 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/pythonCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hotshot/stats.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,555 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hotshot/stones.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,555 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/htmlentitydefs.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,555 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/htmllib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,555 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/httplib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,555 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,555 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/AutoComplete.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,555 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/AutoCompleteWindow.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,555 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/AutoExpand.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,555 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/Bindings.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,555 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/CallTipWindow.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,555 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/CallTips.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,556 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/ClassBrowser.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,556 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/CodeContext.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,556 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/ColorDelegator.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,556 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/Debugger.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,556 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/Delegator.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,556 /2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hotshot/log.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,881 /python2.7/idlelib/EditorWindow.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,882 story.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,882 /python2.7/idlelib/ScrolledList.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,882 /python2.7/idlelib/SearchEngine.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,882 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/WidgetRedirector.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,883 /python2.7/idlelib/ZoomHeight.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,883 /python2.7/idlelib/configHandler.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,883 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/idle_t install_environment.STDOUT DEBUG 2017-11-18 17:03:24,883 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/idle_test/test_io.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,884 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/idle_test/test_text.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,884 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/idle_test/test_widgetredir.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:24,884 Compiling 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,971 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/FileList.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,971 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/FormatParagraph.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,972 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/GrepDialog.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,972 Compiling 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/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/MultiCall.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,972 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/MultiStatusBar.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,972 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/ObjectBrowser.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,972 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/OutputWindow.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:24,972 Compiling 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install_environment.STDOUT DEBUG 2017-11-18 17:03:25,311 /python2.7/lib2to3/fixes/fix_sys_exc.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,311 /python2.7/lib2to3/fixes/fix_unicode.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,311 /python2.7/lib2to3/fixes/fix_xreadlines.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,311 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/fixes/fix_zip.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,311 . install_environment.STDOUT DEBUG 2017-11-18 17:03:25,312 /python2.7/lib2to3/pygram.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,312 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/tests/__init__.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,312 support.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,312 Compiling 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,392 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tk/Tkinter.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,392 ython2.7/lib-tk/test ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,392 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tk/test/runtktests.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,392 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tk/test/test_tkinter ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,392 Compiling 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DEBUG 2017-11-18 17:03:25,394 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tk/test/test_tkinter/test_loadtk.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,395 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tk/test/wiCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-tk/tkColorChooser.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,395 dget_tests.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,395 /python2.7/lib-tk/tkCommonDialog.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,395 Compiling 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17:03:25,398 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/fixes/fix_exitfunc.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,398 /python2.7/lib2to3/fixes/fix_exec.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,398 /python2.7/lib2to3/fixes/fix_filter.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,398 .. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,398 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/fixes/fix_funcattrs.py .Compiling 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,403 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/main.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,403 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/patcomp.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,403 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/fixes/fix_zip.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,403 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/pgen2 ..Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/pgen2/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,403 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/pgen2/conv.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,403 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/pgen2/driver.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,404 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/pgen2/grammar.py ... 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17:03:25,826 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/multiprocessing/dummy/__init__.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,826 /python2.7/multiprocessing/heap.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,826 g/process.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,826 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/multiprocessing/reduction.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,827 g/util.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,827 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/numbers.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,827 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/pickle.py ... install_environment.STDOUT 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c/lib/python2.7/plat-mac/Carbon/Dlg.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,829 s/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Drag.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,829 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libn/File.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,829 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Icn.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,830 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Qd.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,830 /python2.7/plat-mac/Carbon/Qdoffs.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:25,830 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Sound.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,918 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/tests//python2.7/lib2to3/tests/test_rCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/tests/test_util.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,918 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/linecache.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,918 Compiling 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ge_python_2_7/8b09fe018cac/lib/python2.7/markupbase.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,920 ython2.7/multiprocessing/dummy ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,920 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/multiprocessing/dummy/connection.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,920 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/multiprocessing/forking.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,920 Compiling 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,926 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/CarboCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Files.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,926 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Fm.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,926 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Folder.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:25,926 Compiling 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install_environment.STDOUT DEBUG 2017-11-18 17:03:26,324 /python2.7/posixpath.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,324 /python2.7/pstats.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,324 /python2.7/py_compile.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,334 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/CarboCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Windows.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,334 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,334 Compiling 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... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,338 ython2.7/plat-mac/lib-scriptpackages/CodeWarrior ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,338 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior/Metrowerks_Shell_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,338 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior/Required.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,338 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior/Standard_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,338 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,338 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,338 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer/Microsoft_Internet_Explorer.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,339 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer/Netscape_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,339 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer/Required_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,339 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer/Standard_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,339 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer/URL_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,339 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior/CodeWarrior_suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,339 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,339 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,339 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder/Containers_and_folders.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,340 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder/Enumerations.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,340 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder/Files.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,340 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder/Finder_Basics.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,340 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder/Finder_items.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,340 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder/Legacy_suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,341 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder/Standard_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,341 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder/Type_Definitions.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,341 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder/Window_classes.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,341 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,341 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Netscape ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,341 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Netscape/Mozilla_suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,341 /python2.7/plat-mac/lib-scriptpackages/Explorer/Web_Browser_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,341 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Netscape/PowerPlant.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,342 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Netscape/Standard_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,342 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Netscape/Required_suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,342 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-sCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Netscape/Text.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,342 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Netscape/WorldWideWeb_suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,342 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Netscape/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,342 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/StdSuites ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,343 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/StdSuites/AppleScript_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,343 criptpackages/Netscape/Standard_URL_suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,343 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/StdSuites/MacintoCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/StdSuites/QuickDraw_Graphics_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,343 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/StdSuites/QuickDraw_Graphics_Suppleme.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,343 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/StdSuites/Required_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,343 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/StdSuites/Standard_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,344 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/StdSuites/Table_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,344 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/StdSuites/Text_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,344 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/StdSuites/Type_Names_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,344 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/StdSuites/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,344 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/SystemEvents ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,344 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/SystemEvents/Disk_Folder_File_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,344 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/SystemEvents/Folder_Actions_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,345 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/SystemEvents/Hidden_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,345 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/SystemEvents/Login_Items_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,345 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/SystemEvents/Power_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,345 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/SystemEvents/Processes_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,345 Compiling 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... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,345 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Terminal ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,346 sh_Connectivity_Clas.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,346 _Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,346 pendencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Terminal/Terminal_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,346 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Terminal/StandardCompiling /galaxydir/galaxy/database/deCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Terminal/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,347 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/_builtinSuites ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,347 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/_builtinSuites/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,347 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/_builtinSuites/builtin_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,347 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/macerrors.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,347 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/macostools.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,347 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/macresource.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,348 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/pimp.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,348 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/terminalcommand.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,348 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/videoreader.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,348 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/platform.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:26,348 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17:03:26,349 /python2.7/py_compile.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,958 ython2.7/pydoc_data ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,958 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/random.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,959 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/re.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,959 /python2.7/rfc822.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,959 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/rlcompleter.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,959 c/lib/python2.7/robotparser.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,959 Compiling 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17:03:26,961 /python2.7/sqlite3/test/types.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,961 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/sre.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,961 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/stringold.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,961 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/cjkencodings ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,962 ng_bugs.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,962 py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,962 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/relimport.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:26,963 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/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_robotparser.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,095 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_runpy.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,095 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_sax.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,095 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_scope.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,095 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_scriptpackages.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,095 Compiling 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/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_sha.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,096 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_shelve.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,096 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_shlex.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,096 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_shutil.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,096 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_signal.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,096 Compiling 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install_environment.STDOUT DEBUG 2017-11-18 17:03:29,100 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_telnCompiling /galaxydir/galafile.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,100 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_textCompiling /galaxydir/galaad.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,100 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_threCompiling /galaxydir/galaadedtempfile.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,100 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_threCompiling /galaxydir/galaading_local.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,100 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_threCompiling /galaxydir/gala.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,100 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_timeCompiling /galaxydir/galaout.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,100 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_tk.pCompiling /galaxydir/galanize.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,101 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_toolCompiling /galaxydir/galae.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,102 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_tracCompiling /galaxydir/galasformer.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,102 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_ttk_Compiling /galaxydir/galatextonly.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,102 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_tuplCompiling /galaxydir/galachecks.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,102 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_typeCompiling /galaxydir/galapy ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,102 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_unarCompiling /galaxydir/galacumented_details.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,190 /python2.7/test/test_plistlib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,190 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_poll.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,190 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_popen.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,190 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_popen2.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,190 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_poplib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,191 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_posix.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,191 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_posixpath.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,191 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_pprint.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,191 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_print.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,191 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_profile.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,191 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_property.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,191 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_pstats.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,191 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_pty.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,192 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_pwd.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,192 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_py3kwarn.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,192 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_py_compile.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,192 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_pyclbr.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,192 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_pydoc.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,192 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_pyexpat.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,192 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_queue.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,193 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_quopri.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,193 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_random.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,193 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/gala/python2.7/test/test_pow.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,193 /python2.7/test/test_re.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,193 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaline.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,193 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_readCompiling /galaxydir/gala.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,193 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_resource.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,193 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_rfc822.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,193 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_richcmp.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,194 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_rlcompleter.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,194 Compiling 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/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_wait3.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,618 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_wait4.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,618 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_warnings.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,618 /python2.7/test/test_uuid.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,618 /python2.7/test/test_wave.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,618 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_weakref.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,618 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_whichdb.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,618 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_winreg.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,618 Compiling 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,619 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/testcodec.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,619 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/tf_inherit_check.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,620 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/threaded_import_hangers.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,620 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/time_hashlib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,620 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/tracedmodules ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,620 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/tracedmodules/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,620 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/tracedmodules/testmod.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,620 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/warning_tests.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,620 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/win_console_handler.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,620 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/xmltestdata ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,623 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/xmltests.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,623 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/textwrap.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,623 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/this.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,623 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/threading.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,623 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/timeit.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,623 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/toaiff.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,623 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/token.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,625 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/tokenize.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,625 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/trace.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,625 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/traceback.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,625 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/tty.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,626 /python2.7/test/test_zipimport_support.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,626 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/types.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,626 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,627 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,627 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/__main__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,627 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/loader.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:29,627 b/python2.7 DYLD_LIBRARY_PATH=/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,627 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/main.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,628 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/result.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,628 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/runner.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,628 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/signals.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,628 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/suite.py ... 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2017-11-18 17:03:29,630 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/test/test_suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,630 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/util.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,630 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/urllib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,630 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/test/test_assertions.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,630 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/urllib2.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,630 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/user.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,630 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/uu.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,631 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/uuid.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,631 Compiling 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,633 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/wsgiref/simple_server.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,633 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/wsgiref/util.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,633 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/wsgiref/validate.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,633 Compiling 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,638 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xmllib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,638 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xmlrpclib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,638 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/zipfile.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,638 /python2.7/xml/sax/saxutils.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,639 PYTHONPATH=/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li ./python.exe -E -Wi -tt -O /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/compileall.py \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,639 -d /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 -f \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,639 -x 'bad_coding|badsyntax|site-packages|lib2to3/tests/data' \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,639 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:29,639 b/python2.7 DYLD_LIBRARY_PATH=/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 \ 127.0.0.1 - - [18/Nov/2017:17:03:30 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:03:31,394 ython2.7 ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,394 /python2.7/ConfigParser.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,394 /python2.7/MimeWriter.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,395 /python2.7/SimpleXMLRPCServer.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,395 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/StringIO.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,395 . install_environment.STDOUT DEBUG 2017-11-18 17:03:31,395 /python2.7/_MozillaCookieJar.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,395 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/__future__.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,395 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/_strptime.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,396 /python2.7/compiler/future.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,397 /python2.7/compiler/pycodegen.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,397 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/compiler/symbols.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,397 Compiling 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17:03:31,399 ython2.7/distutils/command ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,400 /python2.7/distutils/command/bdist.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,400 /python2.7/distutils/command/build.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,400 /python2.7/distutils/command/build_ext.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,400 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/command/build_py.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,401 /python2.7/distutils/command/upload.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,401 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/debug.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,401 Compiling 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DEBUG 2017-11-18 17:03:31,411 /python2.7/encodings/iso8859_8.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,411 c/lib/python2.7/encodings/iso8859_9.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,411 /python2.7/encodings/mac_cyrillic.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,412 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/mac_farsi.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,412 /python2.7/encodings/mac_latin2.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,412 /python2.7/encodings/mac_turkish.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,412 /python2.7/encodings/string_escape.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,413 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/tis_620.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,413 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/undefined.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,413 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/unicode_escape.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,413 /python2.7/encodings/utf_32_le.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,413 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib8_sig.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,413 abase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/uu_codec.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,413 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/zlib_codec.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,414 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ensurepip ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,414 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ensurepip/__init__.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,414 pendencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ensurepip/__main__.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,414 python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ensurepip/_bundled ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,414 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ensurepip/_uninstall.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,414 Compiling 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install_environment.STDOUT DEBUG 2017-11-18 17:03:31,416 gs.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,416 /python2.7/idlelib/ClassBrowser.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:31,416 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/ColorDelegator.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,489 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/BaseHTTPServer.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,489 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/Bastion.py ... 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DEBUG 2017-11-18 17:03:31,513 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/tests/test_msvc9compiler.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,513 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/tests/test_sdist.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,513 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/tests/test_spawn.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,513 Compiling 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/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/utf_32_be.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,529 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/unicode_escape.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,529 /python2.7/encodings/utf_32_le.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,529 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/utf_7.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,530 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/utf_8.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,530 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib8_sig.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,530 abase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/uu_codec.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,530 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/zlib_codec.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,530 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ensurepip ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,530 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ensurepip/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,530 pendencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ensurepip/__main__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,530 python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ensurepip/_bundled ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,530 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/ensurepip/_uninstall.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,530 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/utf_Compiling /galaxydir/galaxy/datCompiling /galaxydir/galaxy/database/deListing /galaxydir/galaxy/database/dependencies/Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/fileinput.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,530 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/fnmatch.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,531 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/formatter.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,531 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/fpformat.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,531 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/fractions.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,531 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/filecmp.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,531 /python2.7/ftplib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,531 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/functools.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,531 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/getopt.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,531 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/getpass.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,531 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/genericpath.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,531 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/gettext.py ...Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/glob.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,532 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/gzip.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,635 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/heapq.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,635 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hmac.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,635 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hotshot ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,635 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hotshot/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,635 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hotshot/log.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,636 /python2.7/hashlib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,636 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/hotshot/stones.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,636 /python2.7/hotshot/stats.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,636 /python2.7/htmlentitydefs.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,636 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/htmllib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,636 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018caListing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,636 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/AutoComplete.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,636 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/AutoCompleteWindow.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,636 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/AutoExpand.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,636 c/lib/python2.7/httplib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,637 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/BindinCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/CallTipWindow.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,637 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/CallTips.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,637 gs.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,637 /python2.7/idlelib/ClassBrowser.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,637 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/CodeContext.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,637 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/Debugger.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,637 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/Delegator.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:31,637 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/ColorDelegator.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,101 /python2.7/idlelib/EditorWindow.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,102 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/idle_test/mock_tk.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,103 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/json/tests/test_decode.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,103 /python2.7/lib-tk/Tkinter.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,104 Compiling 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install_environment.STDOUT DEBUG 2017-11-18 17:03:33,107 /python2.7/new.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,108 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Dlg.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,108 /python2.7/plat-mac/Carbon/Qd.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,108 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Qdoffs.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,108 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Qt.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,108 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/QuickDraw.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,109 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/QuickTime.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,109 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Res.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,109 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Resources.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,109 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Scrap.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,109 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Snd.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,109 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Sndihooks.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,109 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Sound.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,110 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/TE.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,110 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/TextEdit.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,110 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Win.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,110 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Windows.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,110 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/__init__.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,110 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/EasyDialogs.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,110 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/FrameWork.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,110 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/MiniAEFrame.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,110 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/PixMapWrapper.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,110 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/aepack.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,110 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/aetools.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,111 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/aetypes.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,111 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/applesingle.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,111 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/appletrawmain.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,111 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/appletrunner.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,111 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/argvemulator.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,111 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/bgenlocations.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,111 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/buildtools.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,111 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/bundlebuilder.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,111 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/cfmfile.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,111 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/findertools.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,111 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/gensuitemodule.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,111 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/ic.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,112 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/icopen.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,112 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,112 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,112 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior/CodeWarrior_suite.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,112 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior/Metrowerks_Shell_Suite.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,112 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior/Required.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,112 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior/Standard_Suite.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,112 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior/__init__.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,112 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,112 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer/Microsoft_Internet_Explorer.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,113 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer/Netscape_Suite.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,113 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-s/python2.7/plat-mac/lib-scriptpackages/StdSuites/Type_Names_Suite.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,114 /python2.7/plistlib.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,114 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/popen2.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,114 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/poplib.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:33,114 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/posixfile.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,184 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/FileList.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,184 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/FormatParagraph.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,184 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/GrepDialog.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,184 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/HyperParser.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,185 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/IOBinding.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,185 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/Icons ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,185 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/IdleHistory.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,185 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/MultiCall.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,185 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/MultiStatusBar.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,186 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/ObjectBrowser.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,186 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/OutputWindow.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,186 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/ParenMatch.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,186 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/PathBrowser.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,186 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/Percolator.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,186 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/PyParse.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,187 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/PyShell.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,187 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/RemoteDebugger.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,187 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/RemoteObjectBrowser.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,187 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/ReplaceDialog.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,187 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/RstripExtension.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,188 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/ScriptBinding.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,188 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/ScrolledList.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,188 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/SearchDialog.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,188 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/SearchDialogBase.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,188 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/SearchEngine.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,188 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/StackViewer.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,189 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/ToolTip.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,189 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/TreeWidget.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,189 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/UndoDelegator.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,189 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/WidgetRedirector.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,189 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/WindowList.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,189 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/ZoomHeight.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,189 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,190 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/aboutDialog.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,190 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/configDialog.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,190 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/configHandler.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,190 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/configHelpSourceEdit.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,190 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/configSectionNameDialog.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,191 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/dynOptionMenuWidget.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,191 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/idle.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,191 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/idlelib/idle_test ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,191 Compiling 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17:03:33,215 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/tests/test_pytree.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,215 /python2.7/lib2to3/pgen2/driver.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,215 /python2.7/lib2to3/tests/test_refactor.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,216 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/tests/test_util.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,216 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/linecache.py ... 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/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Audio_mac.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,238 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,238 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/AE.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,238 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/AH.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,238 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Alias.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,238 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Aliases.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,238 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/App.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,239 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Appearance.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,239 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/AppleEvents.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,239 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/AppleHelp.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,239 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/CF.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,239 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/CG.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,240 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/CarbonEvents.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,240 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/CarbonEvt.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,240 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Cm.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,240 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Components.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,240 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/ControlAccessor.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,240 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Controls.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,240 /python2.7/new.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,240 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/CoreFoundation.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,240 /python2.7/plat-mac/Carbon/CoreGraphics.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,240 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Ctl.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,240 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Dialogs.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,240 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Drag.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,240 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Dragconst.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,241 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Events.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,241 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Evt.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,241 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/File.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,241 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Files.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,241 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Fm.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,241 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Folder.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,241 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Folders.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,241 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Fonts.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,241 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Help.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,242 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/IBCarbon.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,242 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/IBCarbonRuntime.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,242 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Icn.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,242 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Icons.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,242 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Launch.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,242 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/LaunchServices.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,242 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/List.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,242 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Lists.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,242 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/MacHelp.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,242 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/MacTextEditor.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,242 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/MediaDescr.py 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,243 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/OSAconst.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,243 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/QDOffscreen.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,243 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Dlg.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,243 /python2.7/plat-mac/Carbon/Qd.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,243 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Qdoffs.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,244 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Qt.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,244 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/QuickDraw.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,244 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/QuickTime.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,244 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Res.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,244 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Resources.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,244 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Scrap.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,244 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Snd.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,244 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Sndihooks.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,244 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/Sound.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,244 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/TE.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,244 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/Carbon/TextEdit.py ... 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,246 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/bundlebuilder.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,246 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/cfmfile.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,246 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/findertools.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,246 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/gensuitemodule.py ... 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,247 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior/CodeWarrior_suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,247 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior/Metrowerks_Shell_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,247 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/CodeWarrior/Required.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,247 Compiling 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,247 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer/Required_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,247 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer/Standard_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,248 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer/URL_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,248 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer/Web_Browser_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,248 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Explorer/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,248 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,248 Compiling 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,249 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder/Finder_items.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,249 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder/Legacy_suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,249 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Finder/Standard_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,249 Compiling 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,249 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Netscape/Mozilla_suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,249 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Netscape/PowerPlant.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,249 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Netscape/Required_suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,250 Compiling 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,250 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/Netscape/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,250 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/StdSuites ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,250 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/StdSuites/AppleScript_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,250 Compiling 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,253 criptpackages/StdSuites/Text_Suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,253 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/StdSuites/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,254 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/plat-mac/lib-scriptpackages/SystemEvents ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:33,254 Compiling 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tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:35,814 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/robotparser.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:35,814 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/runpy.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:35,815 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/sched.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:35,815 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/sets.py ... 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Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/shutil.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:35,815 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:35,815 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:35,815 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/smtpd.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:35,815 Compiling 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2017-11-18 17:03:35,818 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/telnetlib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:35,818 abase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/tabnanny.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:35,818 /python2.7/tempfile.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:35,818 /database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:35,819 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libListing /galaxydir/galaxyCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packaCompiling 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17:03:36,344 /python2.7/test/test_uuid.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,344 /python2.7/test/test_wave.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,344 ref.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,344 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_xmlrpc.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,345 /python2.7/test/test_xpickle.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,345 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_xrange.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,345 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/test/test_zipfile.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,345 Compiling 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2017-11-18 17:03:36,346 . install_environment.STDOUT DEBUG 2017-11-18 17:03:36,346 abase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/test/__init__.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,347 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/test/test_result.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,347 /python2.7/unittest/test/test_suite.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,347 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/util.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,347 /python2.7/warnings.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,347 ython2.7/wsgiref ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,347 /2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/wsgiref/__init__.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,348 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/__init__.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,348 /python2.7/xml/dom/NodeFilter.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,348 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/dom/__init__.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,348 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/etree/ElementPath.py ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,348 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/etree/ElementTree.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 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Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/test/test_functiontestcase.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,378 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/test/test_loader.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,378 abase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/test/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,379 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/unittest/test/test_program.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,379 Compiling 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/python2.7/unittest/test/test_suite.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,379 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/urllib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,379 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/urllib2.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,379 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/urlparse.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,379 Compiling 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/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/wave.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,380 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/weakref.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,380 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/webbrowser.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,380 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/whichdb.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,380 /python2.7/warnings.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,380 ython2.7/wsgiref ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,380 /2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/wsgiref/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,380 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pCompiling /galaxydir/galaxy/database/dependencies/pythonCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/wsgiref/handlers.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,380 /python2.7/wsgiref/headers.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,380 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/wsgiref/simple_server.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,381 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/wsgiref/util.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,381 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/wsgiref/validate.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,381 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xdrlib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,381 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,381 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/dom ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,381 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,381 /python2.7/xml/dom/NodeFilter.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,381 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libCompiling /galaxydir/galaCompiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/dom/domreg.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,381 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/dom/expatbuilder.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,381 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/dom/minicompat.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,382 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/dom/minidom.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,382 xy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/dom/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,382 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/dom/pulldom.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,382 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/dom/xmlbuilder.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,382 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/etree ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,382 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/etree/ElementPath.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,382 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/etree/ElementInclude.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,382 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/etree/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,382 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/etree/cElementTree.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,382 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/parsers ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,382 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/parsers/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,383 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/parsers/expat.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,383 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/sax ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,383 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/sax/__init__.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,383 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/sax/_exceptions.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,383 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/sax/expatreader.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,383 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/sax/handler.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,383 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/sax/saxutils.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,383 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/sax/xmlreader.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,383 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xmllib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,383 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xmlrpclib.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,383 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/zipfile.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,384 Compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/xml/etree/ElementTree.py ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,384 PYTHONPATH=/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,384 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/compileall.py \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,384 -d /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages -f \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,384 -x badsyntax /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages install_environment.STDOUT DEBUG 2017-11-18 17:03:36,401 b/python2.7 DYLD_LIBRARY_PATH=/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 \ ./python.exe -E -Wi -t ython2.7/site-packages ... install_environment.STDOUT DEBUG 2017-11-18 17:03:36,442 axy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 DYLD_LIBRARY_/tmp/tmp-toolshed-mtdP5qH ./python.exe -E -Wi -t -O /gaython2.7/site-packages ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,498 b/python2.7 DYLD_LIBRARY_PATH=/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 \ ./python.exe -E -Wi -t ython2.7/site-packages ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,498 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pPYTHONPATH=/galaxydir/galPATH=/galaxydir/galaxy/databaseBA/Python-2.7.10 \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,498 laxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/compileall.py \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,498 -d /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages -f \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,498 -x badsyntax /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,499 axy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 DYLD_LIBRARY_/tmp/tmp-toolshed-mtdP5qH ./python.exe -E -Wi -t -O /gaython2.7/site-packages ... tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,499 Listing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pPYTHONPATH=/galaxydir/galPATH=/galaxydir/galaxy/databaseBA/Python-2.7.10 \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,499 en2.driver /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/Grammar.txt 127.0.0.1 - - [18/Nov/2017:17:03:36 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:03:36,597 axy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 DYLD_LIBRARY_/tmp/tmp-toolshed-mtdP5qH ./python.exe -E -m lib2to3.pg_2_7/8b09fe018cac/lib/python2.7/lib2to3Writing grammar tables to /galaxydir/galaxy/data.final.0.pickle tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,601 Generating grammar tables from /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/Grammar.txt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,602 axy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 DYLD_LIBRARY_/tmp/tmp-toolshed-mtdP5qH ./python.exe -E -m lib2to3.pg_2_7/8b09fe018cac/lib/python2.7/lib2to3Writing grammar tables to /galaxydir/galaxy/data.final.0.pickle install_environment.STDOUT DEBUG 2017-11-18 17:03:36,639 axy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 DYLD_LIBRARY_/tmp/tmp-toolshed-mtdP5qH ./python.exe -E -m lib2to3.pgb/python2.7/lib2to3/PatternGrammar.txt install_environment.STDOUT DEBUG 2017-11-18 17:03:36,700 from /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pytxt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,705 base/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/Grammar2.7.10PYTHONPATH=/galaxydir/galPATH=/galaxydir/galaxy/databaseBA/Python-2.7.10 \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,705 axy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7 DYLD_LIBRARY_/tmp/tmp-toolshed-mtdP5qH ./python.exe -E -m lib2to3.pgb/python2.7/lib2to3/PatternGrammar.txt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,705 from /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pytxt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,705 en2.driver /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/liGenerating grammar tableshon2.7/lib2to3/PatternGrammar.tWriting grammar tables to /galaxydir/gaernGrammar2.7.10.final.0.pickle install_environment.STDOUT DEBUG 2017-11-18 17:03:36,735 laxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/PattCreating directory /galaxCreating directory /galaxydir/g/usr/bin/install -c -m 644 ./Include/Pyclude/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,744 4 ./Include/Python.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 649fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,751 4 ./Include/asdl.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 648cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,761 4 ./Include/bitset.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64b09fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,766 4 ./Include/bufferobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,782 tearrayobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 647/8b09fe018cac/include/python2./usr/bin/install -c -m 644 ./Include/bynclude/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,791 4 ./Include/cStringIO.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64b09fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,800 4 ./Include/ceval.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 648b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,808 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,808 alaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,809 laxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib2to3/PattCreating directory /galaxCreating directory /galaxydir/g/usr/bin/install -c -m 644 ./Include/Pyclude/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,809 thon-ast.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/in/usr/bin/install -c -m 64e018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,809 4 ./Include/Python.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 649fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,809 4 ./Include/abstract.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 6418cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,809 4 ./Include/asdl.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 648cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,809 4 ./Include/ast.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01/usr/bin/install -c -m 64e018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,809 4 ./Include/bitset.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,809 4 ./Include/bufferobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,809 4 ./Include/boolobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64/8b09fe018cac/include/python2.7/usr/bin/install -c -m 644 ./Include/byac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,810 4 ./Include/bytes_methods.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,810 tearrayobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 647/8b09fe018cac/include/python2./usr/bin/install -c -m 644 ./Include/bynclude/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,810 tesobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/i/usr/bin/install -c -m 6409fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,810 4 ./Include/cStringIO.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,810 4 ./Include/cellobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,810 4 ./Include/ceval.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 648b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,811 4 ./Include/classobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,811 4 ./Include/code.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,822 4 ./Include/cobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 644 ./Include/code/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,827 4 ./Include/complexobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,838 tetime.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/incl/usr/bin/install -c -m 648b09fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,845 4 ./Include/dictobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 6418cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,852 4 ./Include/enumobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,862 4 ./Include/eval.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64b09fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,873 4 ./Include/floatobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 648b09fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,883 4 ./Include/funcobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 6409fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,889 4 ./Include/graminit.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,892 /usr/bin/install -c -m 644 ./Include/grammar.h /galaxydir/galaxy/database/dependencies/python/2.7/iuac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,903 port.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/includ/usr/bin/install -c -m 6409fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,911 /usr/bin/install -c -m 644 ./Include/codecs.h /galaxydir/galaxy/database/dependencies/python/2.7/iucc/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,912 4 ./Include/cobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64/package_python_2_7/8b09fe018ca/usr/bin/install -c -m 644 ./Include/code/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,912 4 ./Include/complexobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,912 mpile.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/inclu/usr/bin/install -c -m 647/8b09fe018cac/include/python2./usr/bin/install -c -m 644 ./Include/daude/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,912 tetime.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/incl/usr/bin/install -c -m 648b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,912 4 ./Include/descrobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,912 4 ./Include/dictobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 6418cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,912 4 ./Include/dtoa.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,912 4 ./Include/enumobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,912 4 ./Include/errcode.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 6418cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,913 4 ./Include/eval.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0/usr/bin/install -c -m 64b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,913 4 ./Include/fileobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 648b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,913 4 ./Include/floatobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 648b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,913 4 ./Include/frameobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,913 4 ./Include/funcobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 6409fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,913 4 ./Include/graminit.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,913 /usr/bin/install -c -m 644 ./Include/grammar.h /galaxydir/galaxy/database/dependencies/python/2.7/iuac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,913 4 ./Include/genobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64c/package_python_2_7/8b09fe018c/usr/bin/install -c -m 644 ./Include/ime/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,913 port.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/includ/usr/bin/install -c -m 6409fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:36,913 4 ./Include/intobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 6409fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,915 4 ./Include/intrcheck.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64b09fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,925 4 ./Include/listobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 648b09fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,936 4 ./Include/longobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,941 4 ./Include/memoryobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,953 tagrammar.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/i/usr/bin/install -c -m 64/8b09fe018cac/include/python2.7/usr/bin/install -c -m 644 ./Include/moclude/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,957 4 ./Include/moduleobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,969 de.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include//usr/bin/install -c -m 64e018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,980 4 ./Include/objimpl.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64e018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,990 4 ./Include/osdefs.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 649fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:36,999 4 ./Include/patchlevel.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8ackage_python_2_7/8b09fe0/usr/bin/install -c -m 644 ./In018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,007 4 ./Include/py_curses.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,021 4 ./Include/intrcheck.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,021 4 ./Include/iterobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,021 4 ./Include/listobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 648b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,021 4 ./Include/longintrepr.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,022 4 ./Include/longobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8/usr/bin/install -c -m 64fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,022 4 ./Include/memoryobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,022 4 ./Include/marshal.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64/8b09fe018cac/include/python2.7/usr/bin/install -c -m 644 ./Include/menclude/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,022 4 ./Include/methodobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,025 tagrammar.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/i/usr/bin/install -c -m 64/8b09fe018cac/include/python2.7/usr/bin/install -c -m 644 ./Include/moclude/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,026 4 ./Include/moduleobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,026 dsupport.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/in/usr/bin/install -c -m 64/8b09fe018cac/include/python2.7/usr/bin/install -c -m 644 ./Include/nopython2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,026 de.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include//usr/bin/install -c -m 64e018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,026 4 ./Include/object.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,026 4 ./Include/objimpl.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64e018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,026 4 ./Include/opcode.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64e018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,026 4 ./Include/osdefs.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 649fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,026 4 ./Include/parsetok.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,026 /usr/bin/install -c -m 644 ./Include/pgen.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/p18cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,026 4 ./Include/patchlevel.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8ackage_python_2_7/8b09fe0/usr/bin/install -c -m 644 ./In018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,027 clude/pgenheaders.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 6409fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,027 4 ./Include/py_curses.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,027 4 ./Include/pyarena.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 6409fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,022 4 ./Include/pycapsule.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,038 4 ./Include/pydebug.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 649fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,045 4 ./Include/pyexpat.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,052 4 ./Include/pygetopt.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 648b09fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,057 4 ./Include/pymactoolbox.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,068 math.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/includ/usr/bin/install -c -m 64018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,078 4 ./Include/pyport.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,089 4 ./Include/pystrcmp.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 649fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,097 4 ./Include/pythonrun.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 649fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,105 4 ./Include/rangeobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 6409fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,122 4 ./Include/sliceobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64/8b09fe018cac/include/python2.7/usr/bin/install -c -m 644 ./Include/stinclude/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,127 4 ./Include/pycapsule.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,128 4 ./Include/pyctype.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,128 4 ./Include/pydebug.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 649fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,128 4 ./Include/pyerrors.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,133 4 ./Include/pyexpat.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 64018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,133 4 ./Include/pyfpe.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 649fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,133 4 ./Include/pygetopt.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 648b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,133 4 ./Include/pymactoolbox.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,133 4 ./Include/pymacconfig.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64/8b09fe018cac/include/python2.7/usr/bin/install -c -m 644 ./Include/pye/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,134 math.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/includ/usr/bin/install -c -m 64018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,134 4 ./Include/pymem.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe/usr/bin/install -c -m 64e018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,134 4 ./Include/pyport.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09f/usr/bin/install -c -m 64fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,134 4 ./Include/pystate.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09/usr/bin/install -c -m 649fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,134 4 ./Include/pystrcmp.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 649fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,134 4 ./Include/pystrtod.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 6409fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,135 4 ./Include/pythonrun.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 649fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,135 4 ./Include/pythread.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 648b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,135 4 ./Include/rangeobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 6409fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,135 4 ./Include/setobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 648b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,135 4 ./Include/stringobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,135 4 ./Include/sliceobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7//usr/bin/install -c -m 64/8b09fe018cac/include/python2.7/usr/bin/install -c -m 644 ./Include/stinclude/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,135 ructmember.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 6409fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,172 4 ./Include/structseq.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64/usr/bin/install -c -m 644 ./Include/tupleobject.h /galaxydir/galaxy/d/usr/bin/install -c -m 644 ./Include/ucnhash.h /2.7/iuc/package_python_2_7/8b09fe018cac/include/python2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,183 4 ./Include/warnings.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64thon2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,200 nfig.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/includ# Substitution happens he# is not available in configuresed -e "s,@EXENAME@,/galaxydir/galaxy/dconfig.in >python-config tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,238 4 ./Include/symtable.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,239 /usr/bin/install -c -m 644 ./Include/sysmodule.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,239 /usr/bin/install -c -m 644 ./Include/timefuncs.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,239 /usr/bin/install -c -m 644 ./Include/token.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,239 /usr/bin/install -c -m 644 ./Include/traceback.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,239 atabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,239 galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,239 4 ./Include/structseq.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b/usr/bin/install -c -m 64/usr/bin/install -c -m 644 ./Include/tupleobject.h /galaxydir/galaxy/d/usr/bin/install -c -m 644 ./Include/ucnhash.h /2.7/iuc/package_python_2_7/8b09fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,239 /usr/bin/install -c -m 644 ./Include/unicodeobject.h /galaxydir/galaxy/database/dependencies/python//usr/bin/install -c -m 649fe018cac/include/python2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,240 4 ./Include/warnings.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b0/usr/bin/install -c -m 64thon2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,240 4 ./Include/weakrefobject.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/include/py/usr/bin/install -c -m 644 pycoe/python2.7/pyconfig.h tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,240 re, as the completely-expanded BINDIR install_environment.STDOUT DEBUG 2017-11-18 17:03:37,273 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/confiCreating directory /galax/usr/bin/install -c -m 644 Modulib/python2.7/config/config.c install_environment.STDOUT DEBUG 2017-11-18 17:03:37,278 4 Modules/python.o /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0on.o install_environment.STDOUT DEBUG 2017-11-18 17:03:37,287 nfig.c.in /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 64b/python2.7/config/Makefile install_environment.STDOUT DEBUG 2017-11-18 17:03:37,302 4 Modules/Setup /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64fe018cac/lib/python2.7/config/S/usr/bin/install -c -m 644 Modules/Setupython2.7/config/Setup.config install_environment.STDOUT DEBUG 2017-11-18 17:03:37,307 4 Misc/python.pc /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,320 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c ./insython2.7/config/install-sh install_environment.STDOUT DEBUG 2017-11-18 17:03:37,332 n-config /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/rm python-config tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,344 nfig.h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/includ# Substitution happens he# is not available in configuresed -e "s,@EXENAME@,/galaxydir/galaxy/dconfig.in >python-config tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,344 atabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/python2.7," < ./Misc/python-Creating directory /galaxg tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,345 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pkgconfig tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,345 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/confiCreating directory /galax/usr/bin/install -c -m 644 Modulib/python2.7/config/config.c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,346 4 Modules/python.o /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0on.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,346 les/config.c /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac//usr/bin/install -c -m 6418cac/lib/python2.7/config/pyth/usr/bin/install -c -m 644 ./Modules/co/python2.7/config/config.c.in tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,346 nfig.c.in /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/usr/bin/install -c -m 64b/python2.7/config/Makefile tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,346 4 Makefile /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/li/usr/bin/install -c -m 64ac/lib/python2.7/config/Setup tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,347 4 Modules/Setup.local /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09etup.local tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,347 4 Modules/Setup /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018c/usr/bin/install -c -m 64fe018cac/lib/python2.7/config/S/usr/bin/install -c -m 644 Modules/Setupython2.7/config/Setup.config tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,347 4 Misc/python.pc /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,347 p.config /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib//usr/bin/install -c -m 64cac/lib/pkgconfig/python-2.7.pc/usr/bin/install -c ./Modules/makesetup7/config/makesetup tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,347 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2./usr/bin/install -c ./insython2.7/config/install-sh tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,347 tall-sh /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/p/usr/bin/install -c pythopython2.7-config tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,348 n-config /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/rm python-config tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,348 /Library/Developer/CommandLineTools/usr/bin/ranlib: file: /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/config/libpython2.7.a(pymath.o) has no symbols install_environment.STDOUT DEBUG 2017-11-18 17:03:37,359 E ./setup.py install \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,452 DYLD_LIBRARY_PATH=/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 ./python.exe - --prefix=/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,452 --install-scripts=/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,452 --install-platlib=/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,452 --root=/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,452 E ./setup.py install \ install_environment.STDOUT DEBUG 2017-11-18 17:03:37,464 running build tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,555 running install tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,555 running build tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,555 running build_ext install_environment.STDOUT DEBUG 2017-11-18 17:03:37,812 building dbm using ndbm install_environment.STDOUT DEBUG 2017-11-18 17:03:37,815 creating /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/copying build/lib.macosx-8b09fe018cac/lib/python2.7/lib-copying build/lib.macosx-10.4-x86_64-2.ib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,816 10.4-x86_64-2.7/_App.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,817 7/_bisect.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-on_2_7/8b09fe018cac/lib/python2copying build/lib.macosx-10.4-x86_64-2.ib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,818 10.4-x86_64-2.7/_CG.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,821 7/_Cm.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-on_2_7/8b09fe018cac/lib/python2copying build/lib.macosx-10.4-x86_64-2.18cac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,822 10.4-x86_64-2.7/_codecs_iso2022.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,824 7/_codecs_jp.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0thon/2.7/iuc/package_pythython2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,825 86_64-2.7/_codecs_tw.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,827 tions.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-/8b09fe018cac/lib/python2.7/libcopying build/lib.macosx-10.4-x86_64-2.lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,827 10.4-x86_64-2.7/_ctypes.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,830 7/_ctypes_test.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fcopying build/lib.macosx-2_7/8b09fe018cac/lib/python2.7/copying build/lib.macosx-10.4-x86_64-2.fe018cac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,830 10.4-x86_64-2.7/_Dlg.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,832 7/_Drag.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018caccopying build/lib.macosx-thon_2_7/8b09fe018cac/lib/pythocopying build/lib.macosx-10.4-x86_64-2.lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,833 10.4-x86_64-2.7/_File.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,835 7/_Fm.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-2_7/8b09fe018cac/lib/python2.7/copying build/lib.macosx-10.4-x86_64-2.18cac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,836 10.4-x86_64-2.7/_heapq.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,838 7/_Help.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018caccopying build/lib.macosx-_2_7/8b09fe018cac/lib/python2.7copying build/lib.macosx-10.4-x86_64-2.8cac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,839 10.4-x86_64-2.7/_Icn.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,841 7/_io.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-7/8b09fe018cac/lib/python2.7/licopying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,841 10.4-x86_64-2.7/_List.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,843 7/_locale.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-2_7/8b09fe018cac/lib/python2.7/copying build/lib.macosx-10.4-x86_64-2.lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,843 10.4-x86_64-2.7/_Menu.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,844 7/_Mlte.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018caces/python/2.7/iuc/packagelib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,845 86_64-2.7/_multiprocessing.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,846 7/_OSA.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/copying build/lib.macosx-8b09fe018cac/lib/python2.7/lib-copying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,848 10.4-x86_64-2.7/_Qt.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,849 7/_random.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-/8b09fe018cac/lib/python2.7/libcopying build/lib.macosx-10.4-x86_64-2.cac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,850 10.4-x86_64-2.7/_Scrap.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,854 7/_sha.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/copying build/lib.macosx-2_7/8b09fe018cac/lib/python2.7/copying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,854 10.4-x86_64-2.7/_Snd.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,858 7/_socket.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-_2_7/8b09fe018cac/lib/python2.7copying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,859 10.4-x86_64-2.7/_sysconfigdata.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,862 7/_sysconfigdata.pyc -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8bcopying build/lib.macosx-_python_2_7/8b09fe018cac/lib/pycopying build/lib.macosx-10.4-x86_64-2.ib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,863 10.4-x86_64-2.7/_testcapi.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,867 7/_tkinter.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018copying build/lib.macosx-/8b09fe018cac/lib/python2.7/libcopying build/lib.macosx-10.4-x86_64-2./lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,868 10.4-x86_64-2.7/audioop.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,870 7/autoGIL.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-_2_7/8b09fe018cac/lib/python2.7copying build/lib.macosx-10.4-x86_64-2.cac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,871 10.4-x86_64-2.7/bz2.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,873 7/cmath.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018caccopying build/lib.macosx-hon_2_7/8b09fe018cac/lib/pythoncopying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,874 10.4-x86_64-2.7/crypt.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,876 7/cStringIO.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01copying build/lib.macosx-_2_7/8b09fe018cac/lib/python2.7copying build/lib.macosx-10.4-x86_64-2.ib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,876 10.4-x86_64-2.7/fcntl.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,878 7/future_builtins.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8bcopying build/lib.macosx-2_7/8b09fe018cac/lib/python2.7/copying build/lib.macosx-10.4-x86_64-2.ib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,879 10.4-x86_64-2.7/icglue.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,881 7/itertools.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01copying build/lib.macosx-7/8b09fe018cac/lib/python2.7/licopying build/lib.macosx-10.4-x86_64-2.lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,884 10.4-x86_64-2.7/mmap.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,891 7/Nav.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-8b09fe018cac/lib/python2.7/lib-on/2.7/iuc/package_python_2_7/8b09fe018load install_environment.STDOUT DEBUG 2017-11-18 17:03:37,893 86_64-2.7/OSATerminology.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythonload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,910 so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pytn/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,917 copying build/lib.macosx-10.4-x86_64-2.7/readline.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,917 n/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,918 copying build/lib.macosx-10.4-x86_64-2.7/time.so -> /galaxydir/galaxy/database/dependencies/python/2copying build/lib.macosx-10.4-x86_64-2.7/unicodedata.so 2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:37,918 cac/lib/python2.7/lib-dynload/_bisect.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,919 ir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynchanging mode of /galaxydload/_CF.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,919 cac/lib/python2.7/lib-dynload/_codecs_cn.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,919 /python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_codecs_hk.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,919 base/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_codecs_iso2022.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,919 ndencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_codecs_jp.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,919 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_codecs_kr.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,920 cac/lib/python2.7/lib-dynload/_ctypes.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,922 cac/lib/python2.7/lib-dynload/_curses.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,922 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_curses_panel.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,923 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynchanging mode of /galaxydir/galbm.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,923 ir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynchanging mode of /galaxydcac/lib/python2.7/lib-dynload/icglue.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,923 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/itertools.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,923 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/MacOS.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,923 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/math.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,923 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/mmap.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,924 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/operator.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,924 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/parser.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,924 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/readline.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,924 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/syslog.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,924 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/termios.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,924 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/time.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,925 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/unicodedata.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,925 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/zlib.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,925 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/ to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,926 running install_scripts install_environment.STDOUT DEBUG 2017-11-18 17:03:37,930 hon_2_7/8b09fe018cac/bin install_environment.STDOUT DEBUG 2017-11-18 17:03:37,931 _python_2_7/8b09fe018cac/bin install_environment.STDOUT DEBUG 2017-11-18 17:03:37,931 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/idle to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,931 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/pydoc to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,931 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/smtpd.py to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,931 running install_egg_info install_environment.STDOUT DEBUG 2017-11-18 17:03:37,950 Writing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/prm /galaxydir/galaxy/datagdata.py* tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,964 Python build finished, but the necessary bits to build these modules were not found: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,964 _bsddb _ssl dl tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,964 gdbm imageop linuxaudiodev tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,964 ossaudiodev spwd sunaudiodev tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:37,964 To find the necessary bits, look in setup.py in detect_modules() for the module's name. install_environment.STDOUT DEBUG 2017-11-18 17:03:37,971 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/share/man install_environment.STDOUT DEBUG 2017-11-18 17:03:37,975 alaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/share/man/man1 install_environment.STDOUT DEBUG 2017-11-18 17:03:37,981 n.man \ install_environment.STDOUT DEBUG 2017-11-18 17:03:37,991 n/python -o -h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cas python2 python) install_environment.STDOUT DEBUG 2017-11-18 17:03:38,000 atabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/python2 install_environment.STDOUT DEBUG 2017-11-18 17:03:38,003 dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin; ln -s python2.7 python2) 127.0.0.1 - - [18/Nov/2017:17:03:37 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/datasets/error?dataset_id=a799d38679e985db&__identifer=9nms4ovms1v" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:03:38,024 rm -f /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/pyt(cd /galaxydir/galaxy/dat2-config) install_environment.STDOUT DEBUG 2017-11-18 17:03:38,038 atabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/python-config tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,067 running build_scripts tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,068 building dbm using ndbm tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,068 running install_lib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,068 python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,068 10.4-x86_64-2.7/_AE.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,068 creating /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/copying build/lib.macosx-8b09fe018cac/lib/python2.7/lib-copying build/lib.macosx-10.4-x86_64-2.ib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,068 10.4-x86_64-2.7/_App.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,068 7/_AH.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-/8b09fe018cac/lib/python2.7/libcopying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,069 10.4-x86_64-2.7/_CarbonEvt.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,069 7/_bisect.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-on_2_7/8b09fe018cac/lib/python2copying build/lib.macosx-10.4-x86_64-2.ib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,069 10.4-x86_64-2.7/_CG.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,069 7/_CF.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-8b09fe018cac/lib/python2.7/lib-copying build/lib.macosx-10.4-x86_64-2.ib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,069 10.4-x86_64-2.7/_codecs_cn.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyth.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,069 7/_Cm.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-on_2_7/8b09fe018cac/lib/python2copying build/lib.macosx-10.4-x86_64-2.18cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,069 10.4-x86_64-2.7/_codecs_iso2022.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,069 7/_codecs_hk.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0copying build/lib.macosx-_python_2_7/8b09fe018cac/lib/pycopying build/lib.macosx-10.4-x86_64-2.18cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,070 7/_codecs_jp.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0thon/2.7/iuc/package_pythython2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,070 86_64-2.7/_codecs_tw.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,070 copying build/lib.macosx-10.4-x86_64-2.7/_codecs_kr.so -> /galaxydir/galaxy/database/dependencies/pyon_2_7/8b09fe018cac/lib/pcopying build/lib.macosx-10.4-x/8b09fe018cac/lib/python2.7/lib-dynloadcopying build/lib.macosx-10.4-x86_64-2.7/_collecib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,070 10.4-x86_64-2.7/_csv.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,070 tions.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-/8b09fe018cac/lib/python2.7/libcopying build/lib.macosx-10.4-x86_64-2.lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,070 10.4-x86_64-2.7/_ctypes.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,070 7/_Ctl.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/copying build/lib.macosx-2_7/8b09fe018cac/lib/python2.7/copying build/lib.macosx-10.4-x86_64-2.e018cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,070 10.4-x86_64-2.7/_curses.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,071 7/_ctypes_test.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fcopying build/lib.macosx-2_7/8b09fe018cac/lib/python2.7/copying build/lib.macosx-10.4-x86_64-2.fe018cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,071 10.4-x86_64-2.7/_Dlg.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,071 7/_curses_panel.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09copying build/lib.macosx-/8b09fe018cac/lib/python2.7/libcopying build/lib.macosx-10.4-x86_64-2./lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,071 10.4-x86_64-2.7/_elementtree.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyn2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,071 7/_Drag.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018caccopying build/lib.macosx-thon_2_7/8b09fe018cac/lib/pythocopying build/lib.macosx-10.4-x86_64-2.lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,071 10.4-x86_64-2.7/_File.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,071 7/_Evt.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/copying build/lib.macosx-7/8b09fe018cac/lib/python2.7/licopying build/lib.macosx-10.4-x86_64-2.ib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,071 10.4-x86_64-2.7/_Folder.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,071 7/_Fm.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-2_7/8b09fe018cac/lib/python2.7/copying build/lib.macosx-10.4-x86_64-2.18cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,071 10.4-x86_64-2.7/_heapq.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,071 7/_functools.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0copying build/lib.macosx-_7/8b09fe018cac/lib/python2.7/lcopying build/lib.macosx-10.4-x86_64-2./lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,071 10.4-x86_64-2.7/_hotshot.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,072 7/_Help.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018caccopying build/lib.macosx-_2_7/8b09fe018cac/lib/python2.7copying build/lib.macosx-10.4-x86_64-2.8cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,072 10.4-x86_64-2.7/_Icn.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,072 7/_IBCarbon.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01copying build/lib.macosx-/8b09fe018cac/lib/python2.7/libcopying build/lib.macosx-10.4-x86_64-2.ib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,072 10.4-x86_64-2.7/_json.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,072 7/_io.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-7/8b09fe018cac/lib/python2.7/licopying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,072 10.4-x86_64-2.7/_List.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,072 7/_Launch.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-7/8b09fe018cac/lib/python2.7/licopying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,072 10.4-x86_64-2.7/_lsprof.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,072 7/_locale.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-2_7/8b09fe018cac/lib/python2.7/copying build/lib.macosx-10.4-x86_64-2.lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,072 10.4-x86_64-2.7/_Menu.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,072 7/_md5.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/copying build/lib.macosx-7/8b09fe018cac/lib/python2.7/licopying build/lib.macosx-10.4-x86_64-2./lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,073 7/_Mlte.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018caces/python/2.7/iuc/packagelib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,073 86_64-2.7/_multiprocessing.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,073 copying build/lib.macosx-10.4-x86_64-2.7/_multibytecodec.so -> /galaxydir/galaxy/database/dependenci_python_2_7/8b09fe018cac/copying build/lib.macosx-10.4-xcopying build/lib.macosx-10.4-x86_64-2.lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,073 10.4-x86_64-2.7/_Qd.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,073 7/_OSA.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/copying build/lib.macosx-8b09fe018cac/lib/python2.7/lib-copying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,073 10.4-x86_64-2.7/_Qt.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,073 7/_Qdoffs.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-8b09fe018cac/lib/python2.7/lib-copying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,073 10.4-x86_64-2.7/_Res.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,074 7/_random.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-/8b09fe018cac/lib/python2.7/libcopying build/lib.macosx-10.4-x86_64-2.cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,074 10.4-x86_64-2.7/_Scrap.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,074 7/_scproxy.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018copying build/lib.macosx-_7/8b09fe018cac/lib/python2.7/lcopying build/lib.macosx-10.4-x86_64-2.lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,075 10.4-x86_64-2.7/_sha256.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,075 7/_sha.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/copying build/lib.macosx-2_7/8b09fe018cac/lib/python2.7/copying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,075 10.4-x86_64-2.7/_Snd.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,075 7/_sha512.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-/8b09fe018cac/lib/python2.7/libcopying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,075 10.4-x86_64-2.7/_sqlite3.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,075 7/_socket.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-_2_7/8b09fe018cac/lib/python2.7copying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,075 10.4-x86_64-2.7/_sysconfigdata.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_hon2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,075 7/_struct.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-python_2_7/8b09fe018cac/lib/pytcopying build/lib.macosx-10.4-x86_64-2.09fe018cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,075 10.4-x86_64-2.7/_sysconfigdata.pyo -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagethon2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,076 7/_sysconfigdata.pyc -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8bcopying build/lib.macosx-_python_2_7/8b09fe018cac/lib/pycopying build/lib.macosx-10.4-x86_64-2.ib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,076 10.4-x86_64-2.7/_testcapi.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytho7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,076 7/_TE.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-n_2_7/8b09fe018cac/lib/python2.copying build/lib.macosx-10.4-x86_64-2.cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,076 10.4-x86_64-2.7/_Win.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,076 7/_tkinter.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018copying build/lib.macosx-/8b09fe018cac/lib/python2.7/libcopying build/lib.macosx-10.4-x86_64-2./lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,076 10.4-x86_64-2.7/audioop.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,076 7/array.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018caccopying build/lib.macosx-2_7/8b09fe018cac/lib/python2.7/copying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,076 10.4-x86_64-2.7/binascii.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,076 7/autoGIL.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-_2_7/8b09fe018cac/lib/python2.7copying build/lib.macosx-10.4-x86_64-2.cac/lib/python2.7/lib-dynload install_environment.STDOUT DEBUG 2017-11-18 17:03:38,077 dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin; ln -s python2-config python-config)test -d /galaxydir/galaxyconfig/python2.pc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,077 10.4-x86_64-2.7/bz2.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,077 7/bsddb185.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018copying build/lib.macosx-8b09fe018cac/lib/python2.7/lib-copying build/lib.macosx-10.4-x86_64-2./lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,077 10.4-x86_64-2.7/ColorPicker.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pyt2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,077 7/cmath.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018caccopying build/lib.macosx-hon_2_7/8b09fe018cac/lib/pythoncopying build/lib.macosx-10.4-x86_64-2.ac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,077 10.4-x86_64-2.7/crypt.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,077 7/cPickle.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ccopying build/lib.macosx-7/8b09fe018cac/lib/python2.7/licopying build/lib.macosx-10.4-x86_64-2.8cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,078 10.4-x86_64-2.7/datetime.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,078 7/cStringIO.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01copying build/lib.macosx-_2_7/8b09fe018cac/lib/python2.7copying build/lib.macosx-10.4-x86_64-2.ib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,078 10.4-x86_64-2.7/fcntl.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,078 7/dbm.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-7/8b09fe018cac/lib/python2.7/licopying build/lib.macosx-10.4-x86_64-2.09fe018cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,078 10.4-x86_64-2.7/gestalt.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,078 7/future_builtins.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8bcopying build/lib.macosx-2_7/8b09fe018cac/lib/python2.7/copying build/lib.macosx-10.4-x86_64-2.ib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,078 10.4-x86_64-2.7/icglue.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2ib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,078 7/grp.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-_7/8b09fe018cac/lib/python2.7/lcopying build/lib.macosx-10.4-x86_64-2.8cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,078 10.4-x86_64-2.7/MacOS.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_b-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,078 7/itertools.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01copying build/lib.macosx-7/8b09fe018cac/lib/python2.7/licopying build/lib.macosx-10.4-x86_64-2.lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,078 10.4-x86_64-2.7/mmap.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,079 7/math.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/copying build/lib.macosx-/8b09fe018cac/lib/python2.7/libcopying build/lib.macosx-10.4-x86_64-2.ib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,079 10.4-x86_64-2.7/nis.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,079 7/Nav.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib.macosx-8b09fe018cac/lib/python2.7/lib-on/2.7/iuc/package_python_2_7/8b09fe018load tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,079 86_64-2.7/OSATerminology.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythonload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,079 copying build/lib.macosx-10.4-x86_64-2.7/operator.so -> /galaxydir/galaxy/database/dependencies/pythcac/lib/python2.7/lib-dyncopying build/lib.macosx-10.4-x_2_7/8b09fe018cac/lib/python2.7/lib-dyncopying build/lib.macosx-10.4-x86_64-2.7/parser.hon2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,080 so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pytn/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,080 copying build/lib.macosx-10.4-x86_64-2.7/pyexpat.so -> /galaxydir/galaxy/database/dependencies/pythocopying build/lib.macosx-10.4-x86_64-2.7/resource.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,080 copying build/lib.macosx-10.4-x86_64-2.7/select.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,080 copying build/lib.macosx-10.4-x86_64-2.7/strop.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,080 copying build/lib.macosx-10.4-x86_64-2.7/syslog.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,080 copying build/lib.macosx-10.4-x86_64-2.7/readline.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,080 n/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,080 copying build/lib.macosx-10.4-x86_64-2.7/termios.so -> /galaxydir/galaxy/database/dependencies/pytho.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,080 -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pythoncopying build/lib.macosx-10.4-x86_64-2.7/zlib.so -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,081 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_AE.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,081 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_AH.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,081 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_App.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,081 copying build/lib.macosx-10.4-x86_64-2.7/time.so -> /galaxydir/galaxy/database/dependencies/python/2copying build/lib.macosx-10.4-x86_64-2.7/unicodedata.so 2.7/lib-dynload tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,081 cac/lib/python2.7/lib-dynload/_bisect.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,081 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018changing mode of /galaxydload/_CarbonEvt.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,081 ir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynchanging mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_CG.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,081 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Cm.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,081 ir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynchanging mode of /galaxydload/_CF.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,081 cac/lib/python2.7/lib-dynload/_codecs_cn.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,081 /python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_codecs_hk.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,082 base/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_codecs_iso2022.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,082 ndencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_codecs_jp.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,082 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018changing mode of /galaxydir/galaxy/database/dependencieschanging mode of /galaxydir/galaxy/datachanging mode of /galaxydir/galaxy/database/depechanging mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_codecs_tw.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,082 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_collections.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,082 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_csv.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,082 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Ctl.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,082 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_codecs_kr.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,082 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_ctypes_test.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,082 cac/lib/python2.7/lib-dynload/_ctypes.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,082 cac/lib/python2.7/lib-dynload/_curses.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,082 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Dlg.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,082 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Drag.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,082 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_elementtree.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,083 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Evt.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,083 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_curses_panel.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,083 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_File.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,083 cac/lib/python2.7/lib-dynload/_Fm.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,083 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Folder.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,083 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_functools.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,083 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_heapq.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,083 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Help.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,083 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_hotshot.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,083 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_IBCarbon.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,083 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Icn.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,083 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_io.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,084 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_json.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,084 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Launch.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,084 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_List.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,084 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_locale.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,084 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_lsprof.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,084 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_md5.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,084 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Menu.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,084 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Mlte.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,084 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_multibytecodec.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,084 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_multiprocessing.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,085 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_OSA.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,085 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Qd.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,085 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Qdoffs.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,085 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Qt.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,085 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_random.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,085 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Res.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,085 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_scproxy.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,085 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Scrap.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,085 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_sha.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,085 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_sha256.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,085 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_sha512.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,086 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Snd.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,086 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_socket.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,086 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_sqlite3.so to 755 install_environment.STDOUT DEBUG 2017-11-18 17:03:38,086 abase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pkgconfig; ln -s python-2.7.pc python2.pc) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,086 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_struct.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,086 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_sysconfigdata.py to 644 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,086 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_sysconfigdata.pyc to 644 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,086 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_sysconfigdata.pyo to 644 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,086 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_TE.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,087 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_testcapi.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,087 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_tkinter.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,087 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_Win.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,087 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/array.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,087 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/audioop.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,087 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/autoGIL.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,091 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/binascii.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,091 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/bsddb185.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,091 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/bz2.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,091 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/cmath.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,091 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/ColorPicker.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,091 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/cPickle.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,091 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/crypt.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,091 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/cStringIO.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,091 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018load/datetime.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,092 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynchanging mode of /galaxydir/galbm.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,092 axy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/dchanging mode of /galaxydload/fcntl.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,092 ir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/future_builtins.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,092 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/gestalt.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,092 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/grp.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,092 ir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynchanging mode of /galaxydcac/lib/python2.7/lib-dynload/icglue.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,092 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/itertools.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,092 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/MacOS.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,092 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/math.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,092 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/mmap.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,092 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/Nav.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,093 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/nis.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,093 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/operator.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,093 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/OSATerminology.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,093 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/parser.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,093 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/pyexpat.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,093 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/resource.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,093 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/select.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,093 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/readline.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,093 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/syslog.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,093 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/termios.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,094 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/time.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,094 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/unicodedata.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,094 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/zlib.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,094 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/ to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,094 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/strop.so to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,094 running install_scripts tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,094 copying build/scripts-2.7/2to3 -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pytcopying build/scripts-2.7/idle -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,095 copying build/scripts-2.7/pydoc -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,096 hon_2_7/8b09fe018cac/bin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,096 _python_2_7/8b09fe018cac/bin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,096 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/idle to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,096 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/pydoc to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,096 changing mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/smtpd.py to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,101 running install_egg_info install_environment.STDOUT DEBUG 2017-11-18 17:03:38,102 e/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pkgconfig/python.pc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,102 copying build/scripts-2.7/smtpd.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagechanging mode of /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/2to3 to 755 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,102 ython2.7/lib-dynload/Python-2.7.10-py2.7.egg-info tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,102 Writing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/prm /galaxydir/galaxy/datagdata.py* tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,102 ydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/share/man tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,102 alaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/share/man/man1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,103 base/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/lib-dynload/_sysconfiCreating directory /galaxCreating directory /galaxydir/g/usr/bin/install -c -m 644 ./Misc/pytho /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/share/man/man1/python2.7.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,103 n.man \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,103 if test -f /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bic/bin/python; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,103 then rm -f /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/python; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,103 else true; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,103 fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,103 n/python -o -h /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cas python2 python) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,103 atabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/python2 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,103 dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin; ln -s python2.7 python2) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,104 (cd /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin; ln -rm -f /galaxydir/galaxy/d(cd /galaxydir/galaxy/database/hon2-config tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,104 rm -f /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/pyt(cd /galaxydir/galaxy/dat2-config) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,104 atabase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/python-config tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,104 abase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin; ln -s python2.7-config pythonrm -f /galaxydir/galaxy/d(cd /galaxydir/galaxy/database/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,104 /database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pkgconfig || /usr/bin/install -c -d -m 755 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pkgconfig tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,104 dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin; ln -s python2-config python-config)test -d /galaxydir/galaxyconfig/python2.pc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,104 abase/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pkgconfig; ln -s python-2.7.pc python2.pc) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,104 e/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pkgconfig/python.pc install_environment.STDOUT DEBUG 2017-11-18 17:03:38,110 cies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pkgconfig; ln -s python2.pc python.pc) install_environment.STDOUT DEBUG 2017-11-18 17:03:38,123 thon/2.7/iuc/package_python_2_7/8b09fe018cac/share/man/man1/python2.1 install_environment.STDOUT DEBUG 2017-11-18 17:03:38,133 ackage_python_2_7/8b09fe018cac/share/man/man1; ln -s python2.7.1 python2.1) install_environment.STDOUT DEBUG 2017-11-18 17:03:38,144 _2_7/8b09fe018cac/share/man/man1/python.1 install_environment.STDOUT DEBUG 2017-11-18 17:03:38,147 re/man/man1; ln -s python2.1 python.1) install_environment.STDOUT DEBUG 2017-11-18 17:03:38,157 case no in \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,211 cies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pkgconfig; ln -s python2.pc python.pc) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,211 thon/2.7/iuc/package_python_2_7/8b09fe018cac/share/man/man1/python2.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,211 ackage_python_2_7/8b09fe018cac/share/man/man1; ln -s python2.7.1 python2.1) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,211 _2_7/8b09fe018cac/share/man/man1/python.1 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,212 re/man/man1; ln -s python2.1 python.1) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,212 rm -f /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pkg(cd /galaxydir/galaxy/datrm -f /galaxydir/galaxy/databas(cd /galaxydir/galaxy/database/dependenrm -f /galaxydir/galaxy/database/dependencies/py(cd /galaxydir/galaxy/database/dependencies/python/2.7/iuc/prm -f /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python(cd /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/shaif test "xno" != "xno" ; then \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,212 upgrade) ensurepip="--upgrade" ;; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,212 install|*) ensurepip="" ;; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,212 esac; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,212 DYLD_LIBRARY_PATH=/galaxydir/galaxy/database/tmp/tmp-toolshed-mtdP5qHBA/Python-2.7.10 ./python.exe -E -m ensurepip \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,213 $ensurepip --root=/ ; \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,214 fi tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,214 case no in \ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment WARNING 2017-11-18 17:03:38,321 Length of stdout > 32K, so only a portion will be saved in the database. tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 17:03:38,321 Attempting to download via url: https://bitbucket.org/pypa/setuptools/get/18.2.tar.bz2 127.0.0.1 - - [18/Nov/2017:17:03:38 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:03:38 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:03:38 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:38,722 + ZLIB_ROOT_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8; export ZLIB_ROOT_PATH PKG_CONFIG_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib/pkgconfig:$PKG_CONFIG_PATH; export PKG_CONFIG_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib:$LIBRARY_PATH; export LIBRARY_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH ZLIB_ROOT_DIR=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8; export ZLIB_ROOT_DIR READLINE_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/include; export READLINE_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH READLINE_LIB_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib; export READLINE_LIB_PATH READLINE_BIN_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/bin; export READLINE_BIN_PATH READLINE_ROOT_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1; export READLINE_ROOT_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib:$LIBRARY_PATH; export LIBRARY_PATH PATH=$PATH:/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/bin; export PATH READLINE_ROOT_DIR=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1; export READLINE_ROOT_DIR PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin:$PATH; export PATH BZLIB_LIB_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib; export BZLIB_LIB_DIR BZLIB_INCLUDE_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include; export BZLIB_INCLUDE_DIR BZLIB_SOURCE_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source; export BZLIB_SOURCE_DIR LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib:$LIBRARY_PATH; export LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source:$LIBRARY_PATH; export LIBRARY_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH BZLIB_ROOT_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595; export BZLIB_ROOT_DIR LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH XZ_ROOT_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594; export XZ_ROOT_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH XZ_ROOT_DIR=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594; export XZ_ROOT_DIR PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/bin:$PATH; export PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib:$LIBRARY_PATH; export LIBRARY_PATH SQLITE_ROOT_DIR=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921; export SQLITE_ROOT_DIR C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH PKG_CONFIG_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib/pkgconfig:$PKG_CONFIG_PATH; export PKG_CONFIG_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH GDBM_ROOT_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc; export GDBM_ROOT_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH GDBM_ROOT_DIR=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc; export GDBM_ROOT_DIR NCURSES_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include; export NCURSES_INCLUDE_PATH NCURSES_LIB_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/; export NCURSES_LIB_PATH NCURSES_ROOT_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd; export NCURSES_ROOT_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib:$LIBRARY_PATH; export LIBRARY_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH NCURSES_ROOT_DIR=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd; export NCURSES_ROOT_DIR tar -xjf 18.2.tar.bz2 127.0.0.1 - - [18/Nov/2017:17:03:38 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,152 + ZLIB_ROOT_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8; export ZLIB_ROOT_PATH PKG_CONFIG_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib/pkgconfig:$PKG_CONFIG_PATH; export PKG_CONFIG_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/lib:$LIBRARY_PATH; export LIBRARY_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH ZLIB_ROOT_DIR=/galaxydir/galaxy/database/dependencies/zlib/1.2.8/iuc/package_zlib_1_2_8/411985b46ae8; export ZLIB_ROOT_DIR READLINE_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/include; export READLINE_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH READLINE_LIB_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib; export READLINE_LIB_PATH READLINE_BIN_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/bin; export READLINE_BIN_PATH READLINE_ROOT_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1; export READLINE_ROOT_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/lib:$LIBRARY_PATH; export LIBRARY_PATH PATH=$PATH:/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1/bin; export PATH READLINE_ROOT_DIR=/galaxydir/galaxy/database/dependencies/readline/6.3/iuc/package_readline_6_3/ca1a9400d4e1; export READLINE_ROOT_DIR PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/bin:$PATH; export PATH BZLIB_LIB_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib; export BZLIB_LIB_DIR BZLIB_INCLUDE_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include; export BZLIB_INCLUDE_DIR BZLIB_SOURCE_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source; export BZLIB_SOURCE_DIR LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/lib:$LIBRARY_PATH; export LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/source:$LIBRARY_PATH; export LIBRARY_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595/bzlib/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH BZLIB_ROOT_DIR=/galaxydir/galaxy/database/dependencies/bzlib/1.0.6/iuc/package_bzlib_1_0/af4887e1f595; export BZLIB_ROOT_DIR LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH XZ_ROOT_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594; export XZ_ROOT_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH XZ_ROOT_DIR=/galaxydir/galaxy/database/dependencies/xz/5.0.5/iuc/package_xz_5_0_5/944f93d45594; export XZ_ROOT_DIR PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/bin:$PATH; export PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib:$LIBRARY_PATH; export LIBRARY_PATH SQLITE_ROOT_DIR=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921; export SQLITE_ROOT_DIR C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH PKG_CONFIG_PATH=/galaxydir/galaxy/database/dependencies/sqlite/3.8.3/iuc/package_sqlite_3_8_3/c8a5c11cc921/lib/pkgconfig:$PKG_CONFIG_PATH; export PKG_CONFIG_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH GDBM_ROOT_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc; export GDBM_ROOT_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH GDBM_ROOT_DIR=/galaxydir/galaxy/database/dependencies/gdbm/1.11/iuc/package_gdbm_1_11/ed2537bccffc; export GDBM_ROOT_DIR NCURSES_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include; export NCURSES_INCLUDE_PATH NCURSES_LIB_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib/; export NCURSES_LIB_PATH NCURSES_ROOT_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd; export NCURSES_ROOT_PATH LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/lib:$LIBRARY_PATH; export LIBRARY_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH C_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses:$C_INCLUDE_PATH; export C_INCLUDE_PATH CPLUS_INCLUDE_PATH=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd/include/ncurses:$CPLUS_INCLUDE_PATH; export CPLUS_INCLUDE_PATH NCURSES_ROOT_DIR=/galaxydir/galaxy/database/dependencies/ncurses/6.0/iuc/package_ncurses_6_0/0efde9889efd; export NCURSES_ROOT_DIR export PATH=$PATH:/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin && export PYTHONHOME=/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac && export PYTHONPATH=$PYTHONPATH:/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac && export PYTHONPATH=$PYTHONPATH:/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/ && export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pkgconfig && export LD_LIBRARY_PATH=/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/:$LD_LIBRARY_PATH && /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/bin/python setup.py install --prefix=/galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac install_environment.STDOUT DEBUG 2017-11-18 17:03:39,495 running build install_environment.STDOUT DEBUG 2017-11-18 17:03:39,497 creating build/lib install_environment.STDOUT DEBUG 2017-11-18 17:03:39,498 creating build/lib/_markerlib install_environment.STDOUT DEBUG 2017-11-18 17:03:39,499 copying _markerlib/markers.py -> build/lib/_markerlib install_environment.STDOUT DEBUG 2017-11-18 17:03:39,499 copying pkg_resources/__init__.py -> build/lib/pkg_resources install_environment.STDOUT DEBUG 2017-11-18 17:03:39,501 copying setuptools/__init__.py -> build/lib/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,503 copying setuptools/compat.py -> build/lib/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,504 copying setuptools/dist.py -> build/lib/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,505 copying setuptools/lib2to3_ex.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,506 running install tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,506 running build_py tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,506 running build tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,506 creating build tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,506 creating build/lib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,506 copying easy_install.py -> build/lib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,506 creating build/lib/_markerlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,507 copying _markerlib/__init__.py -> build/lib/_markerlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,507 copying _markerlib/markers.py -> build/lib/_markerlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,507 creating build/lib/pkg_resources tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,507 copying pkg_resources/__init__.py -> build/lib/pkg_resources tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,507 creating build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,507 copying setuptools/__init__.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,507 copying setuptools/archive_util.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,507 copying setuptools/compat.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,507 copying setuptools/depends.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,508 copying setuptools/dist.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,508 copying setuptools/extension.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,508 copying setuptools/lib2to3_ex.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,508 copying setuptools/msvc9_support.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,508 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'zip_safe' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,509 warnings.warn(msg) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,509 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'setup_requires' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,509 warnings.warn(msg) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,509 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'tests_require' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,509 warnings.warn(msg) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,510 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'extras_require' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,510 warnings.warn(msg) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,510 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'entry_points' tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,510 warnings.warn(msg) install_environment.STDOUT DEBUG 2017-11-18 17:03:39,509 copying setuptools/package_index.py -> build/lib/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,510 copying setuptools/ssl_support.py -> build/lib/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,511 copying setuptools/unicode_utils.py -> build/lib/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,512 copying setuptools/version.py -> build/lib/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,513 creating build/lib/pkg_resources/_vendor install_environment.STDOUT DEBUG 2017-11-18 17:03:39,514 creating build/lib/pkg_resources/_vendor/packaging install_environment.STDOUT DEBUG 2017-11-18 17:03:39,516 copying pkg_resources/_vendor/packaging/_compat.py -> build/lib/pkg_resources/_vendor/packaging install_environment.STDOUT DEBUG 2017-11-18 17:03:39,517 copying pkg_resources/_vendor/packaging/specifiers.py -> build/lib/pkg_resources/_vendor/packaging install_environment.STDOUT DEBUG 2017-11-18 17:03:39,519 creating build/lib/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,520 copying setuptools/command/alias.py -> build/lib/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,522 copying setuptools/command/bdist_rpm.py -> build/lib/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,523 copying setuptools/command/build_ext.py -> build/lib/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,524 copying setuptools/command/develop.py -> build/lib/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,525 copying setuptools/command/egg_info.py -> build/lib/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,527 copying setuptools/command/install_egg_info.py -> build/lib/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,528 copying setuptools/command/install_scripts.py -> build/lib/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,529 copying setuptools/command/rotate.py -> build/lib/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,531 copying setuptools/command/sdist.py -> build/lib/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,533 copying setuptools/command/test.py -> build/lib/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,540 copying setuptools/script (dev).tmpl -> build/lib/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,540 running install_lib install_environment.STDOUT DEBUG 2017-11-18 17:03:39,542 python2.7/site-packages/_markerlib install_environment.STDOUT DEBUG 2017-11-18 17:03:39,542 lib/__init__.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0es/_markerlib install_environment.STDOUT DEBUG 2017-11-18 17:03:39,545 -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pythocopying build/lib/easy_inib/python2.7/site-packages install_environment.STDOUT DEBUG 2017-11-18 17:03:39,547 y/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pcopying build/lib/pkg_resfe018cac/lib/python2.7/site-paccreating /galaxydir/galaxy/database/depvendor install_environment.STDOUT DEBUG 2017-11-18 17:03:39,547 ources/_vendor/__init__.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pkg_resources/_vendor install_environment.STDOUT DEBUG 2017-11-18 17:03:39,548 creating /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/ources/_vendor/packaging install_environment.STDOUT DEBUG 2017-11-18 17:03:39,549 cies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pkg_resources/_vendocopying build/lib/pkg_rese_python_2_7/8b09fe018cac/lib/pg_resources/_vendor/packaging install_environment.STDOUT DEBUG 2017-11-18 17:03:39,550 /_vendor/packaging/_structures.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_ite-packages/pkg_resourcecopying build/lib/pkg_resourcesython_2_7/8b09fe018cac/lib/python2.7/si/_vendor/packaging install_environment.STDOUT DEBUG 2017-11-18 17:03:39,552 /_vendor/packaging/version.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythpackages/pkg_resources/_vcreating /galaxydir/galaxy/dataols install_environment.STDOUT DEBUG 2017-11-18 17:03:39,553 ols/__init__.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0es/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,554 il.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/creating /galaxydir/galaxetuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,556 ols/command/__init__.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7e-packages/setuptools/comcopying build/lib/setuptools/co8cac/lib/python2.7/site-packages/setuptcopying build/lib/setuptools/command/bdist_egg.pon2.7/site-packages/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,558 ols/command/bdist_rpm.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_te-packages/setuptools/cocopying build/lib/setuptools/co8b09fe018cac/lib/python2.7/site-packagecopying build/lib/setuptools/command/build_ext.pon2.7/site-packages/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,559 ols/command/build_py.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7e-packages/setuptools/comcopying build/lib/setuptools/co018cac/lib/python2.7/site-packages/setucopying build/lib/setuptools/command/easy_instalython2.7/site-packages/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,561 ols/command/egg_info.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7e-packages/setuptools/comcopying build/lib/setuptools/co018cac/lib/python2.7/site-packages/setucopying build/lib/setuptools/command/install_eggib/python2.7/site-packages/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,563 ols/command/install_lib.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_site-packages/setuptools/copying build/lib/setuptools/co7/8b09fe018cac/lib/python2.7/site-packacopying build/lib/setuptools/command/register.pyn2.7/site-packages/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,564 ols/command/rotate.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8packages/setuptools/commacopying build/lib/setuptools/coe018cac/lib/python2.7/site-packages/setcopying build/lib/setuptools/command/sdist.py ->7/site-packages/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,566 ols/command/setopt.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8packages/setuptools/commacopying build/lib/setuptools/cocac/lib/python2.7/site-packages/setuptocopying build/lib/setuptools/command/upload_docsthon2.7/site-packages/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,566 ols/compat.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,568 -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pythocopying build/lib/setuptoc/lib/python2.7/site-packages/scopying build/lib/setuptools/extension.hon2.7/site-packages/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,568 ols/lib2to3_ex.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fages/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,570 ort.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libcopying build/lib/setupto09fe018cac/lib/python2.7/site-pcopying build/lib/setuptools/py26compatthon2.7/site-packages/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,570 ols/py27compat.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fages/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,572 .py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pycopying build/lib/setupto8cac/lib/python2.7/site-packagecopying build/lib/setuptools/script (deb/python2.7/site-packages/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,573 ols/script.tmpl -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0es/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,574 .py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pycopying build/lib/setuptofe018cac/lib/python2.7/site-paccopying build/lib/setuptools/unicode_ut/python2.7/site-packages/setuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,575 ols/utils.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018csetuptools install_environment.STDOUT DEBUG 2017-11-18 17:03:39,577 -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pythocopying build/lib/setupto8b09fe018cac/lib/python2.7/sitebyte-compiling /galaxydir/galaxy/databab/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,580 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packarkers.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,620 copying setuptools/py26compat.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,620 copying setuptools/py27compat.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,620 copying setuptools/py31compat.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,621 copying setuptools/sandbox.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,621 copying setuptools/package_index.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,621 copying setuptools/ssl_support.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,621 copying setuptools/site-patch.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,624 copying setuptools/unicode_utils.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,624 copying setuptools/utils.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,624 copying setuptools/version.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,624 copying setuptools/windows_support.py -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,624 creating build/lib/pkg_resources/_vendor tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,624 copying pkg_resources/_vendor/__init__.py -> build/lib/pkg_resources/_vendor tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,635 copying pkg_resources/_vendor/packaging/__about__.py -> build/lib/pkg_resources/_vendor/packaging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,635 creating build/lib/pkg_resources/_vendor/packaging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,635 copying pkg_resources/_vendor/packaging/__init__.py -> build/lib/pkg_resources/_vendor/packaging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,635 copying pkg_resources/_vendor/packaging/_compat.py -> build/lib/pkg_resources/_vendor/packaging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,636 copying pkg_resources/_vendor/packaging/_structures.py -> build/lib/pkg_resources/_vendor/packaging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,636 copying pkg_resources/_vendor/packaging/specifiers.py -> build/lib/pkg_resources/_vendor/packaging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,636 copying pkg_resources/_vendor/packaging/version.py -> build/lib/pkg_resources/_vendor/packaging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,637 creating build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,637 copying setuptools/command/__init__.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,637 copying setuptools/command/alias.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,637 copying setuptools/command/bdist_egg.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,637 copying setuptools/command/bdist_rpm.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,637 copying setuptools/command/bdist_wininst.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,637 copying setuptools/command/build_ext.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,637 copying setuptools/command/build_py.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,638 copying setuptools/command/develop.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,638 copying setuptools/command/easy_install.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,638 copying setuptools/command/egg_info.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,638 copying setuptools/command/install.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,639 copying setuptools/command/install_egg_info.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,639 copying setuptools/command/install_lib.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,639 copying setuptools/command/install_scripts.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,639 copying setuptools/command/register.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,639 copying setuptools/command/rotate.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,639 copying setuptools/command/saveopts.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,640 copying setuptools/command/sdist.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,644 copying setuptools/command/setopt.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,645 copying setuptools/command/test.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,645 copying setuptools/command/upload_docs.py -> build/lib/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,645 copying setuptools/script (dev).tmpl -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,645 copying setuptools/script.tmpl -> build/lib/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,645 running install_lib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,647 python2.7/site-packages/_markerlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,647 lib/__init__.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0es/_markerlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,647 creating /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/copying build/lib/_marker18cac/lib/python2.7/site-packagcopying build/lib/_markerlib/markers.pyn2.7/site-packages/_markerlib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,648 -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pythocopying build/lib/easy_inib/python2.7/site-packages tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,648 stall.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcreating /galaxydir/galaxkg_resources tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,649 ources/__init__.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09kages/pkg_resources tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,649 y/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pcopying build/lib/pkg_resfe018cac/lib/python2.7/site-paccreating /galaxydir/galaxy/database/depvendor tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,649 ources/_vendor/__init__.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pkg_resources/_vendor tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,649 endencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pkg_resources/_copying build/lib/pkg_respython2.7/site-packages/pkg_rescopying build/lib/pkg_resources/_vendor/packaging/__about__.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pkg_resources/_vendor/packaging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,651 creating /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/ources/_vendor/packaging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,651 copying build/lib/pkg_resources/_vendor/packaging/__init__.py -> /galaxydir/galaxy/database/dependenr/packaging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,651 cies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pkg_resources/_vendocopying build/lib/pkg_rese_python_2_7/8b09fe018cac/lib/pg_resources/_vendor/packaging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,656 ources/_vendor/packaging/_compat.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/packagython2.7/site-packages/pkcopying build/lib/pkg_resourcespython_2_7/8b09fe018cac/lib/python2.7/ss/_vendor/packaging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,656 /_vendor/packaging/_structures.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_ite-packages/pkg_resourcecopying build/lib/pkg_resourcesython_2_7/8b09fe018cac/lib/python2.7/si/_vendor/packaging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,657 /_vendor/packaging/specifiers.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pte-packages/pkg_resourcescopying build/lib/pkg_resourceson_2_7/8b09fe018cac/lib/python2.7/site-endor/packaging tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,657 /_vendor/packaging/version.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_pythpackages/pkg_resources/_vcreating /galaxydir/galaxy/dataols tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,658 ols/__init__.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0es/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,659 base/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptocopying build/lib/setupto18cac/lib/python2.7/site-packagcopying build/lib/setuptools/archive_utpython2.7/site-packages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,659 il.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/creating /galaxydir/galaxetuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,659 y/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/scopying build/lib/setupto/8b09fe018cac/lib/python2.7/sitmand tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,659 mmand/alias.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01ools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,660 ols/command/__init__.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7e-packages/setuptools/comcopying build/lib/setuptools/co8cac/lib/python2.7/site-packages/setuptcopying build/lib/setuptools/command/bdist_egg.pon2.7/site-packages/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,660 y -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pythcopying build/lib/setupto7/8b09fe018cac/lib/python2.7/simmand tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,660 mmand/bdist_wininst.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/s/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,660 ols/command/bdist_rpm.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_te-packages/setuptools/cocopying build/lib/setuptools/co8b09fe018cac/lib/python2.7/site-packagecopying build/lib/setuptools/command/build_ext.pon2.7/site-packages/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,660 y -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pythcopying build/lib/setupto/8b09fe018cac/lib/python2.7/sitmand tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,660 mmand/develop.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09feptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,661 ols/command/build_py.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7e-packages/setuptools/comcopying build/lib/setuptools/co018cac/lib/python2.7/site-packages/setucopying build/lib/setuptools/command/easy_instalython2.7/site-packages/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,661 l.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pcopying build/lib/setupto/8b09fe018cac/lib/python2.7/sitmand tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,661 mmand/install.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09feptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,663 ols/command/egg_info.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7e-packages/setuptools/comcopying build/lib/setuptools/co018cac/lib/python2.7/site-packages/setucopying build/lib/setuptools/command/install_eggib/python2.7/site-packages/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,663 _info.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lcopying build/lib/setupto2_7/8b09fe018cac/lib/python2.7/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,663 mmand/install_scripts.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_ges/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,663 ols/command/install_lib.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_site-packages/setuptools/copying build/lib/setuptools/co7/8b09fe018cac/lib/python2.7/site-packacopying build/lib/setuptools/command/register.pyn2.7/site-packages/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,664 -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pythocopying build/lib/setuptob09fe018cac/lib/python2.7/site-nd tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,664 mmand/saveopts.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,664 ols/command/rotate.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8packages/setuptools/commacopying build/lib/setuptools/coe018cac/lib/python2.7/site-packages/setcopying build/lib/setuptools/command/sdist.py ->7/site-packages/setuptools/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,666 /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.copying build/lib/setuptob09fe018cac/lib/python2.7/site-nd tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,666 mmand/test.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018ols/command tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,666 ols/command/setopt.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8packages/setuptools/commacopying build/lib/setuptools/cocac/lib/python2.7/site-packages/setuptocopying build/lib/setuptools/command/upload_docsthon2.7/site-packages/setuptools/command install_environment.STDOUT DEBUG 2017-11-18 17:03:39,624 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/easy_instbyte-compiling /galaxydirages/pkg_resources/__init__.py byte-compiling /galaxydir/galaxy/databarces/_vendor/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,666 ols/compat.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,666 .py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pycopying build/lib/setuptocac/lib/python2.7/site-packagescopying build/lib/setuptools/depends.pyn2.7/site-packages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,667 ols/dist.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018caetuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,667 -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pythocopying build/lib/setuptoc/lib/python2.7/site-packages/scopying build/lib/setuptools/extension.hon2.7/site-packages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,667 ols/lib2to3_ex.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,667 py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pytcopying build/lib/setuptoe018cac/lib/python2.7/site-packcopying build/lib/setuptools/msvc9_supp/python2.7/site-packages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,667 ols/package_index.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8backages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,667 ort.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libcopying build/lib/setupto09fe018cac/lib/python2.7/site-pcopying build/lib/setuptools/py26compatthon2.7/site-packages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,667 ols/py27compat.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,668 .py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pycopying build/lib/setuptoe018cac/lib/python2.7/site-packcopying build/lib/setuptools/py31compatthon2.7/site-packages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,668 ols/sandbox.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe01s/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,668 .py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pycopying build/lib/setupto8cac/lib/python2.7/site-packagecopying build/lib/setuptools/script (deb/python2.7/site-packages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,668 ols/script.tmpl -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe0es/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,668 v).tmpl -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/licopying build/lib/setupto18cac/lib/python2.7/site-packagcopying build/lib/setuptools/site-patchthon2.7/site-packages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,669 ols/ssl_support.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09kages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,669 .py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pycopying build/lib/setuptofe018cac/lib/python2.7/site-paccopying build/lib/setuptools/unicode_ut/python2.7/site-packages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,669 ols/utils.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018csetuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,670 ils.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/libcopying build/lib/setuptoac/lib/python2.7/site-packages/copying build/lib/setuptools/version.pyn2.7/site-packages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,670 ols/windows_support.py -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/-packages/setuptools tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,671 -> /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/pythocopying build/lib/setupto8b09fe018cac/lib/python2.7/sitebyte-compiling /galaxydir/galaxy/databab/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,671 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packarkers.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,672 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/_markerlibyte-compiling /galaxydirages/_markerlib/markers.py to mbyte-compiling /galaxydir/galaxy/databaall.py to easy_install.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,672 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packto __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,672 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pkg_resoubyte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pkg_resources/_vendor/packaging/__about__.py to __about__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,673 byte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pkg_resources/_vendor/packaging/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,673 byte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pkg_resources/_vendor/packaging/_compat.py to _compat.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,674 byte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pkg_resources/_vendor/packaging/_structures.py to _structures.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,674 byte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pkg_resources/_vendor/packaging/specifiers.py to specifiers.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,674 byte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/pkg_resources/_vendor/packaging/version.py to version.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,674 byte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptools/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,674 byte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptools/archive_util.py to archive_util.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,674 byte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptools/command/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,674 byte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptools/command/alias.py to alias.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,674 byte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptools/command/bdist_egg.py to bdist_egg.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,674 byte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptools/command/bdist_rpm.py to bdist_rpm.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,674 byte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptools/command/bdist_wininst.py to bdist_wininst.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,675 byte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptools/command/build_ext.py to build_ext.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,675 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/easy_instbyte-compiling /galaxydirages/pkg_resources/__init__.py byte-compiling /galaxydir/galaxy/databarces/_vendor/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,671 c/lib/python2.7/site-packages/setuptools/command/build_py.py to build_py.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,683 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-pack.py to develop.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,711 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/command/egg_infbyte-compiling /galaxydir/galaxy/databas/command/install.py to install.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,717 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-pack_egg_info.py to install_ebyte-compiling /galaxydir/galaxetuptools/command/install_lib.py to insbyte-compiling /galaxydir/galaxy/database/depend/install_scripts.py to install_scripts.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,719 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packr.py to register.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,725 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/command/saveoptbyte-compiling /galaxydir/galaxy/databas/command/sdist.py to sdist.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,727 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packpy to setopt.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,733 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/command/upload_c install_environment.STDOUT DEBUG 2017-11-18 17:03:39,743 y/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/sbyte-compiling /galaxydirages/setuptools/depends.py to dbyte-compiling /galaxydir/galaxy/databas/dist.py to dist.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,750 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-pack extension.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,754 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/msvc9_support.pbyte-compiling /galaxydir/galaxy/databas/package_index.py to package_index.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,769 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packo py26compat.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,772 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/py31compat.py tbyte-compiling /galaxydir/galaxy/databas/sandbox.py to sandbox.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,779 c/lib/python2.7/site-packages/setuptools/command/build_py.py to build_py.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,779 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-pack.py to develop.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,779 byte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cabyte-compiling /galaxydirages/setuptools/command/developbyte-compiling /galaxydir/galaxy/databas/command/easy_install.py to easy_install.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,779 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packo.py to egg_info.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,780 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/command/egg_infbyte-compiling /galaxydir/galaxy/databas/command/install.py to install.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,780 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/command/installgg_info.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,780 y/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/stall_lib.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,780 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-pack_egg_info.py to install_ebyte-compiling /galaxydir/galaxetuptools/command/install_lib.py to insbyte-compiling /galaxydir/galaxy/database/depend/install_scripts.py to install_scripts.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,780 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packr.py to register.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,780 encies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptools/commandbyte-compiling /galaxydirages/setuptools/command/registebyte-compiling /galaxydir/galaxy/databas/command/rotate.py to rotate.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,780 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packs.py to saveopts.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,780 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/command/saveoptbyte-compiling /galaxydir/galaxy/databas/command/sdist.py to sdist.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,780 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packpy to setopt.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,780 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/command/setopt.byte-compiling /galaxydir/galaxy/databas/command/test.py to test.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,780 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/command/upload_c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,780 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packdocs.py to upload_docs.pybyte-compiling /galaxydir/galaxetuptools/compat.py to compat.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,780 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packepends.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,781 y/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/sbyte-compiling /galaxydirages/setuptools/depends.py to dbyte-compiling /galaxydir/galaxy/databas/dist.py to dist.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,781 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-pack extension.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,781 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/extension.py tobyte-compiling /galaxydir/galaxy/databas/lib2to3_ex.py to lib2to3_ex.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,781 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packy to msvc9_support.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,781 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/msvc9_support.pbyte-compiling /galaxydir/galaxy/databas/package_index.py to package_index.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,781 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packo py26compat.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,781 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/py26compat.py tbyte-compiling /galaxydir/galaxy/databas/py27compat.py to py27compat.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,781 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packo py31compat.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,781 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/py31compat.py tbyte-compiling /galaxydir/galaxy/databas/sandbox.py to sandbox.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,782 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packo site-patch.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,793 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/unicode_utils.pbyte-compiling /galaxydir/galaxy/databas/utils.py to utils.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,796 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packersion.pyc install_environment.STDOUT DEBUG 2017-11-18 17:03:39,799 running install_egg_info tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,885 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packo site-patch.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,885 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/site-patch.py tbyte-compiling /galaxydir/galaxy/databas/ssl_support.py to ssl_support.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,885 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packy to unicode_utils.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,885 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/unicode_utils.pbyte-compiling /galaxydir/galaxy/databas/utils.py to utils.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,885 /galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packersion.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,885 se/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptoolbyte-compiling /galaxydirages/setuptools/version.py to vbyte-compiling /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptools/windows_support.py to windows_support.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,885 Writing /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/site-packages/setuptools-18.2-py2.7.egg-info tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:python DEBUG 2017-11-18 17:03:39,886 running install_egg_info tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 17:03:40,718 Changing status for tool dependency python from Installing to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:03:40,718 Updating an existing record for version 2.7 of tool dependency python for revision 8b09fe018cac of repository package_python_2_7 by updating the status from Installing to Installed. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 17:03:40,785 Tool dependency python version 2.7 has been installed in /galaxydir/galaxy/database/dependencies/python/2.7/iuc/package_python_2_7/8b09fe018cac. 127.0.0.1 - - [18/Nov/2017:17:03:40 -0400] "GET /admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04 HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:03:41 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:03:44 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:03:45,273 Creating a new record for version 3.10.2 of tool dependency atlas for revision 83d12e13dbbd of repository package_numpy_1_9. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:03:45,304 Creating a new record for version 2.7 of tool dependency python for revision 83d12e13dbbd of repository package_numpy_1_9. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:03:45,336 Creating a new record for version 1.9 of tool dependency numpy for revision 83d12e13dbbd of repository package_numpy_1_9. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:03:45,489 Updating an existing record for version 3.10.2 of tool dependency atlas for revision 83d12e13dbbd of repository package_numpy_1_9 by updating the status from Never installed to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:03:45,666 Updating an existing record for version 2.7 of tool dependency python for revision 83d12e13dbbd of repository package_numpy_1_9 by updating the status from Never installed to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:03:45,731 Updating an existing record for version 1.9 of tool dependency numpy for revision 83d12e13dbbd of repository package_numpy_1_9 by updating the status from Never installed to Installing. tool_shed.galaxy_install.tool_dependencies.env_manager DEBUG 2017-11-18 17:03:45,788 Skipping tool dependency definition because unable to locate env.sh file for tool dependency type package, name atlas, version 3.10.2 for repository package_atlas_3_10 tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 17:03:45,789 Attempting to download via url: https://depot.galaxyproject.org/software/numpy/numpy_1.9p1_src_all.tar.gz 127.0.0.1 - - [18/Nov/2017:17:03:47 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 17:03:47,928 Successfully downloaded from url: https://depot.galaxyproject.org/software/numpy/numpy_1.9p1_src_all.tar.gz tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-11-18 17:03:47,940 + export PYTHONPATH=$PYTHONPATH:/galaxydir/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/lib/python && export ATLAS=$ATLAS_ROOT_PATH && python setup.py install --install-lib /galaxydir/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/lib/python --install-scripts /galaxydir/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/bin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-11-18 17:03:48,159 Writing custom site.cfg for ATLAS in Galaxy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-11-18 17:03:48,159 Traceback (most recent call last): tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-11-18 17:03:48,159 File "setup.py", line 264, in <module> tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-11-18 17:03:48,159 setup_package() tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-11-18 17:03:48,160 File "setup.py", line 210, in setup_package tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-11-18 17:03:48,160 raise RuntimeError("Writing custom site.cfg failed! %s" % ex) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-11-18 17:03:48,160 RuntimeError: Writing custom site.cfg failed! 'ATLAS_LIB_DIR' tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:03:48,263 Updating an existing record for version 1.9 of tool dependency numpy for revision 83d12e13dbbd of repository package_numpy_1_9 by updating the status from Installing to Error. 127.0.0.1 - - [18/Nov/2017:17:03:50 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db,5969b1f7201f12ae,0a248a1f62a0cc04" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:03:50,924 Creating a new record for version 1.9 of tool dependency numpy for revision a12f73c3b116 of repository package_biopython_1_67. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:03:50,945 Creating a new record for version 1.67 of tool dependency biopython for revision a12f73c3b116 of repository package_biopython_1_67. The status is being set to Never installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:03:51,071 Updating an existing record for version 1.9 of tool dependency numpy for revision a12f73c3b116 of repository package_biopython_1_67 by updating the status from Never installed to Error. tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler ERROR 2017-11-18 17:03:51,107 Error installing tool dependency for required repository: This tool dependency's required tool dependency numpy version 1.9 has status Error. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:03:51,124 Updating an existing record for version 1.67 of tool dependency biopython for revision a12f73c3b116 of repository package_biopython_1_67 by updating the status from Never installed to Installing. tool_shed.galaxy_install.tool_dependencies.env_manager DEBUG 2017-11-18 17:03:51,170 Skipping tool dependency definition because unable to locate env.sh file for tool dependency type package, name numpy, version 1.9 for repository package_numpy_1_9 tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 17:03:51,170 Attempting to download via url: https://pypi.python.org/packages/f4/35/67d779f52870770c228f9edd0c9d1d1b9bc11afad794e220295d7b88a804/biopython-1.67.tar.gz#md5=542699cc310588c1997806681ee1f65e tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 17:03:55,620 Successfully downloaded from url: https://pypi.python.org/packages/f4/35/67d779f52870770c228f9edd0c9d1d1b9bc11afad794e220295d7b88a804/biopython-1.67.tar.gz#md5=542699cc310588c1997806681ee1f65e tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:55,632 + export PYTHONPATH=$PYTHONPATH:/galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python && export PATH=$PATH:$PATH_NUMPY && export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY && python setup.py install --install-lib /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python install_environment.STDOUT DEBUG 2017-11-18 17:03:56,046 running build tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,054 running install install_environment.STDOUT DEBUG 2017-11-18 17:03:56,054 creating build tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,055 running build install_environment.STDOUT DEBUG 2017-11-18 17:03:56,055 creating build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,055 running build_py tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,056 creating build tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,056 creating build/lib.macosx-10.11-intel-2.7 install_environment.STDOUT DEBUG 2017-11-18 17:03:56,056 copying Bio/bgzf.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,056 copying Bio/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,057 creating build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,057 copying Bio/_utils.py -> build/lib.macosx-10.11-intel-2.7/Bio install_environment.STDOUT DEBUG 2017-11-18 17:03:56,058 copying Bio/File.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,058 copying Bio/bgzf.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,058 copying Bio/DocSQL.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,059 copying Bio/File.py -> build/lib.macosx-10.11-intel-2.7/Bio install_environment.STDOUT DEBUG 2017-11-18 17:03:56,060 copying Bio/kNN.py -> build/lib.macosx-10.11-intel-2.7/Bio install_environment.STDOUT DEBUG 2017-11-18 17:03:56,061 copying Bio/MarkovModel.py -> build/lib.macosx-10.11-intel-2.7/Bio install_environment.STDOUT DEBUG 2017-11-18 17:03:56,062 copying Bio/NaiveBayes.py -> build/lib.macosx-10.11-intel-2.7/Bio install_environment.STDOUT DEBUG 2017-11-18 17:03:56,064 copying Bio/ParserSupport.py -> build/lib.macosx-10.11-intel-2.7/Bio install_environment.STDOUT DEBUG 2017-11-18 17:03:56,066 copying Bio/SeqFeature.py -> build/lib.macosx-10.11-intel-2.7/Bio install_environment.STDOUT DEBUG 2017-11-18 17:03:56,068 copying Bio/triefind.py -> build/lib.macosx-10.11-intel-2.7/Bio install_environment.STDOUT DEBUG 2017-11-18 17:03:56,069 copying Bio/Align/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Align install_environment.STDOUT DEBUG 2017-11-18 17:03:56,070 copying Bio/Align/Generic.py -> build/lib.macosx-10.11-intel-2.7/Bio/Align install_environment.STDOUT DEBUG 2017-11-18 17:03:56,077 copying Bio/Align/Applications/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Align/Applicationcopying Bio/Align/Applicacopying Bio/Align/Applications/copying Bio/Align/Applications/_Dialigncopying Bio/Align/Applications/_Mafft.py -> builcopying Bio/Align/Applications/_MSAProbs.py -> build/lib.maccopying Bio/Align/Applications/_Muscle.py -> build/lib.macosx-10.11-intel-2copying Bio/Align/Applications/_Prank.py -> build/lib.macosx-10.11-intel-2.7/Bio/Align/Applicacopying Bio/Align/Applications/_Probcons.py -> build/lib.macosx-10.11-intel-2.7/Bio/Align/Applications install_environment.STDOUT DEBUG 2017-11-18 17:03:56,078 s install_environment.STDOUT DEBUG 2017-11-18 17:03:56,079 -10.11-intel-2.7/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,079 -> build/lib.macosx-10.11-intel-2.7/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,082 ld/lib.macosx-10.11-intel-2.7/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,083 osx-10.11-intel-2.7/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,088 el-2.7/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,090 lignIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,098 copying Bio/AlignIO/PhylipIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,100 creating build/lib.macosx-10.11-intel-2.7/Bio/Alphabet install_environment.STDOUT DEBUG 2017-11-18 17:03:56,101 copying Bio/Alphabet/Reduced.py -> build/lib.macosx-10.11-intel-2.7/Bio/Alphabet install_environment.STDOUT DEBUG 2017-11-18 17:03:56,102 copying Bio/Application/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Application install_environment.STDOUT DEBUG 2017-11-18 17:03:56,104 copying Bio/Blast/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Blast install_environment.STDOUT DEBUG 2017-11-18 17:03:56,105 copying Bio/Blast/NCBIStandalone.py -> build/lib.macosx-10.11-intel-2.7/Bio/Blast install_environment.STDOUT DEBUG 2017-11-18 17:03:56,107 copying Bio/Blast/NCBIXML.py -> build/lib.macosx-10.11-intel-2.7/Bio/Blast install_environment.STDOUT DEBUG 2017-11-18 17:03:56,108 copying Bio/Blast/Record.py -> build/lib.macosx-10.11-intel-2.7/Bio/Blast install_environment.STDOUT DEBUG 2017-11-18 17:03:56,109 copying Bio/CAPS/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/CAPS install_environment.STDOUT DEBUG 2017-11-18 17:03:56,111 copying Bio/codonalign/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/codonalign install_environment.STDOUT DEBUG 2017-11-18 17:03:56,112 copying Bio/codonalign/codonalignment.py -> build/lib.macosx-10.11-intel-2.7/Bio/codonalign install_environment.STDOUT DEBUG 2017-11-18 17:03:56,133 copying Bio/codonalign/codonseq.py -> build/lib.macosx-10.11-intel-2.7/Bio/codonalign install_environment.STDOUT DEBUG 2017-11-18 17:03:56,138 copying Bio/Compass/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Compass install_environment.STDOUT DEBUG 2017-11-18 17:03:56,142 copying Bio/Crystal/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Crystal install_environment.STDOUT DEBUG 2017-11-18 17:03:56,145 copying Bio/Data/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Data install_environment.STDOUT DEBUG 2017-11-18 17:03:56,147 copying Bio/Data/IUPACData.py -> build/lib.macosx-10.11-intel-2.7/Bio/Data install_environment.STDOUT DEBUG 2017-11-18 17:03:56,152 creating build/lib.macosx-10.11-intel-2.7/Bio/Emboss install_environment.STDOUT DEBUG 2017-11-18 17:03:56,154 copying Bio/Emboss/Applications.py -> build/lib.macosx-10.11-intel-2.7/Bio/Emboss install_environment.STDOUT DEBUG 2017-11-18 17:03:56,158 copying Bio/Emboss/PrimerSearch.py -> build/lib.macosx-10.11-intel-2.7/Bio/Emboss tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,159 copying Bio/Index.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,160 copying Bio/kNN.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,160 copying Bio/LogisticRegression.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,161 copying Bio/MarkovModel.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,161 copying Bio/MaxEntropy.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,161 copying Bio/NaiveBayes.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,162 copying Bio/pairwise2.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,162 copying Bio/ParserSupport.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,163 copying Bio/Seq.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,163 copying Bio/SeqFeature.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,163 copying Bio/SeqRecord.py -> build/lib.macosx-10.11-intel-2.7/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,164 copying Bio/triefind.py -> build/lib.macosx-10.11-intel-2.7/Bio install_environment.STDOUT DEBUG 2017-11-18 17:03:56,164 copying Bio/Entrez/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,165 creating build/lib.macosx-10.11-intel-2.7/Bio/Align tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,165 copying Bio/Align/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Align tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,166 copying Bio/Align/AlignInfo.py -> build/lib.macosx-10.11-intel-2.7/Bio/Align tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,166 copying Bio/Align/Generic.py -> build/lib.macosx-10.11-intel-2.7/Bio/Align tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,167 creating build/lib.macosx-10.11-intel-2.7/Bio/Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,167 s tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,167 tions/_ClustalOmega.py -> build/lib.macosx-10.11-intel-2.7/Bio/Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,167 _Clustalw.py -> build/lib.macosx-10.11-intel-2.7/Bio/Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,167 .py -> build/lib.macosx-10.11-intel-2.7/Bio/Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,167 d/lib.macosx-10.11-intel-2.7/Bio/Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,168 osx-10.11-intel-2.7/Bio/Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,168 .7/Bio/Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,168 tions tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,169 copying Bio/Align/Applications/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Align/Applicationcopying Bio/Align/Applicacopying Bio/Align/Applications/copying Bio/Align/Applications/_Dialigncopying Bio/Align/Applications/_Mafft.py -> builcopying Bio/Align/Applications/_MSAProbs.py -> build/lib.maccopying Bio/Align/Applications/_Muscle.py -> build/lib.macosx-10.11-intel-2copying Bio/Align/Applications/_Prank.py -> build/lib.macosx-10.11-intel-2.7/Bio/Align/Applicacopying Bio/Align/Applications/_Probcons.py -> build/lib.macosx-10.11-intel-2.7/Bio/Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,169 s tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,169 -10.11-intel-2.7/Bio/AlignIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,169 -> build/lib.macosx-10.11-intel-2.7/Bio/AlignIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,169 ld/lib.macosx-10.11-intel-2.7/Bio/AlignIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,169 osx-10.11-intel-2.7/Bio/AlignIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,169 el-2.7/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,169 creating build/lib.macosx-10.11-intel-2.7/Bio/ExPASy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,170 lignIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,170 copying Bio/Align/Applications/_TCoffee.py -> build/lib.macosx-10.11-intel-2.7/Bio/Align/Applicationcreating build/lib.macosxcopying Bio/AlignIO/__init__.pycopying Bio/AlignIO/ClustalIO.py -> buicopying Bio/AlignIO/EmbossIO.py -> build/lib.maccopying Bio/AlignIO/FastaIO.py -> build/lib.macosx-10.11-intcopying Bio/AlignIO/Interfaces.py -> build/lib.macosx-10.11-intel-2.7/Bio/Acopying Bio/AlignIO/NexusIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/AlignIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,171 copying Bio/AlignIO/PhylipIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,171 copying Bio/ExPASy/Enzyme.py -> build/lib.macosx-10.11-intel-2.7/Bio/ExPASy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,171 copying Bio/AlignIO/StockholmIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/AlignIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,171 copying Bio/Alphabet/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Alphabet tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,171 creating build/lib.macosx-10.11-intel-2.7/Bio/Alphabet tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,172 copying Bio/Alphabet/IUPAC.py -> build/lib.macosx-10.11-intel-2.7/Bio/Alphabet tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,172 copying Bio/Alphabet/Reduced.py -> build/lib.macosx-10.11-intel-2.7/Bio/Alphabet tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,172 creating build/lib.macosx-10.11-intel-2.7/Bio/Application tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,172 copying Bio/Application/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Application tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,172 creating build/lib.macosx-10.11-intel-2.7/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,172 copying Bio/Blast/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,172 copying Bio/Blast/Applications.py -> build/lib.macosx-10.11-intel-2.7/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,172 copying Bio/Blast/NCBIStandalone.py -> build/lib.macosx-10.11-intel-2.7/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,172 copying Bio/Blast/NCBIWWW.py -> build/lib.macosx-10.11-intel-2.7/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,173 copying Bio/Blast/NCBIXML.py -> build/lib.macosx-10.11-intel-2.7/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,173 copying Bio/Blast/ParseBlastTable.py -> build/lib.macosx-10.11-intel-2.7/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,173 copying Bio/Blast/Record.py -> build/lib.macosx-10.11-intel-2.7/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,173 creating build/lib.macosx-10.11-intel-2.7/Bio/CAPS tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,173 copying Bio/CAPS/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/CAPS tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,173 creating build/lib.macosx-10.11-intel-2.7/Bio/codonalign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,173 copying Bio/codonalign/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/codonalign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,173 copying Bio/codonalign/chisq.py -> build/lib.macosx-10.11-intel-2.7/Bio/codonalign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,173 copying Bio/codonalign/codonalignment.py -> build/lib.macosx-10.11-intel-2.7/Bio/codonalign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,173 copying Bio/codonalign/codonalphabet.py -> build/lib.macosx-10.11-intel-2.7/Bio/codonalign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,173 copying Bio/codonalign/codonseq.py -> build/lib.macosx-10.11-intel-2.7/Bio/codonalign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,173 creating build/lib.macosx-10.11-intel-2.7/Bio/Compass tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,174 copying Bio/Compass/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Compass tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,174 creating build/lib.macosx-10.11-intel-2.7/Bio/Crystal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,174 copying Bio/Crystal/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Crystal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,174 creating build/lib.macosx-10.11-intel-2.7/Bio/Data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,174 copying Bio/Data/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,174 copying Bio/Data/CodonTable.py -> build/lib.macosx-10.11-intel-2.7/Bio/Data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,174 copying Bio/Data/IUPACData.py -> build/lib.macosx-10.11-intel-2.7/Bio/Data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,174 copying Bio/Data/SCOPData.py -> build/lib.macosx-10.11-intel-2.7/Bio/Data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,174 creating build/lib.macosx-10.11-intel-2.7/Bio/Emboss tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,174 copying Bio/Emboss/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Emboss tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,174 copying Bio/Emboss/Applications.py -> build/lib.macosx-10.11-intel-2.7/Bio/Emboss tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,175 copying Bio/Emboss/Primer3.py -> build/lib.macosx-10.11-intel-2.7/Bio/Emboss tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,175 copying Bio/Emboss/PrimerSearch.py -> build/lib.macosx-10.11-intel-2.7/Bio/Emboss tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,175 creating build/lib.macosx-10.11-intel-2.7/Bio/Entrez tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,175 copying Bio/Entrez/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,175 copying Bio/Entrez/Parser.py -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,175 creating build/lib.macosx-10.11-intel-2.7/Bio/ExPASy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,175 copying Bio/ExPASy/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/ExPASy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,175 copying Bio/ExPASy/Enzyme.py -> build/lib.macosx-10.11-intel-2.7/Bio/ExPASy install_environment.STDOUT DEBUG 2017-11-18 17:03:56,177 copying Bio/ExPASy/Prosite.py -> build/lib.macosx-10.11-intel-2.7/Bio/ExPASy install_environment.STDOUT DEBUG 2017-11-18 17:03:56,179 creating build/lib.macosx-10.11-intel-2.7/Bio/FSSP install_environment.STDOUT DEBUG 2017-11-18 17:03:56,182 copying Bio/FSSP/fssp_rec.py -> build/lib.macosx-10.11-intel-2.7/Bio/FSSP install_environment.STDOUT DEBUG 2017-11-18 17:03:56,184 creating build/lib.macosx-10.11-intel-2.7/Bio/GA install_environment.STDOUT DEBUG 2017-11-18 17:03:56,186 copying Bio/GA/Organism.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA install_environment.STDOUT DEBUG 2017-11-18 17:03:56,187 copying Bio/GA/Crossover/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Crossover install_environment.STDOUT DEBUG 2017-11-18 17:03:56,189 copying Bio/GA/Crossover/GeneralPoint.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Crossover install_environment.STDOUT DEBUG 2017-11-18 17:03:56,190 copying Bio/GA/Crossover/TwoPoint.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Crossover install_environment.STDOUT DEBUG 2017-11-18 17:03:56,191 creating build/lib.macosx-10.11-intel-2.7/Bio/GA/Mutation install_environment.STDOUT DEBUG 2017-11-18 17:03:56,193 copying Bio/GA/Mutation/Simple.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Mutation install_environment.STDOUT DEBUG 2017-11-18 17:03:56,194 copying Bio/GA/Repair/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Repair install_environment.STDOUT DEBUG 2017-11-18 17:03:56,195 creating build/lib.macosx-10.11-intel-2.7/Bio/GA/Selection install_environment.STDOUT DEBUG 2017-11-18 17:03:56,197 copying Bio/GA/Selection/Diversity.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Selection install_environment.STDOUT DEBUG 2017-11-18 17:03:56,198 copying Bio/GA/Selection/Tournament.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Selection install_environment.STDOUT DEBUG 2017-11-18 17:03:56,200 copying Bio/GenBank/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/GenBank install_environment.STDOUT DEBUG 2017-11-18 17:03:56,202 copying Bio/GenBank/Scanner.py -> build/lib.macosx-10.11-intel-2.7/Bio/GenBank install_environment.STDOUT DEBUG 2017-11-18 17:03:56,204 creating build/lib.macosx-10.11-intel-2.7/Bio/Geo install_environment.STDOUT DEBUG 2017-11-18 17:03:56,205 copying Bio/Geo/Record.py -> build/lib.macosx-10.11-intel-2.7/Bio/Geo install_environment.STDOUT DEBUG 2017-11-18 17:03:56,206 copying Bio/Graphics/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics install_environment.STDOUT DEBUG 2017-11-18 17:03:56,207 copying Bio/Graphics/ColorSpiral.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics install_environment.STDOUT DEBUG 2017-11-18 17:03:56,208 copying Bio/Graphics/DisplayRepresentation.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics install_environment.STDOUT DEBUG 2017-11-18 17:03:56,209 copying Bio/Graphics/KGML_vis.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics install_environment.STDOUT DEBUG 2017-11-18 17:03:56,217 copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics/Genocopying Bio/Graphics/Genocopying Bio/Graphics/GenomeDiagcopying Bio/Graphics/GenomeDiagram/_Colcopying Bio/Graphics/GenomeDiagram/_CrossLink.pycopying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.macosx-10.11-incopying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.macosx-10.11-intel-2.7/Bio/Grapcopying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram install_environment.STDOUT DEBUG 2017-11-18 17:03:56,217 omeDiagram install_environment.STDOUT DEBUG 2017-11-18 17:03:56,218 meDiagram/_LinearDrawer.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram install_environment.STDOUT DEBUG 2017-11-18 17:03:56,219 ram/_Track.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram install_environment.STDOUT DEBUG 2017-11-18 17:03:56,220 .7/Bio/HMM install_environment.STDOUT DEBUG 2017-11-18 17:03:56,222 10.11-intel-2.7/Bio/HMM install_environment.STDOUT DEBUG 2017-11-18 17:03:56,223 .11-intel-2.7/Bio/HMM install_environment.STDOUT DEBUG 2017-11-18 17:03:56,225 copying Bio/HMM/Trainer.py -> build/lib.macosx-10.11-intel-2.7/Bio/HMM install_environment.STDOUT DEBUG 2017-11-18 17:03:56,227 creating build/lib.macosx-10.11-intel-2.7/Bio/KEGG install_environment.STDOUT DEBUG 2017-11-18 17:03:56,228 copying Bio/KEGG/REST.py -> build/lib.macosx-10.11-intel-2.7/Bio/KEGG install_environment.STDOUT DEBUG 2017-11-18 17:03:56,229 copying Bio/KEGG/Compound/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/KEGG/Compound install_environment.STDOUT DEBUG 2017-11-18 17:03:56,233 copying Bio/KEGG/Enzyme/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/KEGG/Enzyme install_environment.STDOUT DEBUG 2017-11-18 17:03:56,234 copying Bio/KEGG/Map/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/KEGG/Map install_environment.STDOUT DEBUG 2017-11-18 17:03:56,236 copying Bio/KEGG/KGML/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/KEGG/KGML install_environment.STDOUT DEBUG 2017-11-18 17:03:56,239 copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.macosx-10.11-intel-2.7/Bio/KEGG/KGML install_environment.STDOUT DEBUG 2017-11-18 17:03:56,242 copying Bio/Medline/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Medline install_environment.STDOUT DEBUG 2017-11-18 17:03:56,248 copying Bio/motifs/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/motifs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,249 copying Bio/motifs/mast.py -> build/lib.macosx-10.11-intel-2.7/Bio/motifs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,251 copying Bio/motifs/meme.py -> build/lib.macosx-10.11-intel-2.7/Bio/motifs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,253 copying Bio/motifs/transfac.py -> build/lib.macosx-10.11-intel-2.7/Bio/motifs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,259 copying Bio/motifs/applications/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/motifs/applicaticopying Bio/motifs/appliccreating build/lib.macosx-10.11copying Bio/motifs/jaspar/__init__.py -copying Bio/motifs/jaspar/db.py -> build/lib.maccreating build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork install_environment.STDOUT DEBUG 2017-11-18 17:03:56,260 copying Bio/NeuralNetwork/StopTraining.py -> build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork install_environment.STDOUT DEBUG 2017-11-18 17:03:56,262 creating build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork/BackPropagation install_environment.STDOUT DEBUG 2017-11-18 17:03:56,262 Network/BackPropagation install_environment.STDOUT DEBUG 2017-11-18 17:03:56,273 copying Bio/NeuralNetwork/BackPropagation/Layer.py -> build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetcopying Bio/NeuralNetworkcreating build/lib.macosx-10.11copying Bio/NeuralNetwork/Gene/__init__copying Bio/NeuralNetwork/Gene/Motif.py -> buildcopying Bio/NeuralNetwork/Gene/Pattern.py -> build/lib.macoscopying Bio/NeuralNetwork/Gene/Schema.py -> build/lib.macosx-10.11-intel-2.copying Bio/NeuralNetwork/Gene/Signature.py -> build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwcreating build/lib.macosx-10.11-intel-2.7/Bio/Nexus install_environment.STDOUT DEBUG 2017-11-18 17:03:56,275 copying Bio/Nexus/Nexus.py -> build/lib.macosx-10.11-intel-2.7/Bio/Nexus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,275 copying Bio/ExPASy/Prodoc.py -> build/lib.macosx-10.11-intel-2.7/Bio/ExPASy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,276 copying Bio/ExPASy/Prosite.py -> build/lib.macosx-10.11-intel-2.7/Bio/ExPASy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,276 copying Bio/ExPASy/ScanProsite.py -> build/lib.macosx-10.11-intel-2.7/Bio/ExPASy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,276 creating build/lib.macosx-10.11-intel-2.7/Bio/FSSP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,276 copying Bio/FSSP/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/FSSP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,276 copying Bio/FSSP/fssp_rec.py -> build/lib.macosx-10.11-intel-2.7/Bio/FSSP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,277 copying Bio/FSSP/FSSPTools.py -> build/lib.macosx-10.11-intel-2.7/Bio/FSSP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,277 copying Bio/GA/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,277 creating build/lib.macosx-10.11-intel-2.7/Bio/GA tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,278 copying Bio/GA/Evolver.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,278 copying Bio/GA/Organism.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,278 creating build/lib.macosx-10.11-intel-2.7/Bio/GA/Crossover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,278 copying Bio/GA/Crossover/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Crossover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,278 copying Bio/GA/Crossover/General.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Crossover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,278 copying Bio/GA/Crossover/GeneralPoint.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Crossover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,278 copying Bio/GA/Crossover/Point.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Crossover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,279 copying Bio/GA/Crossover/TwoPoint.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Crossover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,279 copying Bio/GA/Crossover/Uniform.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Crossover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,279 copying Bio/GA/Mutation/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Mutation install_environment.STDOUT DEBUG 2017-11-18 17:03:56,279 copying Bio/Nexus/StandardData.py -> build/lib.macosx-10.11-intel-2.7/Bio/Nexus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,279 creating build/lib.macosx-10.11-intel-2.7/Bio/GA/Mutation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,279 copying Bio/GA/Mutation/General.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Mutation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,279 copying Bio/GA/Mutation/Simple.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Mutation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,280 creating build/lib.macosx-10.11-intel-2.7/Bio/GA/Repair tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,280 copying Bio/GA/Repair/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Repair tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,280 copying Bio/GA/Repair/Stabilizing.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Repair tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,280 copying Bio/GA/Selection/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Selection tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,280 creating build/lib.macosx-10.11-intel-2.7/Bio/GA/Selection tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,280 copying Bio/GA/Selection/Abstract.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Selection tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,281 copying Bio/GA/Selection/Diversity.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Selection tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,281 copying Bio/GA/Selection/RouletteWheel.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Selection tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,281 copying Bio/GA/Selection/Tournament.py -> build/lib.macosx-10.11-intel-2.7/Bio/GA/Selection tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,281 creating build/lib.macosx-10.11-intel-2.7/Bio/GenBank tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,281 copying Bio/GenBank/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/GenBank tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,281 copying Bio/GenBank/Record.py -> build/lib.macosx-10.11-intel-2.7/Bio/GenBank tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,281 copying Bio/GenBank/Scanner.py -> build/lib.macosx-10.11-intel-2.7/Bio/GenBank tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,281 copying Bio/GenBank/utils.py -> build/lib.macosx-10.11-intel-2.7/Bio/GenBank tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,281 creating build/lib.macosx-10.11-intel-2.7/Bio/Geo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,281 copying Bio/Geo/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Geo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,281 copying Bio/Geo/Record.py -> build/lib.macosx-10.11-intel-2.7/Bio/Geo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,281 creating build/lib.macosx-10.11-intel-2.7/Bio/Graphics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,282 copying Bio/Graphics/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,282 copying Bio/Graphics/BasicChromosome.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,282 copying Bio/Graphics/ColorSpiral.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,282 copying Bio/Graphics/Comparative.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,282 copying Bio/Graphics/DisplayRepresentation.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,282 copying Bio/Graphics/Distribution.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,282 copying Bio/Graphics/KGML_vis.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,282 creating build/lib.macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,283 meDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,283 meDiagram/_AbstractDrawer.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,283 ram/_CircularDrawer.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,283 ors.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,283 -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,283 macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,283 tel-2.7/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,283 hics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,284 copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics/Genocopying Bio/Graphics/Genocopying Bio/Graphics/GenomeDiagcopying Bio/Graphics/GenomeDiagram/_Colcopying Bio/Graphics/GenomeDiagram/_CrossLink.pycopying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.macosx-10.11-incopying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.macosx-10.11-intel-2.7/Bio/Grapcopying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,284 omeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,284 meDiagram/_LinearDrawer.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,284 ram/_Track.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,284 .7/Bio/HMM tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,284 10.11-intel-2.7/Bio/HMM tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,284 .11-intel-2.7/Bio/HMM tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,285 copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.macosx-10.11-intel-2.7/Bio/Graphics/Gencopying Bio/Graphics/Genocopying Bio/Graphics/GenomeDiagcreating build/lib.macosx-10.11-intel-2copying Bio/HMM/__init__.py -> build/lib.macosx-copying Bio/HMM/DynamicProgramming.py -> build/lib.macosx-10copying Bio/HMM/MarkovModel.py -> build/lib.macosx-10.11-intel-2.7/Bio/HMM tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,285 copying Bio/HMM/Trainer.py -> build/lib.macosx-10.11-intel-2.7/Bio/HMM tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,285 copying Bio/HMM/Utilities.py -> build/lib.macosx-10.11-intel-2.7/Bio/HMM tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,285 creating build/lib.macosx-10.11-intel-2.7/Bio/KEGG tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,285 copying Bio/KEGG/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/KEGG tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,285 copying Bio/KEGG/REST.py -> build/lib.macosx-10.11-intel-2.7/Bio/KEGG tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,285 creating build/lib.macosx-10.11-intel-2.7/Bio/KEGG/Compound tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,285 copying Bio/KEGG/Compound/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/KEGG/Compound tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,285 creating build/lib.macosx-10.11-intel-2.7/Bio/KEGG/Enzyme tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,285 copying Bio/KEGG/Enzyme/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/KEGG/Enzyme tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,286 creating build/lib.macosx-10.11-intel-2.7/Bio/KEGG/Map tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,286 copying Bio/KEGG/Map/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/KEGG/Map tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,286 creating build/lib.macosx-10.11-intel-2.7/Bio/KEGG/KGML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,286 copying Bio/KEGG/KGML/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/KEGG/KGML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,286 copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.macosx-10.11-intel-2.7/Bio/KEGG/KGML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,286 copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.macosx-10.11-intel-2.7/Bio/KEGG/KGML install_environment.STDOUT DEBUG 2017-11-18 17:03:56,286 creating build/lib.macosx-10.11-intel-2.7/Bio/NMR tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,286 creating build/lib.macosx-10.11-intel-2.7/Bio/Medline tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,286 copying Bio/Medline/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Medline tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,287 creating build/lib.macosx-10.11-intel-2.7/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,287 copying Bio/motifs/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,287 copying Bio/motifs/alignace.py -> build/lib.macosx-10.11-intel-2.7/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,287 copying Bio/motifs/mast.py -> build/lib.macosx-10.11-intel-2.7/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,287 copying Bio/motifs/matrix.py -> build/lib.macosx-10.11-intel-2.7/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,287 copying Bio/motifs/meme.py -> build/lib.macosx-10.11-intel-2.7/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,287 copying Bio/motifs/thresholds.py -> build/lib.macosx-10.11-intel-2.7/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,287 copying Bio/motifs/transfac.py -> build/lib.macosx-10.11-intel-2.7/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,287 creating build/lib.macosx-10.11-intel-2.7/Bio/motifs/applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,287 ons tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,288 ations/_xxmotif.py -> build/lib.macosx-10.11-intel-2.7/Bio/motifs/applications install_environment.STDOUT DEBUG 2017-11-18 17:03:56,288 copying Bio/NMR/NOEtools.py -> build/lib.macosx-10.11-intel-2.7/Bio/NMR tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,288 -intel-2.7/Bio/motifs/jaspar tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,288 > build/lib.macosx-10.11-intel-2.7/Bio/motifs/jaspar tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,288 osx-10.11-intel-2.7/Bio/motifs/jaspar tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,288 copying Bio/motifs/applications/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/motifs/applicaticopying Bio/motifs/appliccreating build/lib.macosx-10.11copying Bio/motifs/jaspar/__init__.py -copying Bio/motifs/jaspar/db.py -> build/lib.maccreating build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,288 copying Bio/NeuralNetwork/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,288 copying Bio/NeuralNetwork/StopTraining.py -> build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,289 copying Bio/NeuralNetwork/Training.py -> build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,289 creating build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork/BackPropagation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,289 Network/BackPropagation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,289 copying Bio/NeuralNetwork/BackPropagation/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Neuralwork/BackPropagation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,289 /BackPropagation/Network.py -> build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork/BackPropagation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,289 -intel-2.7/Bio/NeuralNetwork/Gene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,289 .py -> build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork/Gene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,289 /lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork/Gene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,289 x-10.11-intel-2.7/Bio/NeuralNetwork/Gene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,290 7/Bio/NeuralNetwork/Gene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,290 ork/Gene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,290 copying Bio/NeuralNetwork/BackPropagation/Layer.py -> build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetcopying Bio/NeuralNetworkcreating build/lib.macosx-10.11copying Bio/NeuralNetwork/Gene/__init__copying Bio/NeuralNetwork/Gene/Motif.py -> buildcopying Bio/NeuralNetwork/Gene/Pattern.py -> build/lib.macoscopying Bio/NeuralNetwork/Gene/Schema.py -> build/lib.macosx-10.11-intel-2.copying Bio/NeuralNetwork/Gene/Signature.py -> build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwcreating build/lib.macosx-10.11-intel-2.7/Bio/Nexus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,290 copying Bio/Nexus/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Nexus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,290 copying Bio/Nexus/Nexus.py -> build/lib.macosx-10.11-intel-2.7/Bio/Nexus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,290 copying Bio/Nexus/Nodes.py -> build/lib.macosx-10.11-intel-2.7/Bio/Nexus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,290 copying Bio/Nexus/StandardData.py -> build/lib.macosx-10.11-intel-2.7/Bio/Nexus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,290 copying Bio/Nexus/Trees.py -> build/lib.macosx-10.11-intel-2.7/Bio/Nexus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,290 creating build/lib.macosx-10.11-intel-2.7/Bio/NMR install_environment.STDOUT DEBUG 2017-11-18 17:03:56,290 creating build/lib.macosx-10.11-intel-2.7/Bio/Pathway tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,291 copying Bio/NMR/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/NMR tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,291 copying Bio/NMR/NOEtools.py -> build/lib.macosx-10.11-intel-2.7/Bio/NMR tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,291 copying Bio/NMR/xpktools.py -> build/lib.macosx-10.11-intel-2.7/Bio/NMR tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,291 copying Bio/Pathway/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Pathway tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,291 creating build/lib.macosx-10.11-intel-2.7/Bio/Pathway install_environment.STDOUT DEBUG 2017-11-18 17:03:56,292 copying Bio/Pathway/Rep/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Pathway/Rep install_environment.STDOUT DEBUG 2017-11-18 17:03:56,294 copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.macosx-10.11-intel-2.7/Bio/Pathway/Rep install_environment.STDOUT DEBUG 2017-11-18 17:03:56,296 copying Bio/PDB/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,300 copying Bio/PDB/Atom.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,303 copying Bio/PDB/Dice.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,306 copying Bio/PDB/Entity.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,309 copying Bio/PDB/HSExposure.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,312 copying Bio/PDB/MMCIFParser.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,313 copying Bio/PDB/NACCESS.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,314 copying Bio/PDB/parse_pdb_header.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,316 copying Bio/PDB/PDBIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,318 copying Bio/PDB/PDBParser.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,320 copying Bio/PDB/PSEA.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,321 copying Bio/PDB/ResidueDepth.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,322 copying Bio/PDB/Structure.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,323 copying Bio/PDB/StructureBuilder.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,324 copying Bio/PDB/Vector.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,325 copying Bio/PopGen/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen install_environment.STDOUT DEBUG 2017-11-18 17:03:56,327 copying Bio/PopGen/Async/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/Async install_environment.STDOUT DEBUG 2017-11-18 17:03:56,328 creating build/lib.macosx-10.11-intel-2.7/Bio/PopGen/FDist install_environment.STDOUT DEBUG 2017-11-18 17:03:56,329 copying Bio/PopGen/FDist/Controller.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/FDist install_environment.STDOUT DEBUG 2017-11-18 17:03:56,332 creating build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePop install_environment.STDOUT DEBUG 2017-11-18 17:03:56,333 copying Bio/PopGen/GenePop/Controller.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePop install_environment.STDOUT DEBUG 2017-11-18 17:03:56,334 copying Bio/PopGen/GenePop/FileParser.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePop install_environment.STDOUT DEBUG 2017-11-18 17:03:56,335 install_environment.STDOUT DEBUG 2017-11-18 17:03:56,335 p/Utils.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePop install_environment.STDOUT DEBUG 2017-11-18 17:03:56,336 -intel-2.7/Bio/PopGen/SimCoal install_environment.STDOUT DEBUG 2017-11-18 17:03:56,338 copying Bio/PopGen/SimCoal/Cache.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal install_environment.STDOUT DEBUG 2017-11-18 17:03:56,339 copying Bio/PopGen/SimCoal/Template.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal install_environment.STDOUT DEBUG 2017-11-18 17:03:56,341 copying Bio/Restriction/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Restriction install_environment.STDOUT DEBUG 2017-11-18 17:03:56,342 copying Bio/Restriction/RanaConfig.py -> build/lib.macosx-10.11-intel-2.7/Bio/Restriction install_environment.STDOUT DEBUG 2017-11-18 17:03:56,353 copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.macosx-10.11-intel-2.7/Bio/Restrictiocreating build/lib.macosxcopying Bio/SCOP/__init__.py ->copying Bio/SCOP/Cla.py -> build/lib.macopying Bio/SCOP/Des.py -> build/lib.macosx-10.1copying Bio/SCOP/Dom.py -> build/lib.macosx-10.11-intel-2.7/copying Bio/SCOP/Hie.py -> build/lib.macosx-10.11-intel-2.7/Bio/SCOP install_environment.STDOUT DEBUG 2017-11-18 17:03:56,357 copying Bio/SCOP/Residues.py -> build/lib.macosx-10.11-intel-2.7/Bio/SCOP install_environment.STDOUT DEBUG 2017-11-18 17:03:56,360 copying Bio/SearchIO/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,361 copying Bio/SearchIO/_utils.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,366 copying Bio/SearchIO/FastaIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,368 copying Bio/SearchIO/_model/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/_model install_environment.STDOUT DEBUG 2017-11-18 17:03:56,369 copying Bio/SearchIO/_model/hit.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/_model install_environment.STDOUT DEBUG 2017-11-18 17:03:56,370 copying Bio/SearchIO/_model/query.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/_model install_environment.STDOUT DEBUG 2017-11-18 17:03:56,371 copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/BlastIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,373 copying Bio/SearchIO/BlastIO/blast_text.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/BlastIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,375 creating build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/HmmerIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,382 copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/HmmerIOcopying Bio/SearchIO/Hmmecopying Bio/SearchIO/HmmerIO/hmcopying Bio/SearchIO/HmmerIO/hmmer3_texcreating build/lib.macosx-10.11-intel-2.7/Bio/Secopying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.macopying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.macosx-10.11-intel-2copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.macosx-10.11-intel-2.7/Bio/Secopying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/ExonerateIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,383 O/ExonerateIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,386 -10.11-intel-2.7/Bio/SeqIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,387 copying Bio/SeqIO/_index.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,388 copying Bio/SeqIO/AceIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,390 copying Bio/SeqIO/IgIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,391 copying Bio/SeqIO/Interfaces.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,392 creating build/lib.macosx-10.11-intel-2.7/Bio/Pathway/Rep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,392 copying Bio/Pathway/Rep/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Pathway/Rep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,392 copying Bio/Pathway/Rep/Graph.py -> build/lib.macosx-10.11-intel-2.7/Bio/Pathway/Rep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,392 copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.macosx-10.11-intel-2.7/Bio/Pathway/Rep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,392 creating build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,392 copying Bio/PDB/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,392 copying Bio/PDB/AbstractPropertyMap.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,392 copying Bio/PDB/Atom.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,392 copying Bio/PDB/Chain.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,393 copying Bio/PDB/Dice.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,393 copying Bio/PDB/DSSP.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,393 copying Bio/PDB/Entity.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,393 copying Bio/PDB/FragmentMapper.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,393 copying Bio/PDB/HSExposure.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,393 copying Bio/PDB/MMCIF2Dict.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,393 copying Bio/SeqIO/PhdIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,393 copying Bio/PDB/MMCIFParser.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,394 copying Bio/PDB/Model.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,394 copying Bio/PDB/NACCESS.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,394 copying Bio/PDB/NeighborSearch.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,394 copying Bio/PDB/parse_pdb_header.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,394 copying Bio/PDB/PDBExceptions.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,394 copying Bio/PDB/PDBIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,394 copying Bio/PDB/PDBList.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,394 copying Bio/PDB/PDBParser.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,395 copying Bio/PDB/Polypeptide.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,395 copying Bio/PDB/PSEA.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,395 copying Bio/PDB/Residue.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:03:56,395 copying Bio/SeqIO/QualityIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,395 copying Bio/PDB/ResidueDepth.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,395 copying Bio/PDB/Selection.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,395 copying Bio/PDB/Structure.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,395 copying Bio/PDB/StructureAlignment.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,395 copying Bio/PDB/StructureBuilder.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,395 copying Bio/PDB/Superimposer.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,396 copying Bio/PDB/Vector.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,396 creating build/lib.macosx-10.11-intel-2.7/Bio/PopGen tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,396 copying Bio/PopGen/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,396 creating build/lib.macosx-10.11-intel-2.7/Bio/PopGen/Async tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,396 copying Bio/PopGen/Async/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/Async tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,396 copying Bio/PopGen/Async/Local.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/Async tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,396 copying Bio/PopGen/FDist/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/FDist tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,396 creating build/lib.macosx-10.11-intel-2.7/Bio/PopGen/FDist tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,397 copying Bio/PopGen/FDist/Async.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/FDist tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,397 copying Bio/PopGen/FDist/Controller.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/FDist tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,397 copying Bio/PopGen/FDist/Utils.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/FDist tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,397 creating build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,397 copying Bio/PopGen/GenePop/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,397 copying Bio/PopGen/GenePop/Controller.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,398 copying Bio/PopGen/GenePop/EasyController.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,398 copying Bio/PopGen/GenePop/FileParser.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePop install_environment.STDOUT DEBUG 2017-11-18 17:03:56,398 copying Bio/SeqIO/SffIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,400 copying Bio/SeqIO/TabIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,402 creating build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils install_environment.STDOUT DEBUG 2017-11-18 17:03:56,404 copying Bio/SeqUtils/CodonUsage.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils install_environment.STDOUT DEBUG 2017-11-18 17:03:56,407 copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils install_environment.STDOUT DEBUG 2017-11-18 17:03:56,409 copying Bio/SeqUtils/MeltingTemp.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils install_environment.STDOUT DEBUG 2017-11-18 17:03:56,411 copying Bio/SeqUtils/ProtParamData.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils install_environment.STDOUT DEBUG 2017-11-18 17:03:56,412 copying Bio/Sequencing/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Sequencing install_environment.STDOUT DEBUG 2017-11-18 17:03:56,417 copying Bio/Sequencing/Phd.py -> build/lib.macosx-10.11-intel-2.7/Bio/Sequencing install_environment.STDOUT DEBUG 2017-11-18 17:03:56,424 copying Bio/Sequencing/Applications/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Sequencing/Acopying Bio/Sequencing/Apcopying Bio/Sequencing/Applicatcopying Bio/Sequencing/Applications/_sacreating build/lib.macosx-10.11-intel-2.7/Bio/Stcopying Bio/Statistics/__init__.py -> build/lib.macosx-10.11copying Bio/Statistics/lowess.py -> build/lib.macosx-10.11-intel-2.7/Bio/Stcreating build/lib.macosx-10.11-intel-2.7/Bio/SubsMat install_environment.STDOUT DEBUG 2017-11-18 17:03:56,425 copying Bio/SubsMat/MatrixInfo.py -> build/lib.macosx-10.11-intel-2.7/Bio/SubsMat install_environment.STDOUT DEBUG 2017-11-18 17:03:56,427 copying Bio/SVDSuperimposer/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/SVDSuperimposer install_environment.STDOUT DEBUG 2017-11-18 17:03:56,433 copying Bio/PDB/QCPSuperimposer/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB/QCPSuperimpocreating build/lib.macosxcopying Bio/SwissProt/__init__.copying Bio/SwissProt/KeyWList.py -> bucreating build/lib.macosx-10.11-intel-2.7/Bio/Tocopying Bio/TogoWS/__init__.py -> build/lib.macosx-10.11-intcreating build/lib.macosx-10.11-intel-2.7/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:03:56,434 copying Bio/Phylo/_cdao_owl.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:03:56,436 copying Bio/Phylo/_utils.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:03:56,437 copying Bio/Phylo/CDAO.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:03:56,438 copying Bio/Phylo/Consensus.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:03:56,439 copying Bio/Phylo/NewickIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:03:56,440 copying Bio/Phylo/NeXMLIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:03:56,441 copying Bio/Phylo/PhyloXML.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:03:56,443 copying Bio/Phylo/TreeConstruction.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:03:56,451 copying Bio/Phylo/Applications/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/Applicationcopying Bio/Phylo/Applicacopying Bio/Phylo/Applications/copying Bio/Phylo/Applications/_Raxml.pcreating build/lib.macosx-10.11-intel-2.7/Bio/Phcopying Bio/Phylo/PAML/__init__.py -> build/lib.macosx-10.11copying Bio/Phylo/PAML/_paml.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phycopying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/PAML install_environment.STDOUT DEBUG 2017-11-18 17:03:56,453 copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/PAML install_environment.STDOUT DEBUG 2017-11-18 17:03:56,455 copying Bio/Phylo/PAML/chi2.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/PAML install_environment.STDOUT DEBUG 2017-11-18 17:03:56,458 copying Bio/Phylo/PAML/yn00.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/PAML install_environment.STDOUT DEBUG 2017-11-18 17:03:56,459 copying Bio/UniGene/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/UniGene install_environment.STDOUT DEBUG 2017-11-18 17:03:56,461 copying Bio/UniProt/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/UniProt install_environment.STDOUT DEBUG 2017-11-18 17:03:56,463 creating build/lib.macosx-10.11-intel-2.7/Bio/Wise install_environment.STDOUT DEBUG 2017-11-18 17:03:56,467 copying Bio/Wise/dnal.py -> build/lib.macosx-10.11-intel-2.7/Bio/Wise install_environment.STDOUT DEBUG 2017-11-18 17:03:56,469 creating build/lib.macosx-10.11-intel-2.7/Bio/_py3k install_environment.STDOUT DEBUG 2017-11-18 17:03:56,471 copying Bio/_py3k/_ordereddict.py -> build/lib.macosx-10.11-intel-2.7/Bio/_py3k install_environment.STDOUT DEBUG 2017-11-18 17:03:56,473 copying BioSQL/__init__.py -> build/lib.macosx-10.11-intel-2.7/BioSQL install_environment.STDOUT DEBUG 2017-11-18 17:03:56,476 copying BioSQL/DBUtils.py -> build/lib.macosx-10.11-intel-2.7/BioSQL install_environment.STDOUT DEBUG 2017-11-18 17:03:56,479 creating build/lib.macosx-10.11-intel-2.7/Bio/Affy install_environment.STDOUT DEBUG 2017-11-18 17:03:56,482 copying Bio/KDTree/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/KDTree install_environment.STDOUT DEBUG 2017-11-18 17:03:56,485 creating build/lib.macosx-10.11-intel-2.7/Bio/phenotype install_environment.STDOUT DEBUG 2017-11-18 17:03:56,492 copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,494 copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,501 p/Utils.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,501 copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePopcopying Bio/PopGen/GenePocreating build/lib.macosx-10.11copying Bio/PopGen/SimCoal/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,501 -intel-2.7/Bio/PopGen/SimCoal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,501 copying Bio/PopGen/SimCoal/Async.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,501 copying Bio/PopGen/SimCoal/Cache.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,501 copying Bio/PopGen/SimCoal/Controller.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,501 copying Bio/PopGen/SimCoal/Template.py -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,502 creating build/lib.macosx-10.11-intel-2.7/Bio/Restriction tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,502 copying Bio/Restriction/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Restriction tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,502 copying Bio/Restriction/PrintFormat.py -> build/lib.macosx-10.11-intel-2.7/Bio/Restriction tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,502 copying Bio/Restriction/RanaConfig.py -> build/lib.macosx-10.11-intel-2.7/Bio/Restriction tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,502 copying Bio/Restriction/Restriction.py -> build/lib.macosx-10.11-intel-2.7/Bio/Restriction tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,502 n tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,502 -10.11-intel-2.7/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,502 build/lib.macosx-10.11-intel-2.7/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,502 cosx-10.11-intel-2.7/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,502 1-intel-2.7/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,502 Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,502 copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.macosx-10.11-intel-2.7/Bio/Restrictiocreating build/lib.macosxcopying Bio/SCOP/__init__.py ->copying Bio/SCOP/Cla.py -> build/lib.macopying Bio/SCOP/Des.py -> build/lib.macosx-10.1copying Bio/SCOP/Dom.py -> build/lib.macosx-10.11-intel-2.7/copying Bio/SCOP/Hie.py -> build/lib.macosx-10.11-intel-2.7/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,502 copying Bio/SCOP/Raf.py -> build/lib.macosx-10.11-intel-2.7/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,503 copying Bio/SCOP/Residues.py -> build/lib.macosx-10.11-intel-2.7/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,503 creating build/lib.macosx-10.11-intel-2.7/Bio/SearchIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,503 copying Bio/SearchIO/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,503 copying Bio/SearchIO/_index.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,503 copying Bio/SearchIO/_utils.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,503 copying Bio/SearchIO/BlatIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,503 copying Bio/SearchIO/FastaIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,503 creating build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/_model tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,503 copying Bio/SearchIO/_model/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/_model tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,503 copying Bio/SearchIO/_model/_base.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/_model tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,503 copying Bio/SearchIO/_model/hit.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/_model tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,503 copying Bio/SearchIO/_model/hsp.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/_model tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,504 copying Bio/SearchIO/_model/query.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/_model tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,504 creating build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/BlastIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,504 copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/BlastIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,504 copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/BlastIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,504 copying Bio/SearchIO/BlastIO/blast_text.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/BlastIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,504 copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/BlastIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,504 copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/HmmerIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,504 creating build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/HmmerIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,504 copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/HmmerIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,504 copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,507 copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,510 copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,511 copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,513 copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,514 copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,516 copying Bio/Entrez/DTDs/egquery.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,518 copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,519 copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,520 copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,521 copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,523 copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,524 copying Bio/Entrez/DTDs/esummary-v1.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,525 copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,526 copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,528 copying Bio/Entrez/DTDs/htmltable.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,530 copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,538 copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,540 copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,541 TDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,543 MDB_Features.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,544 atures.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,545 _model.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,546 d.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,547 10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,548 -2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,549 copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,551 copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,553 copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,554 copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,556 copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,557 copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,558 install_environment.STDOUT DEBUG 2017-11-18 17:03:56,558 CBI_Cdd.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,559 d.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,560 > build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,560 ld/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,561 osx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,561 7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,562 Ds install_environment.STDOUT DEBUG 2017-11-18 17:03:56,563 copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,565 copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,566 copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,567 copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,568 copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,570 copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,571 copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,572 copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,574 copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,575 copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,579 copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,587 copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,593 copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,594 copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,596 copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,596 install_environment.STDOUT DEBUG 2017-11-18 17:03:56,597 CBI_Project.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,599 copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,601 copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,602 copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,604 copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,605 copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,605 rIO/hmmer3_domtab.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/HmmerIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,605 mer3_tab.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/HmmerIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,606 t.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/HmmerIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,606 archIO/ExonerateIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,606 cosx-10.11-intel-2.7/Bio/SearchIO/ExonerateIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,606 .7/Bio/SearchIO/ExonerateIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,606 archIO/ExonerateIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,606 copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/HmmerIOcopying Bio/SearchIO/Hmmecopying Bio/SearchIO/HmmerIO/hmcopying Bio/SearchIO/HmmerIO/hmmer3_texcreating build/lib.macosx-10.11-intel-2.7/Bio/Secopying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.macopying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.macosx-10.11-intel-2copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.macosx-10.11-intel-2.7/Bio/Secopying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/ExonerateIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,606 O/ExonerateIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,606 copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.macosx-10.11-intel-2.7/Bio/SearchIcreating build/lib.macosxcopying Bio/SeqIO/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,607 -10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,607 copying Bio/SeqIO/_convert.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,607 copying Bio/SeqIO/_index.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,607 copying Bio/SeqIO/AbiIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,607 copying Bio/SeqIO/AceIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,607 copying Bio/SeqIO/FastaIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,607 copying Bio/SeqIO/IgIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,607 copying Bio/SeqIO/InsdcIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,607 copying Bio/SeqIO/Interfaces.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,608 copying Bio/SeqIO/PdbIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,608 copying Bio/SeqIO/PhdIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO install_environment.STDOUT DEBUG 2017-11-18 17:03:56,608 copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,608 copying Bio/SeqIO/PirIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,608 copying Bio/SeqIO/QualityIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,608 copying Bio/SeqIO/SeqXmlIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,608 copying Bio/SeqIO/SffIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,609 copying Bio/SeqIO/SwissIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,609 copying Bio/SeqIO/TabIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,609 copying Bio/SeqIO/UniprotIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,609 copying Bio/SeqUtils/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,609 creating build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,609 copying Bio/SeqUtils/CheckSum.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,609 copying Bio/SeqUtils/CodonUsage.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils install_environment.STDOUT DEBUG 2017-11-18 17:03:56,609 copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,610 copying Bio/SeqUtils/CodonUsageIndices.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,610 copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,610 copying Bio/SeqUtils/lcc.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,610 copying Bio/SeqUtils/MeltingTemp.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,610 copying Bio/SeqUtils/ProtParam.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,610 copying Bio/SeqUtils/ProtParamData.py -> build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,610 creating build/lib.macosx-10.11-intel-2.7/Bio/Sequencing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,610 copying Bio/Sequencing/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Sequencing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,610 copying Bio/Sequencing/Ace.py -> build/lib.macosx-10.11-intel-2.7/Bio/Sequencing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,610 copying Bio/Sequencing/Phd.py -> build/lib.macosx-10.11-intel-2.7/Bio/Sequencing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,611 creating build/lib.macosx-10.11-intel-2.7/Bio/Sequencing/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,611 pplications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,611 plications/_bwa.py -> build/lib.macosx-10.11-intel-2.7/Bio/Sequencing/Applications install_environment.STDOUT DEBUG 2017-11-18 17:03:56,611 copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,611 ions/_Novoalign.py -> build/lib.macosx-10.11-intel-2.7/Bio/Sequencing/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,611 mtools.py -> build/lib.macosx-10.11-intel-2.7/Bio/Sequencing/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,611 atistics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,612 -intel-2.7/Bio/Statistics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,612 atistics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,612 copying Bio/SubsMat/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/SubsMat tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,612 copying Bio/Sequencing/Applications/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Sequencing/Acopying Bio/Sequencing/Apcopying Bio/Sequencing/Applicatcopying Bio/Sequencing/Applications/_sacreating build/lib.macosx-10.11-intel-2.7/Bio/Stcopying Bio/Statistics/__init__.py -> build/lib.macosx-10.11copying Bio/Statistics/lowess.py -> build/lib.macosx-10.11-intel-2.7/Bio/Stcreating build/lib.macosx-10.11-intel-2.7/Bio/SubsMat tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,612 copying Bio/SubsMat/FreqTable.py -> build/lib.macosx-10.11-intel-2.7/Bio/SubsMat tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,612 copying Bio/SubsMat/MatrixInfo.py -> build/lib.macosx-10.11-intel-2.7/Bio/SubsMat tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,612 creating build/lib.macosx-10.11-intel-2.7/Bio/SVDSuperimposer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,612 copying Bio/SVDSuperimposer/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/SVDSuperimposer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,612 creating build/lib.macosx-10.11-intel-2.7/Bio/PDB/QCPSuperimposer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,613 ser tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,613 -10.11-intel-2.7/Bio/SwissProt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,613 py -> build/lib.macosx-10.11-intel-2.7/Bio/SwissProt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,613 ild/lib.macosx-10.11-intel-2.7/Bio/SwissProt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,613 goWS tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,613 el-2.7/Bio/TogoWS tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,613 copying Bio/PDB/QCPSuperimposer/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/PDB/QCPSuperimpocreating build/lib.macosxcopying Bio/SwissProt/__init__.copying Bio/SwissProt/KeyWList.py -> bucreating build/lib.macosx-10.11-intel-2.7/Bio/Tocopying Bio/TogoWS/__init__.py -> build/lib.macosx-10.11-intcreating build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,613 copying Bio/Phylo/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,613 copying Bio/Phylo/_cdao_owl.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,614 copying Bio/Phylo/_io.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,614 copying Bio/Phylo/_utils.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,614 copying Bio/Phylo/BaseTree.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,614 copying Bio/Phylo/CDAO.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,614 copying Bio/Phylo/CDAOIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,614 copying Bio/Phylo/Consensus.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,614 copying Bio/Phylo/Newick.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,614 copying Bio/Phylo/NewickIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,614 copying Bio/Phylo/NeXML.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,614 copying Bio/Phylo/NeXMLIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,614 copying Bio/Phylo/NexusIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,614 copying Bio/Phylo/PhyloXML.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,615 copying Bio/Phylo/PhyloXMLIO.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,615 copying Bio/Phylo/TreeConstruction.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,615 creating build/lib.macosx-10.11-intel-2.7/Bio/Phylo/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,615 s tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,615 tions/_Fasttree.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,615 _Phyml.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,615 y -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,615 ylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,615 -intel-2.7/Bio/Phylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,615 lo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,616 copying Bio/Phylo/Applications/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/Applicationcopying Bio/Phylo/Applicacopying Bio/Phylo/Applications/copying Bio/Phylo/Applications/_Raxml.pcreating build/lib.macosx-10.11-intel-2.7/Bio/Phcopying Bio/Phylo/PAML/__init__.py -> build/lib.macosx-10.11copying Bio/Phylo/PAML/_paml.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phycopying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,616 copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,616 copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,616 copying Bio/Phylo/PAML/baseml.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,616 copying Bio/Phylo/PAML/chi2.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,616 copying Bio/Phylo/PAML/codeml.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,616 copying Bio/Phylo/PAML/yn00.py -> build/lib.macosx-10.11-intel-2.7/Bio/Phylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,616 creating build/lib.macosx-10.11-intel-2.7/Bio/UniGene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,616 copying Bio/UniGene/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/UniGene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,616 creating build/lib.macosx-10.11-intel-2.7/Bio/UniProt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,616 copying Bio/UniProt/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/UniProt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,617 copying Bio/UniProt/GOA.py -> build/lib.macosx-10.11-intel-2.7/Bio/UniProt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,617 creating build/lib.macosx-10.11-intel-2.7/Bio/Wise tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,617 copying Bio/Wise/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Wise tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,617 copying Bio/Wise/dnal.py -> build/lib.macosx-10.11-intel-2.7/Bio/Wise tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,617 copying Bio/Wise/psw.py -> build/lib.macosx-10.11-intel-2.7/Bio/Wise tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,617 creating build/lib.macosx-10.11-intel-2.7/Bio/_py3k tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,617 copying Bio/_py3k/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/_py3k tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,617 copying Bio/_py3k/_ordereddict.py -> build/lib.macosx-10.11-intel-2.7/Bio/_py3k tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,617 creating build/lib.macosx-10.11-intel-2.7/BioSQL tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,618 copying BioSQL/BioSeq.py -> build/lib.macosx-10.11-intel-2.7/BioSQL tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,618 copying BioSQL/__init__.py -> build/lib.macosx-10.11-intel-2.7/BioSQL tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,618 copying BioSQL/BioSeqDatabase.py -> build/lib.macosx-10.11-intel-2.7/BioSQL tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,618 copying BioSQL/DBUtils.py -> build/lib.macosx-10.11-intel-2.7/BioSQL tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,618 copying BioSQL/Loader.py -> build/lib.macosx-10.11-intel-2.7/BioSQL tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,618 copying Bio/Affy/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Affy install_environment.STDOUT DEBUG 2017-11-18 17:03:56,618 copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,618 copying Bio/Affy/CelFile.py -> build/lib.macosx-10.11-intel-2.7/Bio/Affy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,619 creating build/lib.macosx-10.11-intel-2.7/Bio/Cluster tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,619 copying Bio/Cluster/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/Cluster tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,619 creating build/lib.macosx-10.11-intel-2.7/Bio/Affy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,619 creating build/lib.macosx-10.11-intel-2.7/Bio/KDTree tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,619 copying Bio/KDTree/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/KDTree tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,619 copying Bio/KDTree/KDTree.py -> build/lib.macosx-10.11-intel-2.7/Bio/KDTree tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,619 copying Bio/phenotype/__init__.py -> build/lib.macosx-10.11-intel-2.7/Bio/phenotype tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,619 copying Bio/phenotype/phen_micro.py -> build/lib.macosx-10.11-intel-2.7/Bio/phenotype tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,619 copying Bio/phenotype/pm_fitting.py -> build/lib.macosx-10.11-intel-2.7/Bio/phenotype tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,619 creating build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,620 creating build/lib.macosx-10.11-intel-2.7/Bio/phenotype tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,620 copying Bio/Entrez/DTDs/archivearticle.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,620 copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,620 copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,620 copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,620 copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,620 copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,620 copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,620 copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,621 copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,621 copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,621 copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,621 copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,621 copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,621 copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,621 copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,621 copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,621 copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,622 copying Bio/Entrez/DTDs/egquery.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,622 copying Bio/Entrez/DTDs/einfo.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,622 copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,622 copying Bio/Entrez/DTDs/elink_020122.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,622 copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,622 copying Bio/Entrez/DTDs/eLink_101123.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,622 copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,622 copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,622 copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,623 copying Bio/Entrez/DTDs/esearch.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,623 copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,623 copying Bio/Entrez/DTDs/eSpell.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,623 copying Bio/Entrez/DTDs/esummary-v1.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,623 copying Bio/Entrez/DTDs/eSummary_041029.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,623 copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,623 copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,624 copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,624 copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,624 copying Bio/Entrez/DTDs/htmltable.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,624 copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,624 copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,624 copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,624 copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,624 copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,624 copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,624 TDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,624 MDB_Features.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,625 atures.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,625 _model.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,625 d.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,625 10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,625 -2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,625 copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/Dcopying Bio/Entrez/DTDs/Mcopying Bio/Entrez/DTDs/MMDB_Fecopying Bio/Entrez/DTDs/MMDB_Structuralcopying Bio/Entrez/DTDs/MMDB_Structural_model.mocopying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.macosx-copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.macosx-10.11-intelcopying Bio/Entrez/DTDs/NCBI_all.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,625 copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,625 copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,625 copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,625 copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,625 copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,625 copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,626 copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,626 copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,626 copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,626 copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,626 copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,626 copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,628 copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,629 copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,631 copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,635 copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,638 copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,643 copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,644 copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,646 copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,647 copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,648 /DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,649 lmmedlinecitation_080101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,650 inecitation_090101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,651 ionset_100101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,652 0301.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,653 build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,655 x-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,655 io/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,657 copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,658 lmserials_080101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,659 als_100101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,659 _080101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,660 td -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,661 tel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,661 /Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,663 copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,664 copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,666 copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,668 copying Bio/Entrez/DTDs/PRF_General.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,670 copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,671 copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,673 copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,674 copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,676 copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,677 copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,680 copying Bio/Entrez/DTDs/SP_General.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,687 copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDcopying Bio/Entrez/DTDs/acopying Bio/Entrez/DTDs/archivecopying Bio/Entrez/DTDs/archivecustom-mcopying Bio/Entrez/DTDs/articlemeta.ent -> buildcopying Bio/Entrez/DTDs/backmatter.ent -> build/lib.macosx-1copying Bio/Entrez/DTDs/chars.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Ecopying Bio/Entrez/DTDs/common.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,689 copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,692 copying Bio/Entrez/DTDs/format.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,694 copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,695 copying Bio/Entrez/DTDs/isoamsn.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,697 copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,700 copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,701 copying Bio/Entrez/DTDs/isodia.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,702 copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,703 copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,704 copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,706 copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,707 copying Bio/Entrez/DTDs/isonum.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,708 copying Bio/Entrez/DTDs/isotech.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,710 copying Bio/Entrez/DTDs/link.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,711 copying Bio/Entrez/DTDs/math.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,712 copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,714 copying Bio/Entrez/DTDs/modules.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,720 copying Bio/Entrez/DTDs/para.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,722 copying Bio/Entrez/DTDs/references.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,724 copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,727 copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,730 CBI_Cdd.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,730 d.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,731 > build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,731 ld/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,731 osx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,731 7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,731 Ds tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,731 copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDscopying Bio/Entrez/DTDs/Ncopying Bio/Entrez/DTDs/NCBI_Cdcopying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> buicopying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.maccopying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.macosx-10.11-intel-2.copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTcopying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,731 copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,731 copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,731 copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,731 copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,731 copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,732 copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,732 copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,732 copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,732 copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,732 copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,732 copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,732 copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,732 copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,732 copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,732 copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,732 copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,733 copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,733 copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,733 copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,733 copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,734 copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,734 copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,734 copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,734 copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,734 copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,734 copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,735 copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,735 copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,735 copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,735 copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:03:56,742 copying Bio/PopGen/SimCoal/data/bottle.par -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/dacopying Bio/PopGen/SimCoacopying Bio/PopGen/SimCoal/datacopying Bio/PopGen/SimCoal/data/island.copying Bio/PopGen/SimCoal/data/simple.par -> bucopying Bio/PopGen/SimCoal/data/split_island.par -> build/licopying Bio/PopGen/SimCoal/data/split_ssm_1d.par -> build/lib.macosx-10.11-copying Bio/PopGen/SimCoal/data/split_ssm_2d.par -> build/lib.macosx-10.11-intel-2.7/Bio/PopGecopying Bio/PopGen/SimCoal/data/ssm_1d.par -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/data install_environment.STDOUT DEBUG 2017-11-18 17:03:56,744 ta install_environment.STDOUT DEBUG 2017-11-18 17:03:56,822 building 'Bio.cpairwise2' extension install_environment.STDOUT DEBUG 2017-11-18 17:03:56,832 cc -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -Qunused-arguments -Qunused-arguments -arch i386 -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c Bio/cpairwise2module.c -o build/temp.macosx-10.11-intel-2.7/Bio/cpairwise2module.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,846 copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDscopying Bio/Entrez/DTDs/Ncopying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,847 CBI_Project.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,847 copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,847 copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,847 copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,847 copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,847 copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,848 copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,848 copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,848 copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,848 copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,848 copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,848 copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,848 copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,848 copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,848 copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,848 copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,849 copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,849 copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,849 copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,849 copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,849 copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,849 copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,849 copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,849 copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,849 copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,849 copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,849 copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,850 copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,850 copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,850 copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,850 copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,850 copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,851 copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,851 copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,851 copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,851 copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,851 copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,851 copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,851 copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,851 copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,851 copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,851 copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,851 copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,851 copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,852 copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,852 copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,852 copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,852 copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,852 /DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,852 lmmedlinecitation_080101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,852 inecitation_090101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,852 ionset_100101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,852 0301.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,852 build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,852 x-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,853 io/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,853 copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrezcopying Bio/Entrez/DTDs/ncopying Bio/Entrez/DTDs/nlmmedlcopying Bio/Entrez/DTDs/nlmmedlinecitatcopying Bio/Entrez/DTDs/nlmmedlinecitationset_10copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.macoscopying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.macosx-10.11-intel-2.7/Bcopying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,853 rez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,853 copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,853 lmserials_080101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,853 als_100101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,853 _080101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,853 td -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,853 tel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,853 /Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,853 copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entcopying Bio/Entrez/DTDs/ncopying Bio/Entrez/DTDs/nlmsericopying Bio/Entrez/DTDs/nlmsharedcatcitcopying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dcopying Bio/Entrez/DTDs/NSE.dtd -> build/lib.macosx-10.11-incopying Bio/Entrez/DTDs/NSE.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Biocopying Bio/Entrez/DTDs/OMSSA.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,853 copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,854 copying Bio/Entrez/DTDs/PDB_General.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,854 copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,854 copying Bio/Entrez/DTDs/PIR_General.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,854 copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,854 copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,854 copying Bio/Entrez/DTDs/PRF_General.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,854 copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,854 copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,854 copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,854 copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,854 copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,854 copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,854 copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,855 copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,855 copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,855 copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,855 copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,855 copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,855 copying Bio/Entrez/DTDs/SP_General.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,856 copying Bio/Entrez/DTDs/SP_General.mod.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,856 copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,856 s tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,856 rchivecustom-mixes.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,856 custom-models.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,857 odules.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,857 /lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,858 0.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,858 ntrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,858 copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDcopying Bio/Entrez/DTDs/acopying Bio/Entrez/DTDs/archivecopying Bio/Entrez/DTDs/archivecustom-mcopying Bio/Entrez/DTDs/articlemeta.ent -> buildcopying Bio/Entrez/DTDs/backmatter.ent -> build/lib.macosx-1copying Bio/Entrez/DTDs/chars.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Ecopying Bio/Entrez/DTDs/common.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,863 copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,864 copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,864 copying Bio/Entrez/DTDs/display.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,864 copying Bio/Entrez/DTDs/format.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,864 copying Bio/Entrez/DTDs/isoamsa.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,864 copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,864 copying Bio/Entrez/DTDs/isoamsc.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,864 copying Bio/Entrez/DTDs/isoamsn.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,864 copying Bio/Entrez/DTDs/isoamso.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,864 copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,864 copying Bio/Entrez/DTDs/isobox.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,865 copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,865 copying Bio/Entrez/DTDs/isocyr2.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,865 copying Bio/Entrez/DTDs/isodia.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,865 copying Bio/Entrez/DTDs/isogrk1.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,865 copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,865 copying Bio/Entrez/DTDs/isogrk3.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,865 copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,865 copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,865 copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,865 copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,865 copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,865 copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,866 copying Bio/Entrez/DTDs/isonum.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,866 copying Bio/Entrez/DTDs/isopub.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,868 copying Bio/Entrez/DTDs/isotech.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,868 copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,868 copying Bio/Entrez/DTDs/link.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,868 copying Bio/Entrez/DTDs/list.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,868 copying Bio/Entrez/DTDs/math.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,868 copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,868 copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,869 copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,869 copying Bio/Entrez/DTDs/modules.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,869 copying Bio/Entrez/DTDs/notat.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,869 copying Bio/Entrez/DTDs/para.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,871 copying Bio/Entrez/DTDs/phrase.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,871 copying Bio/Entrez/DTDs/references.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,871 copying Bio/Entrez/DTDs/section.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,872 copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,872 copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,872 copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,872 creating build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,872 ta tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,873 l/data/decline_lambda.par -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,873 /decline_split.par -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,873 par -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,873 ild/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,874 b.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,874 intel-2.7/Bio/PopGen/SimCoal/data 127.0.0.1 - - [18/Nov/2017:17:03:56 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/datasets/error?dataset_id=a799d38679e985db&__identifer=9nms4ovms1v" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,877 n/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,877 copying Bio/PopGen/SimCoal/data/bottle.par -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/dacopying Bio/PopGen/SimCoacopying Bio/PopGen/SimCoal/datacopying Bio/PopGen/SimCoal/data/island.copying Bio/PopGen/SimCoal/data/simple.par -> bucopying Bio/PopGen/SimCoal/data/split_island.par -> build/licopying Bio/PopGen/SimCoal/data/split_ssm_1d.par -> build/lib.macosx-10.11-copying Bio/PopGen/SimCoal/data/split_ssm_2d.par -> build/lib.macosx-10.11-intel-2.7/Bio/PopGecopying Bio/PopGen/SimCoal/data/ssm_1d.par -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,877 ta tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,879 copying Bio/PopGen/SimCoal/data/ssm_2d.par -> build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/darunning build_ext tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,881 creating build/temp.macosx-10.11-intel-2.7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,881 building 'Bio.cpairwise2' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,883 cc -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -Qunused-arguments -Qunused-arguments -arch i386 -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c Bio/cpairwise2module.c -o build/temp.macosx-10.11-intel-2.7/Bio/cpairwise2module.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:56,883 creating build/temp.macosx-10.11-intel-2.7/Bio 127.0.0.1 - - [18/Nov/2017:17:03:57 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:03:57 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:03:57 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:03:57 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:03:57,764 cc -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -Wl,-F. -Qunused-arguments -Qunused-argBio/cpairwise2.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:57,820 cc -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -Wl,-F. -Qunused-arguments -Qunused-argBio/cpairwise2.so install_environment.STDOUT DEBUG 2017-11-18 17:03:57,918 sion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:57,921 sion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:57,922 uments build/temp.macosx-10.11-intel-2.7/Bio/cpairwise2module.o -o build/lib.macosx-10.11-intel-2.7/building 'Bio.trie' extencc -DNDEBUG -g -fwrapv -Os -Walystem/Library/Frameworks/Python.framewoython2.7 -c Bio/triemodule.c -o build/temp.macose.o install_environment.STDOUT DEBUG 2017-11-18 17:03:58,447 l -Wstrict-prototypes -Qunused-arguments -Qunused-arguments -arch i386 -arch x86_64 -pipe -IBio -I/Srk/Versions/2.7/include/px-10.11-intel-2.7/Bio/triemodulcc -DNDEBUG -g -fwrapv -Os -Wall -Wstribrary/Frameworks/Python.framework/Versions/2.7/irie.c -o build/temp.macosx-10.11-intel-2.7/Bio/trie.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:58,538 l -Wstrict-prototypes -Qunused-arguments -Qunused-arguments -arch i386 -arch x86_64 -pipe -IBio -I/Srk/Versions/2.7/include/px-10.11-intel-2.7/Bio/triemodulcc -DNDEBUG -g -fwrapv -Os -Wall -Wstribrary/Frameworks/Python.framework/Versions/2.7/irie.c -o build/temp.macosx-10.11-intel-2.7/Bio/trie.o install_environment.STDOUT DEBUG 2017-11-18 17:03:59,009 ookup -arch i386 -arch x86_64 -Wl,-F. -Qunused-arguments -Qunused-arguments build/temp.macosx-10.11-acosx-10.11-intel-2.7/Bio/trie.o -o build/lib.macosx-10.11-intel-2.7/Bio/trie.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:59,069 ookup -arch i386 -arch x86_64 -Wl,-F. -Qunused-arguments -Qunused-arguments build/temp.macosx-10.11-acosx-10.11-intel-2.7/Bio/trie.o -o build/lib.macosx-10.11-intel-2.7/Bio/trie.so install_environment.STDOUT DEBUG 2017-11-18 17:03:59,104 creating build/temp.macosx-10.11-intel-2.7/Bio/Nexus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:59,172 ct-prototypes -Qunused-arguments -Qunused-arguments -arch i386 -arch x86_64 -pipe -IBio -I/System/Linclude/python2.7 -c Bio/tcc -bundle -undefined dynamic_lintel-2.7/Bio/triemodule.o build/temp.mbuilding 'Bio.Nexus.cnexus' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:59,172 cc -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -Qunused-arguments -Qunused-arguments -arch i386 -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c Bio/Nexus/cnexus.c -o build/temp.macosx-10.11-intel-2.7/Bio/Nexus/cnexus.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:59,172 creating build/temp.macosx-10.11-intel-2.7/Bio/Nexus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:59,379 cc -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -Wl,-F. -Qunused-arguments -Qunused-argNexus/cnexus.so install_environment.STDOUT DEBUG 2017-11-18 17:03:59,454 uments build/temp.macosx-10.11-intel-2.7/Bio/Nexus/cnexus.o -o build/lib.macosx-10.11-intel-2.7/Bio/building 'Bio.Cluster.clucreating build/temp.macosx-10.1cc -DNDEBUG -g -fwrapv -Os -Wall -Wstriy/.venv/lib/python2.7/site-packages/numpy/core/iFrameworks/Python.framework/Versions/2.7/include/python2.7 -o build/temp.macosx-10.11-intel-2.7/Bio/Cluster/clustermodule.o 127.0.0.1 - - [18/Nov/2017:17:03:59 -0400] "GET /admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:59,480 ster' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:59,480 1-intel-2.7/Bio/Cluster tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:03:59,481 uments build/temp.macosx-10.11-intel-2.7/Bio/Nexus/cnexus.o -o build/lib.macosx-10.11-intel-2.7/Bio/building 'Bio.Cluster.clucreating build/temp.macosx-10.1cc -DNDEBUG -g -fwrapv -Os -Wall -Wstriy/.venv/lib/python2.7/site-packages/numpy/core/iFrameworks/Python.framework/Versions/2.7/include/python2.7 -o build/temp.macosx-10.11-intel-2.7/Bio/Cluster/clustermodule.o 127.0.0.1 - - [18/Nov/2017:17:03:59 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:01,339 ct-prototypes -Qunused-arguments -Qunused-arguments -arch i386 -arch x86_64 -pipe -I/galaxydir/galaxnclude -I/System/Library/c Bio/Cluster/clustermodule.c -cc -DNDEBUG -g -fwrapv -Os -Wall -Wstriy/.venv/lib/python2.7/site-packages/numpy/core/iFrameworks/Python.framework/Versions/2.7/include/python2.7 -d/temp.macosx-10.11-intel-2.7/Bio/Cluster/cluster.o 127.0.0.1 - - [18/Nov/2017:17:04:02 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:04:05 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:04:06,227 ct-prototypes -Qunused-arguments -Qunused-arguments -arch i386 -arch x86_64 -pipe -I/galaxydir/galaxnclude -I/System/Library/c Bio/Cluster/cluster.c -o builcc -bundle -undefined dynamic_lookup -a7/Bio/Cluster/clustermodule.o build/temp.macosx-er/cluster.o -o build/lib.macosx-10.11-intel-2.7/Bio/Clusterbuilding 'Bio.KDTree._CKDTree' extension install_environment.STDOUT DEBUG 2017-11-18 17:04:06,228 cc -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -Qunused-arguments -Qunused-arguments -arch i38tem/Library/Frameworks/Py.7/include/python2.7 -c Bio/KDTsx-10.11-intel-2.7/Bio/KDTree/KDTree.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:06,240 rch i386 -arch x86_64 -Wl,-F. -Qunused-arguments -Qunused-arguments build/temp.macosx-10.11-intel-2.10.11-intel-2.7/Bio/Clust/cluster.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:06,240 ct-prototypes -Qunused-arguments -Qunused-arguments -arch i386 -arch x86_64 -pipe -I/galaxydir/galaxnclude -I/System/Library/c Bio/Cluster/cluster.c -o builcc -bundle -undefined dynamic_lookup -a7/Bio/Cluster/clustermodule.o build/temp.macosx-er/cluster.o -o build/lib.macosx-10.11-intel-2.7/Bio/Clusterbuilding 'Bio.KDTree._CKDTree' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:06,240 creating build/temp.macosx-10.11-intel-2.7/Bio/KDTree tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:06,240 cc -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -Qunused-arguments -Qunused-arguments -arch i38tem/Library/Frameworks/Py.7/include/python2.7 -c Bio/KDTsx-10.11-intel-2.7/Bio/KDTree/KDTree.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:06,850 6 -arch x86_64 -pipe -I/galaxydir/galaxy/.venv/lib/python2.7/site-packages/numpy/core/include -I/Systhon.framework/Versions/2ree/KDTree.c -o build/temp.macocc -DNDEBUG -g -fwrapv -Os -Wall -Wstriy/.venv/lib/python2.7/site-packages/numpy/core/iFrameworks/Python.framework/Versions/2.7/include/python2.7 -build/temp.macosx-10.11-intel-2.7/Bio/KDTree/KDTreemodule.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,155 rch i386 -arch x86_64 -Wl,-F. -Qunused-arguments -Qunused-arguments build/temp.macosx-10.11-intel-2.tel-2.7/Bio/KDTree/KDTreeTree.so install_environment.STDOUT DEBUG 2017-11-18 17:04:07,208 ct-prototypes -Qunused-arguments -Qunused-arguments -arch i386 -arch x86_64 -pipe -I/galaxydir/galaxnclude -I/System/Library/c Bio/KDTree/KDTreemodule.c -o cc -bundle -undefined dynamic_lookup -a7/Bio/KDTree/KDTree.o build/temp.macosx-10.11-inmodule.o -o build/lib.macosx-10.11-intel-2.7/Bio/KDTree/_CKDbuilding 'Bio.motifs._pwm' extension install_environment.STDOUT DEBUG 2017-11-18 17:04:07,209 cc -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -Qunused-arguments -Qunused-arguments -arch i38tem/Library/Frameworks/Py.7/include/python2.7 -c Bio/mot-10.11-intel-2.7/Bio/motifs/_pwm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,257 ct-prototypes -Qunused-arguments -Qunused-arguments -arch i386 -arch x86_64 -pipe -I/galaxydir/galaxnclude -I/System/Library/c Bio/KDTree/KDTreemodule.c -o cc -bundle -undefined dynamic_lookup -a7/Bio/KDTree/KDTree.o build/temp.macosx-10.11-inmodule.o -o build/lib.macosx-10.11-intel-2.7/Bio/KDTree/_CKDbuilding 'Bio.motifs._pwm' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,257 creating build/temp.macosx-10.11-intel-2.7/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,257 cc -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -Qunused-arguments -Qunused-arguments -arch i38tem/Library/Frameworks/Py.7/include/python2.7 -c Bio/mot-10.11-intel-2.7/Bio/motifs/_pwm.o tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,463 6 -arch x86_64 -pipe -I/galaxydir/galaxy/.venv/lib/python2.7/site-packages/numpy/core/include -I/Systhon.framework/Versions/2ifs/_pwm.c -o build/temp.macosxcc -bundle -undefined dynamic_lookup -a7/Bio/motifs/_pwm.o -o build/lib.macosx-10.11-intel-2.7/Bio/motifs/_pwm.so tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,568 building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,568 x-10.11-intel-2.7/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,568 1-intel-2.7/Bio/PDB/QCPSuperimposer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,568 ct-prototypes -Qunused-arguments -Qunused-arguments -arch i386 -arch x86_64 -pipe -I/galaxydir/galaxnclude -I/System/Library/c Bio/PDB/QCPSuperimposer/qcprootmodule.o install_environment.STDOUT DEBUG 2017-11-18 17:04:07,699 rch i386 -arch x86_64 -Wl,-F. -Qunused-arguments -Qunused-arguments build/temp.macosx-10.11-intel-2.creating build/temp.macoscreating build/temp.macosx-10.1cc -DNDEBUG -g -fwrapv -Os -Wall -Wstriy/.venv/lib/python2.7/site-packages/numpy/core/iFrameworks/Python.framework/Versions/2.7/include/python2.7 -tmodule.c -o build/temp.macosx-10.11-intel-2.7/Bio/PDB/QCPSuperimposer/qcprcc -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -Wl,-F. -Qunused-arguments -Qunusacosx-10.11-intel-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.so install_environment.STDOUT DEBUG 2017-11-18 17:04:07,746 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12copying build/lib.macosx-package_biopython_1_67/a12f73c3creating /galaxydir/galaxy/database/depcopying build/lib.macosx-10.11-intel-2.7/Bio/_py_1_67/a12f73c3b116/lib/python/Bio/_py3k install_environment.STDOUT DEBUG 2017-11-18 17:04:07,748 10.11-intel-2.7/Bio/_py3k/_ordereddict.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/7/a12f73c3b116/lib/pythoncopying build/lib.macosx-10.11-biopython_1_67/a12f73c3b116/lib/python/creating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/Affy/__init__.p3b116/lib/python/Bio/Affy install_environment.STDOUT DEBUG 2017-11-18 17:04:07,749 10.11-intel-2.7/Bio/Affy/CelFile.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt73c3b116/lib/python/Bio/Acreating /galaxydir/galaxy/datacopying build/lib.macosx-10.11-intel-2.biopython_1_67/a12f73c3b116/lib/python/Bio/Aligncopying build/lib.macosx-10.11-intel-2.7/Bio/Align/AlignInfo3c3b116/lib/python/Bio/Align install_environment.STDOUT DEBUG 2017-11-18 17:04:07,750 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-hon/1.67/biopython/package_biopib/python/Bio/Align/Applications install_environment.STDOUT DEBUG 2017-11-18 17:04:07,752 intel-2.7/Bio/Align/Applications/_ClustalOmega.py -> /galaxydir/galaxy/database/dependencies/biopyth7/a12f73c3b116/lib/pythoncopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Align/Applications install_environment.STDOUT DEBUG 2017-11-18 17:04:07,754 intel-2.7/Bio/Align/Applications/_Dialign.py -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Align/Applications install_environment.STDOUT DEBUG 2017-11-18 17:04:07,754 10.11-intel-2.7/Bio/Align/Applications/_MSAProbs.py -> /galaxydir/galaxy/database/dependencies/biopypython_1_67/a12f73c3b116/copying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12flign/Applications install_environment.STDOUT DEBUG 2017-11-18 17:04:07,756 intel-2.7/Bio/Align/Applications/_Prank.py -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Alcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Align/Applications install_environment.STDOUT DEBUG 2017-11-18 17:04:07,757 intel-2.7/Bio/Align/Applications/_TCoffee.py -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-ackage_biopython_1_67/a12f73c3b116/lib/creating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/AlignIO/__init_73c3b116/lib/python/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:04:07,759 10.11-intel-2.7/Bio/AlignIO/ClustalIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b/a12f73c3b116/lib/python/copying build/lib.macosx-10.11-n/package_biopython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-intel-2.7/Bio/Alin_1_67/a12f73c3b116/lib/python/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:04:07,760 10.11-intel-2.7/Bio/AlignIO/Interfaces.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/7/a12f73c3b116/lib/pythoncopying build/lib.macosx-10.11-/package_biopython_1_67/a12f73c3b116/licopying build/lib.macosx-10.11-intel-2.7/Bio/Alion_1_67/a12f73c3b116/lib/python/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:04:07,762 10.11-intel-2.7/Bio/AlignIO/StockholmIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.6767/a12f73c3b116/lib/pythocreating /galaxydir/galaxy/dataet install_environment.STDOUT DEBUG 2017-11-18 17:04:07,763 10.11-intel-2.7/Bio/Alphabet/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b/a12f73c3b116/lib/python/copying build/lib.macosx-10.11-package_biopython_1_67/a12f73c3b116/libcopying build/lib.macosx-10.11-intel-2.7/Bio/Alpon_1_67/a12f73c3b116/lib/python/Bio/Alphabet install_environment.STDOUT DEBUG 2017-11-18 17:04:07,765 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-7/biopython/package_biopython_1on/Bio/Application install_environment.STDOUT DEBUG 2017-11-18 17:04:07,766 intel-2.7/Bio/bgzf.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_bio install_environment.STDOUT DEBUG 2017-11-18 17:04:07,766 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Blast install_environment.STDOUT DEBUG 2017-11-18 17:04:07,767 endencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Blast install_environment.STDOUT DEBUG 2017-11-18 17:04:07,768 10.11-intel-2.7/Bio/Blast/NCBIStandalone.py -> /galaxydir/galaxy/database/dependencies/biopython/1.6_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-ackage_biopython_1_67/a12f73c3b116/lib/copying build/lib.macosx-10.11-intel-2.7/Bio/Bla1_67/a12f73c3b116/lib/python/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,770 rch i386 -arch x86_64 -Wl,-F. -Qunused-arguments -Qunused-arguments build/temp.macosx-10.11-intel-2.creating build/temp.macoscreating build/temp.macosx-10.1cc -DNDEBUG -g -fwrapv -Os -Wall -Wstriy/.venv/lib/python2.7/site-packages/numpy/core/iFrameworks/Python.framework/Versions/2.7/include/python2.7 -tmodule.c -o build/temp.macosx-10.11-intel-2.7/Bio/PDB/QCPSuperimposer/qcprcc -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -Wl,-F. -Qunused-arguments -Qunusacosx-10.11-intel-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.so install_environment.STDOUT DEBUG 2017-11-18 17:04:07,770 10.11-intel-2.7/Bio/Blast/ParseBlastTable.py -> /galaxydir/galaxy/database/dependencies/biopython/1.1_67/a12f73c3b116/lib/pytcopying build/lib.macosx-10.11-ckage_biopython_1_67/a12f73c3b116/lib/pcreating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/CAPS/__init__.p3b116/lib/python/Bio/CAPS tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,771 ed-arguments build/temp.macosx-10.11-intel-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o -o build/lib.mrunning install_lib tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,771 f73c3b116/lib/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,771 10.11-intel-2.7/Bio/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/b116/lib/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,771 endencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/_py3k install_environment.STDOUT DEBUG 2017-11-18 17:04:07,771 copying build/lib.macosx-10.11-intel-2.7/Bio/Cluster/__init__.py -> /galaxydir/galaxy/database/depenencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Cluster tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,771 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12copying build/lib.macosx-package_biopython_1_67/a12f73c3creating /galaxydir/galaxy/database/depcopying build/lib.macosx-10.11-intel-2.7/Bio/_py_1_67/a12f73c3b116/lib/python/Bio/_py3k tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,772 3k/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythoncopying build/lib.macosx-biopython/package_biopython_1_6/Bio/_py3k tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,772 intel-2.7/Bio/_utils.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,772 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Affy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,772 10.11-intel-2.7/Bio/_py3k/_ordereddict.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/7/a12f73c3b116/lib/pythoncopying build/lib.macosx-10.11-biopython_1_67/a12f73c3b116/lib/python/creating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/Affy/__init__.p3b116/lib/python/Bio/Affy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,772 y -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73ccopying build/lib.macosx-hon/package_biopython_1_67/a12fffy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,773 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Align tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,773 7/Bio/Align/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_ install_environment.STDOUT DEBUG 2017-11-18 17:04:07,773 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/codonalign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,773 10.11-intel-2.7/Bio/Affy/CelFile.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt73c3b116/lib/python/Bio/Acreating /galaxydir/galaxy/datacopying build/lib.macosx-10.11-intel-2.biopython_1_67/a12f73c3b116/lib/python/Bio/Aligncopying build/lib.macosx-10.11-intel-2.7/Bio/Align/AlignInfo3c3b116/lib/python/Bio/Align install_environment.STDOUT DEBUG 2017-11-18 17:04:07,773 /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/codonalign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,773 .py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f7creating /galaxydir/galaxAlign/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,774 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-hon/1.67/biopython/package_biopib/python/Bio/Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,774 10.11-intel-2.7/Bio/Align/Applications/__init__.py -> /galaxydir/galaxy/database/dependencies/biopytython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-on/1.67/biopython/package_biopython_1_6/Bio/Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,774 intel-2.7/Bio/Align/Applications/_ClustalOmega.py -> /galaxydir/galaxy/database/dependencies/biopyth7/a12f73c3b116/lib/pythoncopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,774 intel-2.7/Bio/Align/Applications/_Clustalw.py -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,774 intel-2.7/Bio/Align/Applications/_Dialign.py -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,774 intel-2.7/Bio/Align/Applications/_Mafft.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67copying build/lib.macosx-thon/1.67/biopython/package_biolib/python/Bio/Align/Applications install_environment.STDOUT DEBUG 2017-11-18 17:04:07,774 ase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/codonalse/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/codonalign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,775 10.11-intel-2.7/Bio/Align/Applications/_MSAProbs.py -> /galaxydir/galaxy/database/dependencies/biopypython_1_67/a12f73c3b116/copying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12flign/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,775 intel-2.7/Bio/Align/Applications/_Muscle.py -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Acopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7ign/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,775 intel-2.7/Bio/Align/Applications/_Prank.py -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Alcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,775 intel-2.7/Bio/Align/Applications/_Probcons.py -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Align/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,776 intel-2.7/Bio/Align/Generic.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/ppython/Bio/Align tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,776 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/AlignIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,776 intel-2.7/Bio/Align/Applications/_TCoffee.py -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-ackage_biopython_1_67/a12f73c3b116/lib/creating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/AlignIO/__init_73c3b116/lib/python/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:04:07,776 10.11-intel-2.7/Bio/codonalign/codonseq.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67creating /galaxydir/galaxdencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Compass tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,776 _.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12fcopying build/lib.macosx-iopython/package_biopython_1_67Bio/AlignIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,776 intel-2.7/Bio/AlignIO/EmbossIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythoib/python/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:04:07,776 10.11-intel-2.7/Bio/cpairwise2.so -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,777 10.11-intel-2.7/Bio/AlignIO/ClustalIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b/a12f73c3b116/lib/python/copying build/lib.macosx-10.11-n/package_biopython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-intel-2.7/Bio/Alin_1_67/a12f73c3b116/lib/python/Bio/AlignIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,777 gnIO/FastaIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythocopying build/lib.macosx-biopython/package_biopython_1_6/Bio/AlignIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,777 intel-2.7/Bio/AlignIO/NexusIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythonb/python/Bio/AlignIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,777 10.11-intel-2.7/Bio/AlignIO/Interfaces.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/7/a12f73c3b116/lib/pythoncopying build/lib.macosx-10.11-/package_biopython_1_67/a12f73c3b116/licopying build/lib.macosx-10.11-intel-2.7/Bio/Alion_1_67/a12f73c3b116/lib/python/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:04:07,777 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12l install_environment.STDOUT DEBUG 2017-11-18 17:04:07,778 atabase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Crystal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,778 gnIO/PhylipIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythcopying build/lib.macosx-/biopython/package_biopython_1_n/Bio/AlignIO install_environment.STDOUT DEBUG 2017-11-18 17:04:07,778 .67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,778 10.11-intel-2.7/Bio/AlignIO/StockholmIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.6767/a12f73c3b116/lib/pythocreating /galaxydir/galaxy/dataet tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,779 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Alphabcopying build/lib.macosx-iopython/package_biopython_1_67Bio/Alphabet tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,779 intel-2.7/Bio/Alphabet/IUPAC.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython//python/Bio/Alphabet tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,779 10.11-intel-2.7/Bio/Alphabet/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b/a12f73c3b116/lib/python/copying build/lib.macosx-10.11-package_biopython_1_67/a12f73c3b116/libcopying build/lib.macosx-10.11-intel-2.7/Bio/Alpon_1_67/a12f73c3b116/lib/python/Bio/Alphabet tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,779 habet/Reduced.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythcreating /galaxydir/galaxApplication tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,779 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-7/biopython/package_biopython_1on/Bio/Application tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,779 intel-2.7/Bio/bgzf.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,780 10.11-intel-2.7/Bio/Application/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.6_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-opython_1_67/a12f73c3b116/lib/python/Bicreating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/Blast/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,780 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,780 endencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,780 copying build/lib.macosx-10.11-intel-2.7/Bio/Blast/Applications.py -> /galaxydir/galaxy/database/depcopying build/lib.macosx-7/biopython/package_biopython_1on/Bio/Blast install_environment.STDOUT DEBUG 2017-11-18 17:04:07,780 copying build/lib.macosx-10.11-intel-2.7/Bio/Data/CodonTable.py -> /galaxydir/galaxy/database/dependncies/biopython/1.67/biopf73c3b116/lib/python/Bio/Data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,780 intel-2.7/Bio/Blast/NCBIWWW.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/ppython/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,781 10.11-intel-2.7/Bio/Blast/NCBIStandalone.py -> /galaxydir/galaxy/database/dependencies/biopython/1.6_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-ackage_biopython_1_67/a12f73c3b116/lib/copying build/lib.macosx-10.11-intel-2.7/Bio/Bla1_67/a12f73c3b116/lib/python/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,781 st/NCBIXML.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_copying build/lib.macosx-67/biopython/package_biopython_hon/Bio/Blast install_environment.STDOUT DEBUG 2017-11-18 17:04:07,781 7/Bio/DocSQL.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,781 intel-2.7/Bio/Blast/Record.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/paython/Bio/Blast tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,781 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/CAPS install_environment.STDOUT DEBUG 2017-11-18 17:04:07,782 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Emboss tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,782 10.11-intel-2.7/Bio/Blast/ParseBlastTable.py -> /galaxydir/galaxy/database/dependencies/biopython/1.1_67/a12f73c3b116/lib/pytcopying build/lib.macosx-10.11-ckage_biopython_1_67/a12f73c3b116/lib/pcreating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/CAPS/__init__.p3b116/lib/python/Bio/CAPS install_environment.STDOUT DEBUG 2017-11-18 17:04:07,782 .py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Emboss tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,782 y -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73ccreating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Cluster tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,782 dencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Cluster tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,782 copying build/lib.macosx-10.11-intel-2.7/Bio/Cluster/__init__.py -> /galaxydir/galaxy/database/depenencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Cluster tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,783 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/codonalign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,783 copying build/lib.macosx-10.11-intel-2.7/Bio/Cluster/cluster.so -> /galaxydir/galaxy/database/dependcreating /galaxydir/galaxcopying build/lib.macosx-10.11-intel-2.7/Bio/codonalign/__init__.py ->copying build/lib.macosx-10.11-intel-2.7/Bio/codonalign/chisq.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/codonalign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,783 /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/codonalign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,783 copying build/lib.macosx-10.11-intel-2.7/Bio/codonalign/codonalignment.py -> /galaxydir/galaxy/databign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,783 ase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/codonalse/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/codonalign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,784 copying build/lib.macosx-10.11-intel-2.7/Bio/codonalign/codonalphabet.py -> /galaxydir/galaxy/databacopying build/lib.macosx-/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/codonalign tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,784 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Compass tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,784 10.11-intel-2.7/Bio/codonalign/codonseq.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67creating /galaxydir/galaxdencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Compass tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,784 10.11-intel-2.7/Bio/cpairwise2.so -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio install_environment.STDOUT DEBUG 2017-11-18 17:04:07,784 axydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/libncies/biopython/1.67/biopython/package_biopython_1_67/a1f73c3b116/lib/python/Bio/Entrez tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,784 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12l tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,785 atabase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Crystal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,785 .67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,785 copying build/lib.macosx-10.11-intel-2.7/Bio/Compass/__init__.py -> /galaxydir/galaxy/database/depencopying build/lib.macosx-f73c3b116/lib/python/Bio/Crystacopying build/lib.macosx-10.11-intel-2.7/Bio/Crystal/__init__.py -> /galaxydir/galaxy/dcreating /galaxydir/galaxy/database/dependencies/biopython/1copying build/lib.macosx-10.11-intel-2.7/Bio/Data/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,785 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,785 copying build/lib.macosx-10.11-intel-2.7/Bio/Data/IUPACData.py -> /galaxydir/galaxy/database/dependeython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,785 copying build/lib.macosx-10.11-intel-2.7/Bio/Data/CodonTable.py -> /galaxydir/galaxy/database/dependncies/biopython/1.67/biopf73c3b116/lib/python/Bio/Data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,785 7/Bio/DocSQL.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio install_environment.STDOUT DEBUG 2017-11-18 17:04:07,785 f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,785 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Emboss tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,786 .py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Emboss tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,786 copying build/lib.macosx-10.11-intel-2.7/Bio/Data/SCOPData.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12copying build/lib.macosx-10.11-intel-2.creating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/Emboss/__init__copying build/lib.macosx-10.11-intel-2.7/Bio/Emboss/Applications.py -> /gal/python/Bio/Emboss tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,786 copying build/lib.macosx-10.11-intel-2.7/Bio/Emboss/Primer3.py -> /galaxydir/galaxy/database/depende2f73c3b116/lib/python/Bio/Emboss tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,786 copying build/lib.macosx-10.11-intel-2.7/Bio/Emboss/PrimerSearch.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Emboss tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,787 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,787 axydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/libncies/biopython/1.67/biopython/package_biopython_1_67/a1f73c3b116/lib/python/Bio/Entrez tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,787 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/archivearticle.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,787 f73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,787 axy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bicopying build/lib.macosx-iopython/1.67/biopython/package116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,788 intel-2.7/Bio/Entrez/DTDs/archivecustom-models.ent -> /galaxydir/galaxy/database/dependencies/biopyt67/a12f73c3b116/lib/pythocopying build/lib.macosx-10.11-thon/1.67/biopython/package_biopython_1on/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,789 intel-2.7/Bio/Entrez/DTDs/articlemeta.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,790 intel-2.7/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,791 intel-2.7/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,792 intel-2.7/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,793 intel-2.7/Bio/Entrez/DTDs/chars.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt/lib/python/Bio/Entrez/DTcopying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11TDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,795 intel-2.7/Bio/Entrez/DTDs/default-classes.ent -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,796 intel-2.7/Bio/Entrez/DTDs/display.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,797 intel-2.7/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,798 intel-2.7/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,799 intel-2.7/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,800 intel-2.7/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,802 intel-2.7/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,803 intel-2.7/Bio/Entrez/DTDs/einfo.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt/lib/python/Bio/Entrez/DTcopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,805 intel-2.7/Bio/Entrez/DTDs/elink_020122.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,805 intel-2.7/Bio/Entrez/DTDs/eLink_101123.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,806 intel-2.7/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,808 intel-2.7/Bio/Entrez/DTDs/esearch.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,809 intel-2.7/Bio/Entrez/DTDs/eSpell.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopy6/lib/python/Bio/Entrez/Dcopying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,810 intel-2.7/Bio/Entrez/DTDs/eSummary_041029.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11TDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,811 intel-2.7/Bio/Entrez/DTDs/GenBank_General.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-on/1.67/biopython/package_biopython_1_6/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,812 intel-2.7/Bio/Entrez/DTDs/HomoloGene.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/Entrcopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,814 intel-2.7/Bio/Entrez/DTDs/htmltable.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bib116/lib/python/Bio/Entrecopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,815 intel-2.7/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,817 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/isoamsa.ent -> /galaxydir/galaxy/database/dpython_1_67/a12f73c3b116/copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,818 intel-2.7/Bio/Entrez/DTDs/isoamsc.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,822 intel-2.7/Bio/Entrez/DTDs/isoamso.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,822 intel-2.7/Bio/Entrez/DTDs/isobox.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopy6/lib/python/Bio/Entrez/Dcopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,823 intel-2.7/Bio/Entrez/DTDs/isocyr2.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11TDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,823 intel-2.7/Bio/Entrez/DTDs/isogrk1.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,827 ependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,827 10.11-intel-2.7/Bio/Entrez/DTDs/isomscr.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.6_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11TDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,828 intel-2.7/Bio/Entrez/DTDs/isopub.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopy6/lib/python/Bio/Entrez/Dcopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,829 intel-2.7/Bio/Entrez/DTDs/journalmeta.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-on/package_biopython_1_67/a12f73c3b116/s install_environment.STDOUT DEBUG 2017-11-18 17:04:07,832 intel-2.7/Bio/Entrez/DTDs/list.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythlib/python/Bio/Entrez/DTDcopying build/lib.macosx-10.11-on/package_biopython_1_67/a12f73c3b116/s install_environment.STDOUT DEBUG 2017-11-18 17:04:07,832 intel-2.7/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,834 intel-2.7/Bio/Entrez/DTDs/mathmlsetup.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-on/package_biopython_1_67/a12f73c3b116/s install_environment.STDOUT DEBUG 2017-11-18 17:04:07,834 intel-2.7/Bio/Entrez/DTDs/MMDB.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,835 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,835 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /galaxydir/g.67/biopython/package_bioTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,837 B_Features.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythoncopying build/lib.macosx-python/1.67/biopython/package_b6/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,838 intel-2.7/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /galaxydir/galaxy/database/dependencies/biopy_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-iopython/1.67/biopython/package_biopythpython/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,840 intel-2.7/Bio/Entrez/DTDs/mmlalias.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/Entrezcopying build/lib.macosx-10.11-python/package_biopython_1_67/a12f73c3b/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,843 intel-2.7/Bio/Entrez/DTDs/modules.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,843 intel-2.7/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-python/package_biopython_1_67/a12f73c3b/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,846 intel-2.7/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,848 intel-2.7/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-n/1.67/biopython/package_biopython_1_67Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,848 intel-2.7/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,851 intel-2.7/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,851 intel-2.7/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,853 intel-2.7/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-hon/1.67/biopython/package_biopython_1_n/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,857 intel-2.7/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/Entrezcopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,857 intel-2.7/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bib116/lib/python/Bio/Entrecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,860 intel-2.7/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,868 ase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/atabase/dependencies/biopage_biopython_1_67/a12f73c3b116copying build/lib.macosx-10.11-intel-2./package_biopython_1_67/a12f73c3b116/lib/python/copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBn_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,870 10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1_1_67/a12f73c3b116/lib/pycopying build/lib.macosx-10.11-atabase/dependencies/biopython/1.67/bio1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,871 intel-2.7/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-n/1.67/biopython/package_biopython_1_67Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,873 intel-2.7/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-n/1.67/biopython/package_biopython_1_67Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,875 intel-2.7/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-on/1.67/biopython/package_biopython_1_6/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,876 intel-2.7/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,878 intel-2.7/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,879 intel-2.7/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/Entrezcopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,880 intel-2.7/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bib116/lib/python/Bio/Entrecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,882 intel-2.7/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,882 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,884 intel-2.7/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopythona12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,885 atabase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entcopying build/lib.macosx-biopython/1.67/biopython/packagb116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,886 intel-2.7/Bio/Entrez/DTDs/NCBI_Project.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,887 intel-2.7/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,888 intel-2.7/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/Entrezcopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,889 intel-2.7/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,890 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/archivecustom-classes.ent -> /galaxydir/galo/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,890 axy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bicopying build/lib.macosx-iopython/1.67/biopython/package116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,890 10.11-intel-2.7/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /galaxydir/galaxy/database/dependencies/b_biopython_1_67/a12f73c3bcopying build/lib.macosx-10.11-hon/1.67/biopython/package_biopython_1_n/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,890 intel-2.7/Bio/Entrez/DTDs/archivecustom-models.ent -> /galaxydir/galaxy/database/dependencies/biopyt67/a12f73c3b116/lib/pythocopying build/lib.macosx-10.11-thon/1.67/biopython/package_biopython_1on/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,890 intel-2.7/Bio/Entrez/DTDs/archivecustom-modules.ent -> /galaxydir/galaxy/database/dependencies/biopy_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,890 intel-2.7/Bio/Entrez/DTDs/articlemeta.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,890 intel-2.7/Bio/Entrez/DTDs/backmatter.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/Entrcopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,890 intel-2.7/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,891 intel-2.7/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,891 intel-2.7/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,891 intel-2.7/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,891 intel-2.7/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,891 intel-2.7/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-hon/package_biopython_1_67/a12f73c3b116Ds tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,891 intel-2.7/Bio/Entrez/DTDs/chars.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt/lib/python/Bio/Entrez/DTcopying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11TDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,891 intel-2.7/Bio/Entrez/DTDs/common.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopy6/lib/python/Bio/Entrez/Dcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,891 intel-2.7/Bio/Entrez/DTDs/default-classes.ent -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,891 intel-2.7/Bio/Entrez/DTDs/default-mixes.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,892 intel-2.7/Bio/Entrez/DTDs/display.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,892 intel-2.7/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/Entrcopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,892 intel-2.7/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,892 intel-2.7/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/Entrcopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,891 intel-2.7/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/Entrcopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12copying build/lib.macosx-10.11-intel-2.7/Bio/Entcopying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,892 abase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,892 intel-2.7/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,892 intel-2.7/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/Entrcopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,893 intel-2.7/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,893 intel-2.7/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/Entrcopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,893 intel-2.7/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,893 intel-2.7/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/Entrcopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,893 intel-2.7/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,893 intel-2.7/Bio/Entrez/DTDs/egquery.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-hon/package_biopython_1_67/a12f73c3b116Ds tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,893 intel-2.7/Bio/Entrez/DTDs/einfo.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt/lib/python/Bio/Entrez/DTcopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,893 intel-2.7/Bio/Entrez/DTDs/eInfo_020511.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,893 intel-2.7/Bio/Entrez/DTDs/elink_020122.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,893 intel-2.7/Bio/Entrez/DTDs/eLink_090910.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,894 intel-2.7/Bio/Entrez/DTDs/eLink_101123.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,894 intel-2.7/Bio/Entrez/DTDs/EMBL_General.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,894 intel-2.7/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,894 intel-2.7/Bio/Entrez/DTDs/ePost_020511.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,894 intel-2.7/Bio/Entrez/DTDs/esearch.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,894 intel-2.7/Bio/Entrez/DTDs/eSearch_020511.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11TDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,894 intel-2.7/Bio/Entrez/DTDs/eSpell.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopy6/lib/python/Bio/Entrez/Dcopying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,895 intel-2.7/Bio/Entrez/DTDs/esummary-v1.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,895 intel-2.7/Bio/Entrez/DTDs/eSummary_041029.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11TDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,895 intel-2.7/Bio/Entrez/DTDs/format.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopy6/lib/python/Bio/Entrez/Dcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,895 intel-2.7/Bio/Entrez/DTDs/GenBank_General.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-on/1.67/biopython/package_biopython_1_6/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,895 intel-2.7/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopyth7/a12f73c3b116/lib/pythoncopying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,895 intel-2.7/Bio/Entrez/DTDs/HomoloGene.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/Entrcopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,895 intel-2.7/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-opython/package_biopython_1_67/a12f73c3z/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,895 intel-2.7/Bio/Entrez/DTDs/htmltable.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bib116/lib/python/Bio/Entrecopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,895 intel-2.7/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,895 intel-2.7/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/aependencies/biopython/1.67/biopython/package_biolib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,896 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/isoamsa.ent -> /galaxydir/galaxy/database/dpython_1_67/a12f73c3b116/copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,896 intel-2.7/Bio/Entrez/DTDs/isoamsb.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,896 intel-2.7/Bio/Entrez/DTDs/isoamsc.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,896 intel-2.7/Bio/Entrez/DTDs/isoamsn.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,896 intel-2.7/Bio/Entrez/DTDs/isoamso.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,896 intel-2.7/Bio/Entrez/DTDs/isoamsr.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11TDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,896 intel-2.7/Bio/Entrez/DTDs/isobox.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopy6/lib/python/Bio/Entrez/Dcopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,896 intel-2.7/Bio/Entrez/DTDs/isocyr1.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,896 intel-2.7/Bio/Entrez/DTDs/isocyr2.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11TDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,897 intel-2.7/Bio/Entrez/DTDs/isodia.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopy6/lib/python/Bio/Entrez/Dcopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,897 intel-2.7/Bio/Entrez/DTDs/isogrk2.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/isogrk3.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,897 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/isogrk4.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,897 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/isolat1.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,897 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/isolat2.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,897 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/isomfrk.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,897 intel-2.7/Bio/Entrez/DTDs/isogrk1.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,897 ependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,897 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/isomopf.ent -> /galaxydir/galaxy/database/dcopying build/lib.macosx-7/biopython/package_biopython_1on/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,898 10.11-intel-2.7/Bio/Entrez/DTDs/isomscr.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.6_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11TDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,897 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /galaxydir/galaxy/dataon/1.67/biopython/packageiopython_1_67/a12f73c3b116/lib/copying build/lib.macosx-10.11-intel-2.n/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,898 intel-2.7/Bio/Entrez/DTDs/isonum.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopy6/lib/python/Bio/Entrez/Dcopying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11TDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,898 intel-2.7/Bio/Entrez/DTDs/isopub.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopy6/lib/python/Bio/Entrez/Dcopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,898 intel-2.7/Bio/Entrez/DTDs/isotech.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,898 intel-2.7/Bio/Entrez/DTDs/journalmeta.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-on/package_biopython_1_67/a12f73c3b116/s tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,898 intel-2.7/Bio/Entrez/DTDs/link.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythlib/python/Bio/Entrez/DTDcopying build/lib.macosx-10.11-on/package_biopython_1_67/a12f73c3b116/s tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,898 intel-2.7/Bio/Entrez/DTDs/list.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythlib/python/Bio/Entrez/DTDcopying build/lib.macosx-10.11-on/package_biopython_1_67/a12f73c3b116/s tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,898 intel-2.7/Bio/Entrez/DTDs/math.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythlib/python/Bio/Entrez/DTDcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,898 intel-2.7/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,899 intel-2.7/Bio/Entrez/DTDs/mathml2.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,899 intel-2.7/Bio/Entrez/DTDs/mathmlsetup.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-on/package_biopython_1_67/a12f73c3b116/s tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,899 intel-2.7/Bio/Entrez/DTDs/MMDB.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,899 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,899 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /galaxydir/g.67/biopython/package_bioTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,899 intel-2.7/Bio/Entrez/DTDs/MMDB.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythlib/python/Bio/Entrez/DTDcopying build/lib.macosx-10.11-alaxy/database/dependencies/biopython/1python_1_67/a12f73c3b116/lib/python/Bio/Entrez/Dcopying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/MMD_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,899 B_Features.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythoncopying build/lib.macosx-python/1.67/biopython/package_b6/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,899 10.11-intel-2.7/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /galaxydir/galaxy/database/dependencies/bioiopython_1_67/a12f73c3b11copying build/lib.macosx-10.11-thon/1.67/biopython/package_biopython_1on/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,899 intel-2.7/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /galaxydir/galaxy/database/dependencies/biopy_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-iopython/1.67/biopython/package_biopythpython/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,900 intel-2.7/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /galaxydir/galaxy/database/dependencies/bon_1_67/a12f73c3b116/lib/copying build/lib.macosx-10.11-python/package_biopython_1_67/a12f73c3b/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,900 intel-2.7/Bio/Entrez/DTDs/mmlalias.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/Entrezcopying build/lib.macosx-10.11-python/package_biopython_1_67/a12f73c3b/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,900 intel-2.7/Bio/Entrez/DTDs/mmlextra.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/Entrezcopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,900 intel-2.7/Bio/Entrez/DTDs/modules.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,900 atabase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entse/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,900 intel-2.7/Bio/Entrez/DTDs/NCBI_Access.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,900 intel-2.7/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-python/package_biopython_1_67/a12f73c3b/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,900 intel-2.7/Bio/Entrez/DTDs/NCBI_all.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/Entrezcopying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,900 intel-2.7/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,901 intel-2.7/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,901 intel-2.7/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-n/1.67/biopython/package_biopython_1_67Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,901 intel-2.7/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopytho/a12f73c3b116/lib/python/copying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,901 intel-2.7/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,901 intel-2.7/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,901 intel-2.7/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,901 intel-2.7/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,901 intel-2.7/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,902 intel-2.7/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,902 intel-2.7/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-hon/1.67/biopython/package_biopython_1_n/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,902 intel-2.7/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopyt67/a12f73c3b116/lib/pythocopying build/lib.macosx-10.11-python/package_biopython_1_67/a12f73c3b/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,902 intel-2.7/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/Entrezcopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,902 intel-2.7/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-opython/package_biopython_1_67/a12f73c3z/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,902 intel-2.7/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bib116/lib/python/Bio/Entrecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,902 intel-2.7/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,902 intel-2.7/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,902 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,903 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,903 intel-2.7/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,903 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /galaxydir/galaxy/databDTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,903 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /galaxydir/galaxy/dython/1.67/biopython/pack/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,903 7/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythonBio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,903 ase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/atabase/dependencies/biopage_biopython_1_67/a12f73c3b116copying build/lib.macosx-10.11-intel-2./package_biopython_1_67/a12f73c3b116/lib/python/copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBn_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,903 I_GBSeq.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythocopying build/lib.macosx-.67/biopython/package_biopythonthon/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,903 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/Dcopying build/lib.macosx-copying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,904 intel-2.7/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,904 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_General.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,904 10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1_1_67/a12f73c3b116/lib/pycopying build/lib.macosx-10.11-atabase/dependencies/biopython/1.67/bio1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,904 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /galaxydir/galaxy/dpython/package_biopython_copying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,904 intel-2.7/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-n/1.67/biopython/package_biopython_1_67Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,904 intel-2.7/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopytho/a12f73c3b116/lib/python/copying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,904 intel-2.7/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-n/1.67/biopython/package_biopython_1_67Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,904 intel-2.7/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopytho/a12f73c3b116/lib/python/copying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,905 intel-2.7/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-on/1.67/biopython/package_biopython_1_6/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,905 intel-2.7/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopyth7/a12f73c3b116/lib/pythoncopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,905 intel-2.7/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,905 intel-2.7/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,905 intel-2.7/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,905 intel-2.7/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-python/package_biopython_1_67/a12f73c3b/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,905 database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Encopying build/lib.macosx-database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,905 intel-2.7/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/Entrezcopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,906 intel-2.7/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-opython/package_biopython_1_67/a12f73c3z/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,906 intel-2.7/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bib116/lib/python/Bio/Entrecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,906 intel-2.7/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,906 intel-2.7/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,906 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,906 intel-2.7/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-/1.67/biopython/package_biopython_1_67/io/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,906 intel-2.7/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,906 intel-2.7/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopythona12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,907 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /galaxydir/galaxy/drez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,907 atabase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entcopying build/lib.macosx-biopython/1.67/biopython/packagb116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,907 10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /galaxydir/galaxy/database/dependencies/e_biopython_1_67/a12f73c3copying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,907 intel-2.7/Bio/Entrez/DTDs/NCBI_Project.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,907 intel-2.7/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,907 intel-2.7/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,907 intel-2.7/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-python/package_biopython_1_67/a12f73c3b/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,907 intel-2.7/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/Entrezcopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,907 intel-2.7/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,908 intel-2.7/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,908 intel-2.7/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,908 intel-2.7/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,908 rez/DTDs/NCBI_RNA.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,908 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,908 intel-2.7/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/Entrcopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12copying build/lib.macosx-10.11-intel-2.7/Bio/Entcopying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,908 abase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,908 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /galaxydir/galaxy/datbase/dependencies/biopyth_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,908 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_bpython/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,908 7/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,909 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,909 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,909 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,909 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /galaxydir/galaxy/database/dependencies/biopythocopying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,909 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,909 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /galaxydir/galaxy/dataon/1.67/biopython/packageiopython_1_67/a12f73c3b116/lib/copying build/lib.macosx-10.11-intel-2.n/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,909 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /galaxydir/galaxy/drez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,909 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /galaxydir/galaxy/databacopying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,909 atabase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entse/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,910 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /galaxydir/galaxy/databaTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,910 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,910 10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,910 intel-2.7/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,910 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/Dcopying build/lib.macosx-copying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,910 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /galaxydir/galaxy/trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,910 10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,910 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /galaxydir/galaxy/copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,910 database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Encopying build/lib.macosx-database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,911 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /galaxydir/galaxy/daez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,911 10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:07,911 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /galaxydir/galaxy/data73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,912 tabase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrcopying build/lib.macosx-base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12fse/dependencies/biopython/1.67/biopython/package116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,915 intel-2.7/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-/database/dependencies/biopython/1.67/bn_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,918 intel-2.7/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /galaxydir/galaxy/database/dependencies/biopytho/a12f73c3b116/lib/python/copying build/lib.macosx-10.11-atabase/dependencies/biopython/1.67/bio1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,920 intel-2.7/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-database/dependencies/biopython/1.67/bi_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,922 intel-2.7/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /galaxydir/galaxy/database/dependencies/biopythona12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-iopython/1.67/biopython/package_biopythpython/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,924 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /galaxydir/galaxy/database/dependencies/bon_1_67/a12f73c3b116/lib/copying build/lib.macosx-10.11-iopython/1.67/biopython/package_biopythpython/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,925 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /galaxydir/galaxy/database/dependencieython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-s/biopython/1.67/biopython/package_biopib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,928 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /galaxydir/galaxy/database/dependencieython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-s/biopython/1.67/biopython/package_biopib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,930 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /galaxydir/galaxy/database/dependencieython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-s/biopython/1.67/biopython/package_biopib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,934 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /galaxydir/galaxy/database/dependencieython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-database/dependencies/biopython/1.67/bi_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,935 intel-2.7/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /galaxydir/galaxy/database/dependencies/biopythona12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-ython/1.67/biopython/package_biopython_hon/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,936 intel-2.7/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /galaxydir/galaxy/database/dependencies/biop1_67/a12f73c3b116/lib/pytcopying build/lib.macosx-10.11-hon/package_biopython_1_67/a12f73c3b116Ds install_environment.STDOUT DEBUG 2017-11-18 17:04:07,937 intel-2.7/Bio/Entrez/DTDs/NSE.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythoib/python/Bio/Entrez/DTDscopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,938 intel-2.7/Bio/Entrez/DTDs/OMSSA.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt/lib/python/Bio/Entrez/DTcopying build/lib.macosx-10.11-opython/package_biopython_1_67/a12f73c3z/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,939 intel-2.7/Bio/Entrez/DTDs/para.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythlib/python/Bio/Entrez/DTDcopying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,940 intel-2.7/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11TDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,941 intel-2.7/Bio/Entrez/DTDs/PIR_General.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,943 intel-2.7/Bio/Entrez/DTDs/pmc-1.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt/lib/python/Bio/Entrez/DTcopying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,943 intel-2.7/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,944 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/pubmed_020114.dtd -> /galaxydir/galaxy/datahon/package_biopython_1_6copying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,946 intel-2.7/Bio/Entrez/DTDs/pubmed_090101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,948 intel-2.7/Bio/Entrez/DTDs/pubmed_100301.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,949 intel-2.7/Bio/Entrez/DTDs/pubmed_120101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,949 intel-2.7/Bio/Entrez/DTDs/pubmed_130501.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,951 intel-2.7/Bio/Entrez/DTDs/pubmed_150101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,952 intel-2.7/Bio/Entrez/DTDs/section.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,953 intel-2.7/Bio/Entrez/DTDs/SP_General.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-hon/package_biopython_1_67/a12f73c3b116Ds install_environment.STDOUT DEBUG 2017-11-18 17:04:07,954 intel-2.7/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,955 intel-2.7/Bio/Entrez/Parser.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/ppython/Bio/Entrez install_environment.STDOUT DEBUG 2017-11-18 17:04:07,956 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/ExPASy install_environment.STDOUT DEBUG 2017-11-18 17:04:07,956 .py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f7copying build/lib.macosx-thon/package_biopython_1_67/a12ExPASy install_environment.STDOUT DEBUG 2017-11-18 17:04:07,957 intel-2.7/Bio/ExPASy/Prodoc.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/ppython/Bio/ExPASy install_environment.STDOUT DEBUG 2017-11-18 17:04:07,958 ASy/Prosite.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythoncopying build/lib.macosx-biopython/package_biopython_1_6/Bio/ExPASy install_environment.STDOUT DEBUG 2017-11-18 17:04:07,959 intel-2.7/Bio/File.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_bio install_environment.STDOUT DEBUG 2017-11-18 17:04:07,959 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/FSSP install_environment.STDOUT DEBUG 2017-11-18 17:04:07,960 y -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73ccopying build/lib.macosx-thon/package_biopython_1_67/a12FSSP install_environment.STDOUT DEBUG 2017-11-18 17:04:07,960 intel-2.7/Bio/FSSP/FSSPTools.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython//python/Bio/FSSP install_environment.STDOUT DEBUG 2017-11-18 17:04:07,961 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA install_environment.STDOUT DEBUG 2017-11-18 17:04:07,961 -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3bcreating /galaxydir/galaxGA/Crossover install_environment.STDOUT DEBUG 2017-11-18 17:04:07,962 10.11-intel-2.7/Bio/GA/Crossover/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.1_67/a12f73c3b116/lib/pytcopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1sover install_environment.STDOUT DEBUG 2017-11-18 17:04:07,964 intel-2.7/Bio/GA/Crossover/GeneralPoint.py -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/GAcopying build/lib.macosx-10.11-hon/package_biopython_1_67/a12f73c3b116ver install_environment.STDOUT DEBUG 2017-11-18 17:04:07,965 intel-2.7/Bio/GA/Crossover/TwoPoint.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/GA/Crocopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1sover install_environment.STDOUT DEBUG 2017-11-18 17:04:07,965 intel-2.7/Bio/GA/Evolver.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/packhon/Bio/GA install_environment.STDOUT DEBUG 2017-11-18 17:04:07,966 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Mutation install_environment.STDOUT DEBUG 2017-11-18 17:04:07,967 nit__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Mutation install_environment.STDOUT DEBUG 2017-11-18 17:04:07,967 copying build/lib.macosx-10.11-intel-2.7/Bio/GA/Mutation/General.py -> /galaxydir/galaxy/database/de/python/Bio/GA/Mutation install_environment.STDOUT DEBUG 2017-11-18 17:04:07,968 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Mutatcopying build/lib.macosx-on/package_biopython_1_67/a12f7 install_environment.STDOUT DEBUG 2017-11-18 17:04:07,969 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Repcopying build/lib.macosx-10.11-intel-2.7/Bio/GA/Repair/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Repair install_environment.STDOUT DEBUG 2017-11-18 17:04:07,970 copying build/lib.macosx-10.11-intel-2.7/Bio/GA/Repair/Stabilizing.py -> /galaxydir/galaxy/database/creating /galaxydir/galaxGA/Selection install_environment.STDOUT DEBUG 2017-11-18 17:04:07,972 10.11-intel-2.7/Bio/GA/Selection/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.1_67/a12f73c3b116/lib/pytcopying build/lib.macosx-10.11-python/package_biopython_1_67/a12f73c3bection install_environment.STDOUT DEBUG 2017-11-18 17:04:07,973 intel-2.7/Bio/GA/Selection/Diversity.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bib116/lib/python/Bio/GA/Secopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fA/Selection install_environment.STDOUT DEBUG 2017-11-18 17:04:07,974 intel-2.7/Bio/GA/Selection/Tournament.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/GA/Screating /galaxydir/galaxy/datak install_environment.STDOUT DEBUG 2017-11-18 17:04:07,976 10.11-intel-2.7/Bio/GenBank/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bia12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-package_biopython_1_67/a12f73c3b116/libcopying build/lib.macosx-10.11-intel-2.7/Bio/Genn_1_67/a12f73c3b116/lib/python/Bio/GenBank install_environment.STDOUT DEBUG 2017-11-18 17:04:07,978 10.11-intel-2.7/Bio/GenBank/utils.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyf73c3b116/lib/python/Bio/creating /galaxydir/galaxy/datacopying build/lib.macosx-10.11-intel-2.opython_1_67/a12f73c3b116/lib/python/Bio/Geo install_environment.STDOUT DEBUG 2017-11-18 17:04:07,980 10.11-intel-2.7/Bio/Geo/Record.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythoc3b116/lib/python/Bio/Geocreating /galaxydir/galaxy/datacs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,980 10.11-intel-2.7/Bio/Graphics/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics install_environment.STDOUT DEBUG 2017-11-18 17:04:07,981 copying build/lib.macosx-10.11-intel-2.7/Bio/Graphics/BasicChromosome.py -> /galaxydir/galaxy/datababiopython/package_biopythphics install_environment.STDOUT DEBUG 2017-11-18 17:04:07,982 phics/ColorSpiral.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biocopying build/lib.macosx-7/biopython/package_biopython_1on/Bio/Graphics install_environment.STDOUT DEBUG 2017-11-18 17:04:07,983 intel-2.7/Bio/Graphics/DisplayRepresentation.py -> /galaxydir/galaxy/database/dependencies/biopythona12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-python/package_biopython_1_67/a12f73c3bcs install_environment.STDOUT DEBUG 2017-11-18 17:04:07,985 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphicopying build/lib.macosx-opython/1.67/biopython/package_16/lib/python/Bio/Graphics/GenomeDiagracopying build/lib.macosx-10.11-intel-2.7/Bio/Grapython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Grcopying build/lib.macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram/_Circul67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDiagram install_environment.STDOUT DEBUG 2017-11-18 17:04:07,985 10.11-intel-2.7/Bio/Graphics/GenomeDiagram/_Colors.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDiagram install_environment.STDOUT DEBUG 2017-11-18 17:04:07,986 intel-2.7/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /galaxydir/galaxy/database/dependencies/biopyt/database/dependencies/bickage_biopython_1_67/a12f73c3b1meDiagram install_environment.STDOUT DEBUG 2017-11-18 17:04:07,987 7/Bio/Graphics/GenomeDiagram/_Feature.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b/python/Bio/Graphics/Genocopying build/lib.macosx-10.11-thon/1.67/biopython/package_biopython_1on/Bio/Graphics/GenomeDiagram install_environment.STDOUT DEBUG 2017-11-18 17:04:07,988 intel-2.7/Bio/Graphics/GenomeDiagram/_Graph.py -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-on/1.67/biopython/package_biopython_1_6/Bio/Graphics/GenomeDiagram install_environment.STDOUT DEBUG 2017-11-18 17:04:07,989 intel-2.7/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /galaxydir/galaxy/database/dependencies/bio_1_67/a12f73c3b116/lib/pycopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Graphics/GenomeDiagram install_environment.STDOUT DEBUG 2017-11-18 17:04:07,990 intel-2.7/Bio/Graphics/KGML_vis.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythlib/python/Bio/Graphics install_environment.STDOUT DEBUG 2017-11-18 17:04:07,991 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/HMM install_environment.STDOUT DEBUG 2017-11-18 17:04:07,991 -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3copying build/lib.macosx-.67/biopython/package_biopythonthon/Bio/HMM install_environment.STDOUT DEBUG 2017-11-18 17:04:07,992 intel-2.7/Bio/HMM/MarkovModel.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythonb/python/Bio/HMM install_environment.STDOUT DEBUG 2017-11-18 17:04:07,993 /Trainer.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_copying build/lib.macosx-thon/package_biopython_1_67/a12HMM install_environment.STDOUT DEBUG 2017-11-18 17:04:07,993 intel-2.7/Bio/Index.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio install_environment.STDOUT DEBUG 2017-11-18 17:04:07,994 endencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KDTree install_environment.STDOUT DEBUG 2017-11-18 17:04:07,995 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KDTree install_environment.STDOUT DEBUG 2017-11-18 17:04:07,998 10.11-intel-2.7/Bio/KDTree/KDTree.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyf73c3b116/lib/python/Bio/creating /galaxydir/galaxy/datacopying build/lib.macosx-10.11-intel-2.iopython_1_67/a12f73c3b116/lib/python/Bio/KEGG install_environment.STDOUT DEBUG 2017-11-18 17:04:08,000 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-.67/biopython/package_biopythoncreating /galaxydir/galaxy/database/depcopying build/lib.macosx-10.11-intel-2.7/Bio/KEGpython_1_67/a12f73c3b116/lib/python/Bio/KEGG/Enzyme install_environment.STDOUT DEBUG 2017-11-18 17:04:08,003 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-dependencies/biopython/1.67/bio1_67/a12f73c3b116/lib/python/Bio/KEGG/Kcopying build/lib.macosx-10.11-intel-2.7/Bio/KEGf73c3b116/lib/python/Bio/KEGG/Map install_environment.STDOUT DEBUG 2017-11-18 17:04:08,006 10.11-intel-2.7/Bio/KEGG/Map/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b/a12f73c3b116/lib/python/copying build/lib.macosx-10.11-thon/1.67/biopython/package_biopython_1endencies/biopython/1.67/biopython/package_biopyb/python/Bio install_environment.STDOUT DEBUG 2017-11-18 17:04:08,007 intel-2.7/Bio/MarkovModel.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/pacthon/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,013 tabase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrcopying build/lib.macosx-base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12fse/dependencies/biopython/1.67/biopython/package116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,013 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /galaxydir/galaxy/databa_biopython_1_67/a12f73c3bcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,013 intel-2.7/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,013 intel-2.7/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-/database/dependencies/biopython/1.67/bn_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,013 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /galaxydir/galaxyiopython/package_biopythocopying build/lib.macosx-10.11-n/1.67/biopython/package_biopython_1_67Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,013 intel-2.7/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,013 intel-2.7/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /galaxydir/galaxy/database/dependencies/biopytho/a12f73c3b116/lib/python/copying build/lib.macosx-10.11-atabase/dependencies/biopython/1.67/bio1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,013 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /galaxydir/galaxy/dpython/package_biopython_copying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:08,014 Entropy.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_6creating /galaxydir/galaxcopying build/lib.macosx-10.11-intel-2.7/Bio/Medline/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Medline tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,014 intel-2.7/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,014 intel-2.7/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-database/dependencies/biopython/1.67/bi_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,014 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /galaxydir/galaxy/opython/package_biopythoncopying build/lib.macosx-10.11-/1.67/biopython/package_biopython_1_67/io/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,014 intel-2.7/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /galaxydir/galaxy/database/dependencies/biopythona12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-iopython/1.67/biopython/package_biopythpython/Bio/Entrez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:08,014 f73c3b116/lib/python/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,014 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /galaxydir/galaxy/database/dependencies/bon_1_67/a12f73c3b116/lib/copying build/lib.macosx-10.11-iopython/1.67/biopython/package_biopythpython/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,015 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /galaxydir/galaxy/database/dependencies/bon_1_67/a12f73c3b116/lib/copying build/lib.macosx-10.11-iopython/1.67/biopython/package_biopythpython/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,015 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /galaxydir/galaxy/database/dependencies/bon_1_67/a12f73c3b116/lib/copying build/lib.macosx-10.11-s/biopython/1.67/biopython/package_biopib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,015 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /galaxydir/galaxy/database/dependencieython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-s/biopython/1.67/biopython/package_biopib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,015 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /galaxydir/galaxy/database/dependencieython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-s/biopython/1.67/biopython/package_biopib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,015 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /galaxydir/galaxy/database/dependencieython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-s/biopython/1.67/biopython/package_biopib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,015 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /galaxydir/galaxy/database/dependencieython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-s/biopython/1.67/biopython/package_biopib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,015 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /galaxydir/galaxy/database/dependencieython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-s/biopython/1.67/biopython/package_biopib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,015 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /galaxydir/galaxy/database/dependencieython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-s/biopython/1.67/biopython/package_biopib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,015 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,015 intel-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /galaxydir/galaxy/database/dependencieython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-database/dependencies/biopython/1.67/bi_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,016 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /galaxydir/galaxy/opython/package_biopythoncopying build/lib.macosx-10.11-/1.67/biopython/package_biopython_1_67/io/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,016 intel-2.7/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /galaxydir/galaxy/database/dependencies/biopythona12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-ython/1.67/biopython/package_biopython_hon/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,016 intel-2.7/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /galaxydir/galaxy/database/dependencies/biop1_67/a12f73c3b116/lib/pytcopying build/lib.macosx-10.11-ython/1.67/biopython/package_biopython_hon/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,016 intel-2.7/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /galaxydir/galaxy/database/dependencies/biop1_67/a12f73c3b116/lib/pytcopying build/lib.macosx-10.11-hon/package_biopython_1_67/a12f73c3b116Ds tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,016 intel-2.7/Bio/Entrez/DTDs/notat.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt/lib/python/Bio/Entrez/DTcopying build/lib.macosx-10.11-n/package_biopython_1_67/a12f73c3b116/l tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,016 intel-2.7/Bio/Entrez/DTDs/NSE.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythoib/python/Bio/Entrez/DTDscopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,016 intel-2.7/Bio/Entrez/DTDs/NSE.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-hon/package_biopython_1_67/a12f73c3b116Ds tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,017 intel-2.7/Bio/Entrez/DTDs/OMSSA.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt/lib/python/Bio/Entrez/DTcopying build/lib.macosx-10.11-opython/package_biopython_1_67/a12f73c3z/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,017 intel-2.7/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bib116/lib/python/Bio/Entrecopying build/lib.macosx-10.11-on/package_biopython_1_67/a12f73c3b116/s tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,017 intel-2.7/Bio/Entrez/DTDs/para.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythlib/python/Bio/Entrez/DTDcopying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,017 intel-2.7/Bio/Entrez/DTDs/PDB_General.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,017 intel-2.7/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11TDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,017 intel-2.7/Bio/Entrez/DTDs/phrase.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopy6/lib/python/Bio/Entrez/Dcopying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,017 intel-2.7/Bio/Entrez/DTDs/PIR_General.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,017 intel-2.7/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-hon/package_biopython_1_67/a12f73c3b116Ds tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,017 intel-2.7/Bio/Entrez/DTDs/pmc-1.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt/lib/python/Bio/Entrez/DTcopying build/lib.macosx-10.11-biopython/package_biopython_1_67/a12f73rez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,018 intel-2.7/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,018 intel-2.7/Bio/Entrez/DTDs/PRF_General.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/c3b116/lib/python/Bio/Entcopying build/lib.macosx-10.11-base/dependencies/biopython/1.67/biopyt7/a12f73c3b116/lib/python/Bio/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,018 copying build/lib.macosx-10.11-intel-2.7/Bio/Entrez/DTDs/pubmed_020114.dtd -> /galaxydir/galaxy/datahon/package_biopython_1_6copying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,018 intel-2.7/Bio/Entrez/DTDs/pubmed_080101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,018 intel-2.7/Bio/Entrez/DTDs/pubmed_090101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,018 intel-2.7/Bio/Entrez/DTDs/pubmed_100101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,018 intel-2.7/Bio/Entrez/DTDs/pubmed_100301.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,018 intel-2.7/Bio/Entrez/DTDs/pubmed_110101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,018 intel-2.7/Bio/Entrez/DTDs/pubmed_120101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,019 intel-2.7/Bio/Entrez/DTDs/pubmed_130101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,019 intel-2.7/Bio/Entrez/DTDs/pubmed_130501.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,019 intel-2.7/Bio/Entrez/DTDs/pubmed_140101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fntrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,019 intel-2.7/Bio/Entrez/DTDs/pubmed_150101.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Ecopying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,019 intel-2.7/Bio/Entrez/DTDs/references.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/Entrcopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,019 intel-2.7/Bio/Entrez/DTDs/section.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/Entrez/copying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cez/DTDs install_environment.STDOUT DEBUG 2017-11-18 17:04:08,019 10.11-intel-2.7/Bio/motifs/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biocopying build/lib.macosx-copying build/lib.macosx-10.11-thon/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,019 intel-2.7/Bio/Entrez/DTDs/SP_General.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/Entrcopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,020 intel-2.7/Bio/Entrez/DTDs/SP_General.mod.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-hon/package_biopython_1_67/a12f73c3b116Ds tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,020 intel-2.7/Bio/Entrez/DTDs/taxon.dtd -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt/lib/python/Bio/Entrez/DTcopying build/lib.macosx-10.11-.67/biopython/package_biopython_1_67/a1/Entrez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,020 intel-2.7/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7trez/DTDs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,020 intel-2.7/Bio/Entrez/Parser.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/ppython/Bio/Entrez tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,020 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/ExPASy install_environment.STDOUT DEBUG 2017-11-18 17:04:08,020 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/jaspar tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,020 intel-2.7/Bio/Entrez/DTDs/xmlspecchars.ent -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Encopying build/lib.macosx-10.11-ackage_biopython_1_67/a12f73c3b116/lib/creating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/ExPASy/__init__3c3b116/lib/python/Bio/ExPASy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,021 .py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f7copying build/lib.macosx-thon/package_biopython_1_67/a12ExPASy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,021 intel-2.7/Bio/ExPASy/Prodoc.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/ppython/Bio/ExPASy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,021 10.11-intel-2.7/Bio/ExPASy/Enzyme.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyf73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-ackage_biopython_1_67/a12f73c3b116/lib/copying build/lib.macosx-10.11-intel-2.7/Bio/ExP_1_67/a12f73c3b116/lib/python/Bio/ExPASy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,021 ASy/Prosite.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythoncopying build/lib.macosx-biopython/package_biopython_1_6/Bio/ExPASy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,021 intel-2.7/Bio/File.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,021 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/FSSP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,021 10.11-intel-2.7/Bio/ExPASy/ScanProsite.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/7/a12f73c3b116/lib/pythoncopying build/lib.macosx-10.11-opython_1_67/a12f73c3b116/lib/python/Bicreating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/FSSP/__init__.p3b116/lib/python/Bio/FSSP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,021 y -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73ccopying build/lib.macosx-thon/package_biopython_1_67/a12FSSP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,021 intel-2.7/Bio/FSSP/FSSPTools.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython//python/Bio/FSSP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,022 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,022 10.11-intel-2.7/Bio/FSSP/fssp_rec.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyf73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-package_biopython_1_67/a12f73c3b116/libcreating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/GA/__init__.py 116/lib/python/Bio/GA tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,022 -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3bcreating /galaxydir/galaxGA/Crossover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,022 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-67/biopython/package_biopython_hon/Bio/GA/Crossover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,022 10.11-intel-2.7/Bio/GA/Crossover/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.1_67/a12f73c3b116/lib/pytcopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1sover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,022 intel-2.7/Bio/GA/Crossover/General.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/GA/Croscopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7/Crossover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,022 intel-2.7/Bio/GA/Crossover/GeneralPoint.py -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/GAcopying build/lib.macosx-10.11-hon/package_biopython_1_67/a12f73c3b116ver tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,022 intel-2.7/Bio/GA/Crossover/Point.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt/lib/python/Bio/GA/Crossocopying build/lib.macosx-10.11-python/package_biopython_1_67/a12f73c3bssover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,022 intel-2.7/Bio/GA/Crossover/TwoPoint.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/GA/Crocopying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1sover tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,022 intel-2.7/Bio/GA/Evolver.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/packhon/Bio/GA tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,023 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Mutation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,023 nit__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Mutation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,023 copying build/lib.macosx-10.11-intel-2.7/Bio/GA/Mutation/General.py -> /galaxydir/galaxy/database/de/python/Bio/GA/Mutation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,023 intel-2.7/Bio/GA/Crossover/Uniform.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/GA/Croscopying build/lib.macosx-10.11-age_biopython_1_67/a12f73c3b116/lib/pytcreating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/GA/Mutation/__ipendencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/libcopying build/lib.macosx-10.11-intel-2.7/Bio/GA/Mutation/Simple.py -> /galaxydir/galaxy/databaion tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,023 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Mutatcopying build/lib.macosx-on/package_biopython_1_67/a12f7 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,023 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Repcopying build/lib.macosx-10.11-intel-2.7/Bio/GA/Repair/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Repair tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,023 10.11-intel-2.7/Bio/GA/Organism.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyth3c3b116/lib/python/Bio/GAcreating /galaxydir/galaxy/dataair install_environment.STDOUT DEBUG 2017-11-18 17:04:08,023 7/Bio/motifs/jaspar/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/copying build/lib.macosx-copying build/lib.macosx-10.11-kage_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs install_environment.STDOUT DEBUG 2017-11-18 17:04:08,023 10.11-intel-2.7/Bio/motifs/matrix.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,024 dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Repair tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,024 copying build/lib.macosx-10.11-intel-2.7/Bio/GA/Repair/Stabilizing.py -> /galaxydir/galaxy/database/creating /galaxydir/galaxGA/Selection tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,024 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-67/biopython/package_biopython_hon/Bio/GA/Selection tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,024 10.11-intel-2.7/Bio/GA/Selection/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.1_67/a12f73c3b116/lib/pytcopying build/lib.macosx-10.11-python/package_biopython_1_67/a12f73c3bection tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,024 intel-2.7/Bio/GA/Selection/Abstract.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/GA/Selcopying build/lib.macosx-10.11-opython/package_biopython_1_67/a12f73c3lection tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,024 intel-2.7/Bio/GA/Selection/Diversity.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bib116/lib/python/Bio/GA/Secopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fA/Selection tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,024 intel-2.7/Bio/GA/Selection/RouletteWheel.py -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Gcopying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73celection tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,025 intel-2.7/Bio/GA/Selection/Tournament.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/GA/Screating /galaxydir/galaxy/datak tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,025 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GenBancopying build/lib.macosx-opython/package_biopython_1_67/io/GenBank tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,025 intel-2.7/Bio/GenBank/Record.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython//python/Bio/GenBank tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,025 10.11-intel-2.7/Bio/GenBank/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bia12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-package_biopython_1_67/a12f73c3b116/libcopying build/lib.macosx-10.11-intel-2.7/Bio/Genn_1_67/a12f73c3b116/lib/python/Bio/GenBank tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,025 Bank/Scanner.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythocopying build/lib.macosx-thon/package_biopython_1_67/a12GenBank tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,025 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Geo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,025 10.11-intel-2.7/Bio/GenBank/utils.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyf73c3b116/lib/python/Bio/creating /galaxydir/galaxy/datacopying build/lib.macosx-10.11-intel-2.opython_1_67/a12f73c3b116/lib/python/Bio/Geo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,025 7/Bio/Geo/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_bicopying build/lib.macosx-n/package_biopython_1_67/a12f73 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,025 10.11-intel-2.7/Bio/Geo/Record.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythoc3b116/lib/python/Bio/Geocreating /galaxydir/galaxy/datacs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,025 10.11-intel-2.7/Bio/Graphics/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,026 copying build/lib.macosx-10.11-intel-2.7/Bio/Graphics/BasicChromosome.py -> /galaxydir/galaxy/datababiopython/package_biopythphics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,026 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphicopying build/lib.macosx-se/dependencies/biopython/1.67/on_1_67/a12f73c3b116/lib/python/Bio/Gracopying build/lib.macosx-10.11-intel-2.7/Bio/Grapython_1_67/a12f73c3b116/lib/python/Bio/Graphics install_environment.STDOUT DEBUG 2017-11-18 17:04:08,026 intel-2.7/Bio/motifs/meme.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/paccopying build/lib.macosx-iopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,026 phics/ColorSpiral.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biocopying build/lib.macosx-7/biopython/package_biopython_1on/Bio/Graphics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,026 10.11-intel-2.7/Bio/Graphics/Comparative.py -> /galaxydir/galaxy/database/dependencies/biopython/1.6_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-/1.67/biopython/package_biopython_1_67/io/Graphics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,026 intel-2.7/Bio/Graphics/DisplayRepresentation.py -> /galaxydir/galaxy/database/dependencies/biopythona12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-python/package_biopython_1_67/a12f73c3bcs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,026 intel-2.7/Bio/Graphics/Distribution.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/Graphicreating /galaxydir/galaxy/datacs/GenomeDiagram install_environment.STDOUT DEBUG 2017-11-18 17:04:08,026 10.11-intel-2.7/Bio/motifs/transfac.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio12f73c3b116/lib/python/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,027 10.11-intel-2.7/Bio/Graphics/GenomeDiagram/__init__.py -> /galaxydir/galaxy/database/dependencies/bibiopython_1_67/a12f73c3b1m tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,027 phics/GenomeDiagram/_AbstractDrawer.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bioaphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,027 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphicopying build/lib.macosx-opython/1.67/biopython/package_16/lib/python/Bio/Graphics/GenomeDiagracopying build/lib.macosx-10.11-intel-2.7/Bio/Grapython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Grcopying build/lib.macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram/_Circul67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,027 10.11-intel-2.7/Bio/Graphics/GenomeDiagram/_Colors.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,027 arDrawer.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_copying build/lib.macosx-copying build/lib.macosx-10.11-hon/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,027 intel-2.7/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /galaxydir/galaxy/database/dependencies/biopyt/database/dependencies/bickage_biopython_1_67/a12f73c3b1meDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,027 copying build/lib.macosx-10.11-intel-2.7/Bio/Graphics/GenomeDiagram/_Diagram.py -> /galaxydir/galaxyopython/1.67/biopython/pa16/lib/python/Bio/Graphics/Genocopying build/lib.macosx-10.11-intel-2.iopython/package_biopython_1_67/a12f73c3b116/libmeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,027 7/Bio/Graphics/GenomeDiagram/_Feature.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b/python/Bio/Graphics/Genocopying build/lib.macosx-10.11-thon/1.67/biopython/package_biopython_1on/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,028 intel-2.7/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /galaxydir/galaxy/database/dependencies/biopy_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,028 intel-2.7/Bio/Graphics/GenomeDiagram/_Graph.py -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-on/1.67/biopython/package_biopython_1_6/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,028 intel-2.7/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /galaxydir/galaxy/database/dependencies/biopyth7/a12f73c3b116/lib/pythoncopying build/lib.macosx-10.11-python/1.67/biopython/package_biopythonthon/Bio/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,028 intel-2.7/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /galaxydir/galaxy/database/dependencies/bio_1_67/a12f73c3b116/lib/pycopying build/lib.macosx-10.11-1.67/biopython/package_biopython_1_67/ao/Graphics/GenomeDiagram tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,028 intel-2.7/Bio/Graphics/KGML_vis.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythlib/python/Bio/Graphics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,028 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/HMM tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,028 intel-2.7/Bio/Graphics/GenomeDiagram/_Track.py -> /galaxydir/galaxy/database/dependencies/biopython/12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-on/package_biopython_1_67/a12f73c3b116/creating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/HMM/__init__.pyb116/lib/python/Bio/HMM tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,028 -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3copying build/lib.macosx-.67/biopython/package_biopythonthon/Bio/HMM tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,028 intel-2.7/Bio/HMM/MarkovModel.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythonb/python/Bio/HMM tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,028 10.11-intel-2.7/Bio/HMM/DynamicProgramming.py -> /galaxydir/galaxy/database/dependencies/biopython/1_1_67/a12f73c3b116/lib/pycopying build/lib.macosx-10.11-/package_biopython_1_67/a12f73c3b116/licopying build/lib.macosx-10.11-intel-2.7/Bio/HMM67/a12f73c3b116/lib/python/Bio/HMM tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,028 /Trainer.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_copying build/lib.macosx-thon/package_biopython_1_67/a12HMM tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,028 intel-2.7/Bio/Index.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,029 10.11-intel-2.7/Bio/HMM/Utilities.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyf73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-creating /galaxydir/galaxy/database/depcopying build/lib.macosx-10.11-intel-2.7/Bio/KDTree/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KDTree tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,029 endencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KDTree tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,029 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KDTree tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,029 copying build/lib.macosx-10.11-intel-2.7/Bio/KDTree/_CKDTree.so -> /galaxydir/galaxy/database/dependcopying build/lib.macosx-thon/package_biopython_1_67/a12KDTree tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,029 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KEGG tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,029 10.11-intel-2.7/Bio/KDTree/KDTree.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyf73c3b116/lib/python/Bio/creating /galaxydir/galaxy/datacopying build/lib.macosx-10.11-intel-2.iopython_1_67/a12f73c3b116/lib/python/Bio/KEGG tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,029 7/Bio/KEGG/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_bcreating /galaxydir/galaxKEGG/Compound tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,029 10.11-intel-2.7/Bio/KEGG/Compound/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1_1_67/a12f73c3b116/lib/python/Bio/KEGG/Compound tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,029 endencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KEGG/Enzyme tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,029 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-.67/biopython/package_biopythoncreating /galaxydir/galaxy/database/depcopying build/lib.macosx-10.11-intel-2.7/Bio/KEGpython_1_67/a12f73c3b116/lib/python/Bio/KEGG/Enzyme tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,029 G/Enzyme/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biocreating /galaxydir/galaxKEGG/KGML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,029 10.11-intel-2.7/Bio/KEGG/KGML/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KEGG/KGML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,030 copying build/lib.macosx-10.11-intel-2.7/Bio/KEGG/KGML/KGML_parser.py -> /galaxydir/galaxy/database/python/package_biopython_GML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,030 G/KGML/KGML_pathway.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KEGG/KGML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,030 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-dependencies/biopython/1.67/bio1_67/a12f73c3b116/lib/python/Bio/KEGG/Kcopying build/lib.macosx-10.11-intel-2.7/Bio/KEGf73c3b116/lib/python/Bio/KEGG/Map tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,030 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12copying build/lib.macosx-iopython/package_biopython_1_67Bio/KEGG/Map tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,030 intel-2.7/Bio/KEGG/REST.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KEGG tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,030 copying build/lib.macosx-10.11-intel-2.7/Bio/kNN.py -> /galaxydir/galaxy/database/dependencies/biopy_67/a12f73c3b116/lib/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,031 10.11-intel-2.7/Bio/KEGG/Map/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b/a12f73c3b116/lib/python/copying build/lib.macosx-10.11-thon/1.67/biopython/package_biopython_1endencies/biopython/1.67/biopython/package_biopyb/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,031 intel-2.7/Bio/MarkovModel.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/pacthon/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,031 copying build/lib.macosx-10.11-intel-2.7/Bio/LogisticRegression.py -> /galaxydir/galaxy/database/depthon_1_67/a12f73c3b116/licopying build/lib.macosx-10.11-kage_biopython_1_67/a12f73c3b116/lib/pycopying build/lib.macosx-10.11-intel-2.7/Bio/Max7/a12f73c3b116/lib/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,031 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Medline tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,031 Entropy.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_6creating /galaxydir/galaxcopying build/lib.macosx-10.11-intel-2.7/Bio/Medline/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Medline tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,031 f73c3b116/lib/python/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,031 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12copying build/lib.macosx-python/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,031 10.11-intel-2.7/Bio/motifs/_pwm.so -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,031 copying build/lib.macosx-10.11-intel-2.7/Bio/motifs/alignace.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,031 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,031 intel-2.7/Bio/motifs/applications/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,032 10.11-intel-2.7/Bio/motifs/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biocopying build/lib.macosx-copying build/lib.macosx-10.11-thon/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,032 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/jaspar tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,032 copying build/lib.macosx-10.11-intel-2.7/Bio/motifs/applications/_xxmotif.py -> /galaxydir/galaxy/database/dependencies/biopycreating /galaxydir/galaxy/datacopying build/lib.macosx-10.11-intel-2.package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/jaspar install_environment.STDOUT DEBUG 2017-11-18 17:04:08,032 7/Bio/NaiveBayes.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopcreating /galaxydir/galax/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,032 10.11-intel-2.7/Bio/motifs/jaspar/db.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/jaspar tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,032 7/Bio/motifs/jaspar/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/copying build/lib.macosx-copying build/lib.macosx-10.11-kage_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,033 10.11-intel-2.7/Bio/motifs/matrix.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,033 intel-2.7/Bio/motifs/mast.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/paccopying build/lib.macosx-copying build/lib.macosx-10.11-kage_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,033 intel-2.7/Bio/motifs/meme.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/paccopying build/lib.macosx-iopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,033 10.11-intel-2.7/Bio/motifs/transfac.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio12f73c3b116/lib/python/Bio/motifs tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,033 10.11-intel-2.7/Bio/motifs/thresholds.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bcopying build/lib.macosx-python/package_biopython_1_67/acopying build/lib.macosx-10.11-intel-2.ython_1_67/a12f73c3b116/lib/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,033 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,033 7/Bio/NaiveBayes.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopcreating /galaxydir/galax/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork install_environment.STDOUT DEBUG 2017-11-18 17:04:08,034 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12NeuralNetwork/BackPropagalaxy/database/dependencies/biopage_biopython_1_67/a12f73c3b116/lib/pytgation install_environment.STDOUT DEBUG 2017-11-18 17:04:08,035 7/Bio/NeuralNetwork/BackPropagation/Network.py -> /galaxydir/galaxy/database/dependencies/biopython/16/lib/python/Bio/NeuralNcreating /galaxydir/galaxy/dataNetwork/Gene install_environment.STDOUT DEBUG 2017-11-18 17:04:08,038 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNecopying build/lib.macosx-ase/dependencies/biopython/1.67hon_1_67/a12f73c3b116/lib/python/Bio/Necopying build/lib.macosx-10.11-intel-2.7/Bio/Neukage_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetworcopying build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork/StopTraining.py 116/lib/python/Bio/NeuralNetwork install_environment.STDOUT DEBUG 2017-11-18 17:04:08,040 10.11-intel-2.7/Bio/NeuralNetwork/Training.py -> /galaxydir/galaxy/database/dependencies/biopython/1_1_67/a12f73c3b116/lib/pycreating /galaxydir/galaxy/datacopying build/lib.macosx-10.11-intel-2.biopython_1_67/a12f73c3b116/lib/python/Bio/Nexuscopying build/lib.macosx-10.11-intel-2.7/Bio/Nexus/cnexus.sob116/lib/python/Bio/Nexus install_environment.STDOUT DEBUG 2017-11-18 17:04:08,041 10.11-intel-2.7/Bio/Nexus/Nexus.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyth3c3b116/lib/python/Bio/Necopying build/lib.macosx-10.11-kage_biopython_1_67/a12f73c3b116/lib/pycopying build/lib.macosx-10.11-intel-2.7/Bio/Nexthon_1_67/a12f73c3b116/lib/python/Bio/Nexus install_environment.STDOUT DEBUG 2017-11-18 17:04:08,043 10.11-intel-2.7/Bio/Nexus/Trees.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyth3c3b116/lib/python/Bio/Necreating /galaxydir/galaxy/datacopying build/lib.macosx-10.11-intel-2.opython_1_67/a12f73c3b116/lib/python/Bio/NMR install_environment.STDOUT DEBUG 2017-11-18 17:04:08,045 10.11-intel-2.7/Bio/NMR/NOEtools.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyties/biopython/1.67/biopyt7/a12f73c3b116/lib/python/Bio/Ncopying build/lib.macosx-10.11-intel-2.cies/biopython/1.67/biopython/package_biopython_hon/Bio install_environment.STDOUT DEBUG 2017-11-18 17:04:08,048 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Pathwacopying build/lib.macosx-f73c3b116/lib/python/Bio/Pathwacopying build/lib.macosx-10.11-intel-2.ndencies/biopython/1.67/biopython/package_biopyt/python/Bio/Pathway/Rep install_environment.STDOUT DEBUG 2017-11-18 17:04:08,050 intel-2.7/Bio/Pathway/Rep/MultiGraph.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bib116/lib/python/Bio/Pathwcreating /galaxydir/galaxy/datae/dependencies/biopython/1.67/biopython12f73c3b116/lib/python/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,051 intel-2.7/Bio/PDB/Atom.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/packagn/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,053 /Chain.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67copying build/lib.macosx-package_biopython_1_67/a12f73c3biopython/1.67/biopython/package_biopyt/python/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,054 intel-2.7/Bio/PDB/Entity.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/packhon/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,056 /FragmentMapper.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopycopying build/lib.macosx-ncies/biopython/1.67/biopython/2f73c3b116/lib/python/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,058 intel-2.7/Bio/PDB/MMCIFParser.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythonb/python/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,060 /Model.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67copying build/lib.macosx-endencies/biopython/1.67/biopyt7/a12f73c3b116/lib/python/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,061 intel-2.7/Bio/PDB/parse_pdb_header.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,064 /PDBExceptions.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopytcopying build/lib.macosx-/package_biopython_1_67/a12f73ccopying build/lib.macosx-10.11-intel-2.python_1_67/a12f73c3b116/lib/python/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,066 10.11-intel-2.7/Bio/PDB/PDBParser.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyf73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-/package_biopython_1_67/a12f73c3b116/licopying build/lib.macosx-10.11-intel-2.7/Bio/PDBa12f73c3b116/lib/python/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,067 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-thon/1.67/biopython/package_biolib/python/Bio/PDB/QCPSuperimposer install_environment.STDOUT DEBUG 2017-11-18 17:04:08,069 intel-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.so -> /galaxydir/galaxy/database/dependencies/biopyth7/a12f73c3b116/lib/pythoncopying build/lib.macosx-10.11-kage_biopython_1_67/a12f73c3b116/lib/pycopying build/lib.macosx-10.11-intel-2.7/Bio/PDBon_1_67/a12f73c3b116/lib/python/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,070 10.11-intel-2.7/Bio/PDB/Selection.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyf73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-/dependencies/biopython/1.67/biopython/2f73c3b116/lib/python/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,070 intel-2.7/Bio/PDB/StructureBuilder.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,072 /Superimposer.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythcopying build/lib.macosx-n/package_biopython_1_67/a12f73f73c3b116/lib/python/Bio/phenotype install_environment.STDOUT DEBUG 2017-11-18 17:04:08,073 ependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/phenotype install_environment.STDOUT DEBUG 2017-11-18 17:04:08,075 10.11-intel-2.7/Bio/phenotype/pm_fitting.py -> /galaxydir/galaxy/database/dependencies/biopython/1.6_67/a12f73c3b116/lib/pythcreating /galaxydir/galaxy/datacopying build/lib.macosx-10.11-intel-2.encies/biopython/1.67/biopython/package_biopythoython/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:04:08,075 intel-2.7/Bio/Phylo/_io.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/packaon/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:04:08,077 lo/_utils.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1creating /galaxydir/galaxPhylo/Applications install_environment.STDOUT DEBUG 2017-11-18 17:04:08,078 tabase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylcopying build/lib.macosx-n/1.67/biopython/package_biopytase/dependencies/biopython/1.67/biopyth/a12f73c3b116/lib/python/Bio/Phylo/Applications install_environment.STDOUT DEBUG 2017-11-18 17:04:08,081 intel-2.7/Bio/Phylo/BaseTree.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/s/biopython/1.67/biopythoa12f73c3b116/lib/python/Bio/Phycopying build/lib.macosx-10.11-intel-2.opython_1_67/a12f73c3b116/lib/python/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:04:08,083 10.11-intel-2.7/Bio/Phylo/Consensus.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-ckage_biopython_1_67/a12f73c3b116/lib/pcopying build/lib.macosx-10.11-intel-2.7/Bio/Phy_1_67/a12f73c3b116/lib/python/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:04:08,085 10.11-intel-2.7/Bio/Phylo/NeXML.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyth3c3b116/lib/python/Bio/Phcopying build/lib.macosx-10.11-ackage_biopython_1_67/a12f73c3b116/lib/copying build/lib.macosx-10.11-intel-2.7/Bio/Phy1_67/a12f73c3b116/lib/python/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:04:08,086 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/PAML install_environment.STDOUT DEBUG 2017-11-18 17:04:08,087 10.11-intel-2.7/Bio/Phylo/PAML/_paml.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bia12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-se/dependencies/biopython/1.67/biopythoa12f73c3b116/lib/python/Bio/Phylo/PAML install_environment.STDOUT DEBUG 2017-11-18 17:04:08,088 intel-2.7/Bio/Phylo/PAML/_parse_yn00.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bib116/lib/python/Bio/Phylocopying build/lib.macosx-10.11-on/package_biopython_1_67/a12f73c3b116/ install_environment.STDOUT DEBUG 2017-11-18 17:04:08,089 intel-2.7/Bio/Phylo/PAML/chi2.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythonb/python/Bio/Phylo/PAML install_environment.STDOUT DEBUG 2017-11-18 17:04:08,090 lo/PAML/codeml.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopytcopying build/lib.macosx-python/package_biopython_1_67/ao/Phylo/PAML install_environment.STDOUT DEBUG 2017-11-18 17:04:08,090 intel-2.7/Bio/Phylo/PhyloXML.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython//python/Bio/Phylo install_environment.STDOUT DEBUG 2017-11-18 17:04:08,092 lo/PhyloXMLIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythcopying build/lib.macosx-.67/biopython/package_biopythonf73c3b116/lib/python/Bio/PopGen install_environment.STDOUT DEBUG 2017-11-18 17:04:08,093 f73c3b116/lib/python/Bio/PopGen/Async install_environment.STDOUT DEBUG 2017-11-18 17:04:08,093 endencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/Async install_environment.STDOUT DEBUG 2017-11-18 17:04:08,095 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/dependencies/biopython/1.endencies/biopython/1.67/biopyt7/a12f73c3b116/lib/python/Bio/PopGen/FDcopying build/lib.macosx-10.11-intel-2.7/Bio/Popbiopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/FDist install_environment.STDOUT DEBUG 2017-11-18 17:04:08,097 10.11-intel-2.7/Bio/PopGen/FDist/Utils.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/7/a12f73c3b116/lib/pythoncreating /galaxydir/galaxy/data/GenePop install_environment.STDOUT DEBUG 2017-11-18 17:04:08,100 atabase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Popcopying build/lib.macosx-database/dependencies/biopythoniopython_1_67/a12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-intel-2.7/Bio/Popf73c3b116/lib/python/Bio/PopGen/SimCoal install_environment.STDOUT DEBUG 2017-11-18 17:04:08,104 ependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/SimCocopying build/lib.macosx-ase/dependencies/biopython/1.67hon_1_67/a12f73c3b116/lib/python/Bio/Pocreating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/laxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/io/PopGen/SimCoal/data install_environment.STDOUT DEBUG 2017-11-18 17:04:08,106 intel-2.7/Bio/PopGen/SimCoal/data/decline_split.par -> /galaxydir/galaxy/database/dependencies/biopy_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12abase/dependencies/biopython/1.67/biopython/packc3b116/lib/python/Bio/PopGen/SimCoal/data install_environment.STDOUT DEBUG 2017-11-18 17:04:08,109 intel-2.7/Bio/PopGen/SimCoal/data/split_island.par -> /galaxydir/galaxy/database/dependencies/biopyt67/a12f73c3b116/lib/pythocopying build/lib.macosx-10.11-xy/database/dependencies/biopython/1.67hon_1_67/a12f73c3b116/lib/python/Bio/PopGen/SimCcopying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/abase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3n/SimCoal/data install_environment.STDOUT DEBUG 2017-11-18 17:04:08,113 intel-2.7/Bio/PopGen/SimCoal/Template.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/PopGcreating /galaxydir/galaxy/dataction install_environment.STDOUT DEBUG 2017-11-18 17:04:08,115 e/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Restricticopying build/lib.macosx-.67/biopython/package_biopythonthon/Bio/Restriction install_environment.STDOUT DEBUG 2017-11-18 17:04:08,116 intel-2.7/Bio/Restriction/Restriction.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/Restcopying build/lib.macosx-10.11-thon/1.67/biopython/package_biopython_1on/Bio/Restriction install_environment.STDOUT DEBUG 2017-11-18 17:04:08,118 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SCOP install_environment.STDOUT DEBUG 2017-11-18 17:04:08,118 biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SCOP install_environment.STDOUT DEBUG 2017-11-18 17:04:08,119 10.11-intel-2.7/Bio/SCOP/Des.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/b116/lib/python/Bio/SCOP install_environment.STDOUT DEBUG 2017-11-18 17:04:08,120 7/Bio/SCOP/Dom.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopytcopying build/lib.macosx-package_biopython_1_67/a12f73c3copying build/lib.macosx-10.11-intel-2.hon_1_67/a12f73c3b116/lib/python/Bio/SCOP install_environment.STDOUT DEBUG 2017-11-18 17:04:08,120 10.11-intel-2.7/Bio/SCOP/Residues.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SCOP install_environment.STDOUT DEBUG 2017-11-18 17:04:08,121 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12IO install_environment.STDOUT DEBUG 2017-11-18 17:04:08,122 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO install_environment.STDOUT DEBUG 2017-11-18 17:04:08,123 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-/1.67/biopython/package_biopythpython/Bio/SearchIO/_model install_environment.STDOUT DEBUG 2017-11-18 17:04:08,123 intel-2.7/Bio/SearchIO/_model/_base.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/Searchcopying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11/_model install_environment.STDOUT DEBUG 2017-11-18 17:04:08,124 intel-2.7/Bio/SearchIO/_model/hsp.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/_model install_environment.STDOUT DEBUG 2017-11-18 17:04:08,124 7/Bio/SearchIO/_model/query.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/po/SearchIO/_model install_environment.STDOUT DEBUG 2017-11-18 17:04:08,125 .py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f7creating /galaxydir/galaxSearchIO/BlastIO install_environment.STDOUT DEBUG 2017-11-18 17:04:08,126 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Searchcopying build/lib.macosx-hon/1.67/biopython/package_biopib/python/Bio/SearchIO/BlastIO install_environment.STDOUT DEBUG 2017-11-18 17:04:08,128 intel-2.7/Bio/SearchIO/BlastIO/blast_xml.py -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Scopying build/lib.macosx-10.11-/package_biopython_1_67/a12f73c3b116/licreating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/Exonerhon_1_67/a12f73c3b116/lib/python/Bio/SearchIO/ExonerateIO install_environment.STDOUT DEBUG 2017-11-18 17:04:08,130 10.11-intel-2.7/Bio/SearchIO/ExonerateIO/_base.py -> /galaxydir/galaxy/database/dependencies/biopyththon_1_67/a12f73c3b116/licopying build/lib.macosx-10.11-python/1.67/biopython/package_biopythonthon/Bio/SearchIO/ExonerateIO install_environment.STDOUT DEBUG 2017-11-18 17:04:08,131 intel-2.7/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /galaxydir/galaxy/database/dependencies/biop1_67/a12f73c3b116/lib/pytcopying build/lib.macosx-10.11-opython/1.67/biopython/package_biopythoython/Bio/SearchIO/ExonerateIO install_environment.STDOUT DEBUG 2017-11-18 17:04:08,132 intel-2.7/Bio/SearchIO/FastaIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythoib/python/Bio/SearchIO install_environment.STDOUT DEBUG 2017-11-18 17:04:08,132 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/HmmerIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,134 copying build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork/__init__.py -> /galaxydir/galaxy/databasef73c3b116/lib/python/Bio/tion install_environment.STDOUT DEBUG 2017-11-18 17:04:08,134 /dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/Hcopying build/lib.macosx-thon/1.67/biopython/package_biolib/python/Bio/SearchIO/HmmerIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,134 copying build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork/BackPropagation/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork/BackPropagation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,134 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12NeuralNetwork/BackPropagalaxy/database/dependencies/biopage_biopython_1_67/a12f73c3b116/lib/pytgation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,135 copying build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork/BackPropagation/Layer.py -> /galaxydir/gaython/1.67/biopython/packhon/Bio/NeuralNetwork/BackPropacopying build/lib.macosx-10.11-intel-2.1.67/biopython/package_biopython_1_67/a12f73c3b1etwork/BackPropagation tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,135 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Neuralcopying build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork/Gene/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork/Gene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,135 7/Bio/NeuralNetwork/BackPropagation/Network.py -> /galaxydir/galaxy/database/dependencies/biopython/16/lib/python/Bio/NeuralNcreating /galaxydir/galaxy/dataNetwork/Gene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,135 copying build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork/Gene/Motif.py -> /galaxydir/galaxy/databatwork/Gene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,135 10.11-intel-2.7/Bio/NeuralNetwork/Gene/Pattern.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork/Gene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,135 copying build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork/Gene/Schema.py -> /galaxydir/galaxy/datab/biopython/package_biopyturalNetwork/Gene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,135 ralNetwork/Gene/Signature.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/pack/Gene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,135 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNecopying build/lib.macosx-ase/dependencies/biopython/1.67hon_1_67/a12f73c3b116/lib/python/Bio/Necopying build/lib.macosx-10.11-intel-2.7/Bio/Neukage_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetworcopying build/lib.macosx-10.11-intel-2.7/Bio/NeuralNetwork/StopTraining.py 116/lib/python/Bio/NeuralNetwork tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,136 -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3bcopying build/lib.macosx-.67/biopython/package_biopythonthon/Bio/NeuralNetwork tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,136 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Nexus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,136 7/Bio/Nexus/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,136 10.11-intel-2.7/Bio/NeuralNetwork/Training.py -> /galaxydir/galaxy/database/dependencies/biopython/1_1_67/a12f73c3b116/lib/pycreating /galaxydir/galaxy/datacopying build/lib.macosx-10.11-intel-2.biopython_1_67/a12f73c3b116/lib/python/Bio/Nexuscopying build/lib.macosx-10.11-intel-2.7/Bio/Nexus/cnexus.sob116/lib/python/Bio/Nexus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,136 -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3copying build/lib.macosx-on/package_biopython_1_67/a12f7xus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,136 intel-2.7/Bio/Nexus/Nodes.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/pacthon/Bio/Nexus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,136 10.11-intel-2.7/Bio/Nexus/Nexus.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyth3c3b116/lib/python/Bio/Necopying build/lib.macosx-10.11-kage_biopython_1_67/a12f73c3b116/lib/pycopying build/lib.macosx-10.11-intel-2.7/Bio/Nexthon_1_67/a12f73c3b116/lib/python/Bio/Nexus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,136 us/StandardData.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopycopying build/lib.macosx-on/package_biopython_1_67/a12f7xus tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,137 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NMR tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,137 10.11-intel-2.7/Bio/Nexus/Trees.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyth3c3b116/lib/python/Bio/Necreating /galaxydir/galaxy/datacopying build/lib.macosx-10.11-intel-2.opython_1_67/a12f73c3b116/lib/python/Bio/NMR tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,137 7/Bio/NMR/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_bicopying build/lib.macosx-hon/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NMR tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,137 copying build/lib.macosx-10.11-intel-2.7/Bio/NMR/xpktools.py -> /galaxydir/galaxy/database/dependenchon/package_biopython_1_6MR tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,137 7/Bio/pairwise2.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,137 10.11-intel-2.7/Bio/NMR/NOEtools.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyties/biopython/1.67/biopyt7/a12f73c3b116/lib/python/Bio/Ncopying build/lib.macosx-10.11-intel-2.cies/biopython/1.67/biopython/package_biopython_hon/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,137 copying build/lib.macosx-10.11-intel-2.7/Bio/ParserSupport.py -> /galaxydir/galaxy/database/dependen1_67/a12f73c3b116/lib/pytcreating /galaxydir/galaxy/datay tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,137 10.11-intel-2.7/Bio/Pathway/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Pathway tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,137 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12y/Rep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,137 7/Bio/Pathway/Rep/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Pathway/Rep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,138 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Pathwacopying build/lib.macosx-f73c3b116/lib/python/Bio/Pathwacopying build/lib.macosx-10.11-intel-2.ndencies/biopython/1.67/biopython/package_biopyt/python/Bio/Pathway/Rep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,138 copying build/lib.macosx-10.11-intel-2.7/Bio/Pathway/Rep/Graph.py -> /galaxydir/galaxy/database/depehon_1_67/a12f73c3b116/libcopying build/lib.macosx-10.11-opython/package_biopython_1_67/a12f73c3ay/Rep tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,138 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,138 copying build/lib.macosx-10.11-intel-2.7/Bio/PDB/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,138 intel-2.7/Bio/Pathway/Rep/MultiGraph.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bib116/lib/python/Bio/Pathwcreating /galaxydir/galaxy/datae/dependencies/biopython/1.67/biopython12f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,138 intel-2.7/Bio/PDB/Atom.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/packagn/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,138 copying build/lib.macosx-10.11-intel-2.7/Bio/PDB/AbstractPropertyMap.py -> /galaxydir/galaxy/databas/package_biopython_1_67/acopying build/lib.macosx-10.11-e_biopython_1_67/a12f73c3b116/lib/pythocopying build/lib.macosx-10.11-intel-2.7/Bio/PDB/a12f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,138 10.11-intel-2.7/Bio/PDB/Dice.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,138 /Chain.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67copying build/lib.macosx-package_biopython_1_67/a12f73c3biopython/1.67/biopython/package_biopyt/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,139 intel-2.7/Bio/PDB/Entity.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/packhon/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,139 copying build/lib.macosx-10.11-intel-2.7/Bio/PDB/DSSP.py -> /galaxydir/galaxy/database/dependencies/hon_1_67/a12f73c3b116/libcopying build/lib.macosx-10.11-age_biopython_1_67/a12f73c3b116/lib/pytcopying build/lib.macosx-10.11-intel-2.7/Bio/PDBthon_1_67/a12f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,139 10.11-intel-2.7/Bio/PDB/HSExposure.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,139 /FragmentMapper.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopycopying build/lib.macosx-ncies/biopython/1.67/biopython/2f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,139 intel-2.7/Bio/PDB/MMCIFParser.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythonb/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,139 copying build/lib.macosx-10.11-intel-2.7/Bio/PDB/MMCIF2Dict.py -> /galaxydir/galaxy/database/dependepackage_biopython_1_67/a1copying build/lib.macosx-10.11-/package_biopython_1_67/a12f73c3b116/licopying build/lib.macosx-10.11-intel-2.7/Bio/PDB/a12f73c3b116/lib/python/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,139 abase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Searccopying build/lib.macosx-s/biopython/1.67/biopython/packncies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,139 10.11-intel-2.7/Bio/PDB/NACCESS.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,140 /Model.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67copying build/lib.macosx-endencies/biopython/1.67/biopyt7/a12f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,140 intel-2.7/Bio/PDB/parse_pdb_header.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,140 copying build/lib.macosx-10.11-intel-2.7/Bio/PDB/NeighborSearch.py -> /galaxydir/galaxy/database/dephon/package_biopython_1_6copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1copying build/lib.macosx-10.11-intel-2.7/Bio/PDBhon_1_67/a12f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,140 10.11-intel-2.7/Bio/PDB/PDBIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,140 /PDBExceptions.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopytcopying build/lib.macosx-/package_biopython_1_67/a12f73ccopying build/lib.macosx-10.11-intel-2.python_1_67/a12f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,140 7/Bio/PDB/PDBList.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biocopying build/lib.macosx-thon/package_biopython_1_67/a12PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,141 intel-2.7/Bio/PDB/Polypeptide.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythonb/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,141 10.11-intel-2.7/Bio/PDB/PDBParser.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyf73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-/package_biopython_1_67/a12f73c3b116/licopying build/lib.macosx-10.11-intel-2.7/Bio/PDBa12f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,141 /PSEA.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/creating /galaxydir/galaxPDB/QCPSuperimposer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,141 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-thon/1.67/biopython/package_biolib/python/Bio/PDB/QCPSuperimposer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,141 10.11-intel-2.7/Bio/PDB/QCPSuperimposer/__init__.py -> /galaxydir/galaxy/database/dependencies/biopypython_1_67/a12f73c3b116/copying build/lib.macosx-10.11-on/1.67/biopython/package_biopython_1_6/Bio/PDB/QCPSuperimposer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,141 intel-2.7/Bio/PDB/Residue.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/pacthon/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,141 intel-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.so -> /galaxydir/galaxy/database/dependencies/biopyth7/a12f73c3b116/lib/pythoncopying build/lib.macosx-10.11-kage_biopython_1_67/a12f73c3b116/lib/pycopying build/lib.macosx-10.11-intel-2.7/Bio/PDBon_1_67/a12f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,141 /ResidueDepth.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythcopying build/lib.macosx-thon/package_biopython_1_67/a12PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,141 intel-2.7/Bio/PDB/Structure.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,141 10.11-intel-2.7/Bio/PDB/Selection.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyf73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-/dependencies/biopython/1.67/biopython/2f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,142 intel-2.7/Bio/PDB/StructureBuilder.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biop16/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,142 copying build/lib.macosx-10.11-intel-2.7/Bio/PDB/StructureAlignment.py -> /galaxydir/galaxy/databasepackage_biopython_1_67/a1copying build/lib.macosx-10.11-ython/package_biopython_1_67/a12f73c3b1copying build/lib.macosx-10.11-intel-2.7/Bio/PDBon_1_67/a12f73c3b116/lib/python/Bio/PDB tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,142 10.11-intel-2.7/Bio/PDB/Vector.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythoc3b116/lib/python/Bio/PDB install_environment.STDOUT DEBUG 2017-11-18 17:04:08,142 10.11-intel-2.7/Bio/SeqIO/_index.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Scopying build/lib.macosx-10.11-intel-2.cies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,142 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12copying build/lib.macosx-10.11-intel-2.7/Bio/phenotype/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/phenotype tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,142 /Superimposer.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythcopying build/lib.macosx-n/package_biopython_1_67/a12f73f73c3b116/lib/python/Bio/phenotype tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,143 ependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/phenotype tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,143 copying build/lib.macosx-10.11-intel-2.7/Bio/phenotype/phen_micro.py -> /galaxydir/galaxy/database/dcopying build/lib.macosx-7/biopython/package_biopython_1on/Bio/phenotype tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,143 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,143 7/Bio/Phylo/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,143 10.11-intel-2.7/Bio/phenotype/pm_fitting.py -> /galaxydir/galaxy/database/dependencies/biopython/1.6_67/a12f73c3b116/lib/pythcreating /galaxydir/galaxy/datacopying build/lib.macosx-10.11-intel-2.encies/biopython/1.67/biopython/package_biopythoython/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,143 intel-2.7/Bio/Phylo/_io.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/packaon/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,144 copying build/lib.macosx-10.11-intel-2.7/Bio/Phylo/_cdao_owl.py -> /galaxydir/galaxy/database/dependn_1_67/a12f73c3b116/lib/pcopying build/lib.macosx-10.11-ge_biopython_1_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-intel-2.7/Bio/Phy_67/a12f73c3b116/lib/python/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,144 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-intel-2.7/Bio/Phylo/Applications/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,144 lo/_utils.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1creating /galaxydir/galaxPhylo/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,144 copying build/lib.macosx-10.11-intel-2.7/Bio/Phylo/Applications/_Fasttree.py -> /galaxydir/galaxy/dao/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,144 10.11-intel-2.7/Bio/Phylo/Applications/_Phyml.py -> /galaxydir/galaxy/database/dependencies/biopythohon_1_67/a12f73c3b116/lib/python/Bio/Phylo/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,144 tabase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylcopying build/lib.macosx-n/1.67/biopython/package_biopytase/dependencies/biopython/1.67/biopyth/a12f73c3b116/lib/python/Bio/Phylo/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,144 copying build/lib.macosx-10.11-intel-2.7/Bio/Phylo/Applications/_Raxml.py -> /galaxydir/galaxy/databon/package_biopython_1_67copying build/lib.macosx-10.11-package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,144 copying build/lib.macosx-10.11-intel-2.7/Bio/Phylo/CDAO.py -> /galaxydir/galaxy/database/dependencien/package_biopython_1_67/lo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,144 intel-2.7/Bio/Phylo/BaseTree.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/s/biopython/1.67/biopythoa12f73c3b116/lib/python/Bio/Phycopying build/lib.macosx-10.11-intel-2.opython_1_67/a12f73c3b116/lib/python/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,145 7/Bio/Phylo/CDAOIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_bicopying build/lib.macosx-python/package_biopython_1_67/ao/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,145 intel-2.7/Bio/Phylo/Newick.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/paython/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,145 10.11-intel-2.7/Bio/Phylo/Consensus.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-ckage_biopython_1_67/a12f73c3b116/lib/pcopying build/lib.macosx-10.11-intel-2.7/Bio/Phy_1_67/a12f73c3b116/lib/python/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,145 lo/NewickIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythoncopying build/lib.macosx-on/package_biopython_1_67/a12f7ylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,145 intel-2.7/Bio/Phylo/NeXMLIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/ppython/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,145 10.11-intel-2.7/Bio/Phylo/NeXML.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyth3c3b116/lib/python/Bio/Phcopying build/lib.macosx-10.11-ackage_biopython_1_67/a12f73c3b116/lib/copying build/lib.macosx-10.11-intel-2.7/Bio/Phy1_67/a12f73c3b116/lib/python/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,146 lo/NexusIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_creating /galaxydir/galaxPhylo/PAML install_environment.STDOUT DEBUG 2017-11-18 17:04:08,145 10.11-intel-2.7/Bio/SeqIO/IgIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythoes/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,146 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,146 10.11-intel-2.7/Bio/Phylo/PAML/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67copying build/lib.macosx-opython/package_biopython_1_67/io/Phylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,146 intel-2.7/Bio/Phylo/PAML/_parse_baseml.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,146 10.11-intel-2.7/Bio/Phylo/PAML/_paml.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bia12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-se/dependencies/biopython/1.67/biopythoa12f73c3b116/lib/python/Bio/Phylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,146 copying build/lib.macosx-10.11-intel-2.7/Bio/Phylo/PAML/_parse_codeml.py -> /galaxydir/galaxy/databan/package_biopython_1_67/copying build/lib.macosx-10.11-opython/package_biopython_1_67/a12f73c3/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,146 intel-2.7/Bio/Phylo/PAML/_parse_yn00.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bib116/lib/python/Bio/Phylocopying build/lib.macosx-10.11-on/package_biopython_1_67/a12f73c3b116/ tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,146 intel-2.7/Bio/Phylo/PAML/chi2.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythonb/python/Bio/Phylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,146 intel-2.7/Bio/Phylo/PAML/baseml.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythlib/python/Bio/Phylo/PAMLcopying build/lib.macosx-10.11-/package_biopython_1_67/a12f73c3b116/licopying build/lib.macosx-10.11-intel-2.7/Bio/Phyhon_1_67/a12f73c3b116/lib/python/Bio/Phylo/PAML install_environment.STDOUT DEBUG 2017-11-18 17:04:08,147 10.11-intel-2.7/Bio/SeqIO/PirIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,147 lo/PAML/codeml.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopytcopying build/lib.macosx-python/package_biopython_1_67/ao/Phylo/PAML tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,147 intel-2.7/Bio/Phylo/PhyloXML.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython//python/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,147 10.11-intel-2.7/Bio/Phylo/PAML/yn00.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-package_biopython_1_67/a12f73c3b116/libcopying build/lib.macosx-10.11-intel-2.7/Bio/Phyon_1_67/a12f73c3b116/lib/python/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,147 10.11-intel-2.7/Bio/Phylo/TreeConstruction.py -> /galaxydir/galaxy/database/dependencies/biopython/1_1_67/a12f73c3b116/lib/python/Bio/Phylo tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,147 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,148 lo/PhyloXMLIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythcopying build/lib.macosx-.67/biopython/package_biopythonf73c3b116/lib/python/Bio/PopGen tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,148 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/Async/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/Async tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,148 f73c3b116/lib/python/Bio/PopGen/Async tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,148 endencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/Async tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,148 copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/Async/Local.py -> /galaxydir/galaxy/database/depcreating /galaxydir/galaxPopGen/FDist tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,148 copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/FDist/__init__.py -> /galaxydir/galaxy/database/67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/FDist tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,148 copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/FDist/Async.py -> /galaxydir/galaxy/database/dephon/package_biopython_1_6ist tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,148 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/dependencies/biopython/1.endencies/biopython/1.67/biopyt7/a12f73c3b116/lib/python/Bio/PopGen/FDcopying build/lib.macosx-10.11-intel-2.7/Bio/Popbiopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/FDist tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,148 Gen/FDist/Controller.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_copying build/lib.macosx-biopython/package_biopython_1_6/Bio/PopGen/FDist tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,149 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGencopying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePop/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/GenePop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,149 copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePop/Controller.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/GenePop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,149 10.11-intel-2.7/Bio/PopGen/FDist/Utils.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/7/a12f73c3b116/lib/pythoncreating /galaxydir/galaxy/data/GenePop install_environment.STDOUT DEBUG 2017-11-18 17:04:08,148 10.11-intel-2.7/Bio/SeqIO/SeqXmlIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopes/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,149 copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePop/EasyController.py -> /galaxydir/galaxy/dGen/GenePop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,149 10.11-intel-2.7/Bio/PopGen/GenePop/FileParser.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/GenePop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,150 copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/GenePop/LargeFileParser.py -> /galaxydir/galaxy//1.67/biopython/package_bio/PopGen/GenePop tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,150 Gen/GenePop/Utils.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/GenePop install_environment.STDOUT DEBUG 2017-11-18 17:04:08,150 es/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,150 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/SimCoal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,150 atabase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Popcopying build/lib.macosx-database/dependencies/biopythoniopython_1_67/a12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-intel-2.7/Bio/Popf73c3b116/lib/python/Bio/PopGen/SimCoal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,151 copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/Async.py -> /galaxydir/galaxy/database/dal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,151 10.11-intel-2.7/Bio/PopGen/SimCoal/Cache.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/SimCoal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,151 copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/Controller.py -> /galaxydir/galaxy/datab/biopython/package_biopytpGen/SimCoal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,151 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,151 data/bottle.par -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,151 ependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/SimCocopying build/lib.macosx-ase/dependencies/biopython/1.67hon_1_67/a12f73c3b116/lib/python/Bio/Pocreating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/laxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/io/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,151 copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/data/decline_lambda.par -> /galaxydir/gaa12f73c3b116/lib/python/Bcopying build/lib.macosx-10.11-thon/1.67/biopython/package_biopython_1on/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,151 intel-2.7/Bio/PopGen/SimCoal/data/island.par -> /galaxydir/galaxy/database/dependencies/biopython/1.f73c3b116/lib/python/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,151 intel-2.7/Bio/PopGen/SimCoal/data/decline_split.par -> /galaxydir/galaxy/database/dependencies/biopy_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-67/biopython/package_biopython_1_67/a12abase/dependencies/biopython/1.67/biopython/packc3b116/lib/python/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,151 copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/data/simple.par -> /galaxydir/galaxy/datage_biopython_1_67/a12f73copying build/lib.macosx-10.11-hon/1.67/biopython/package_biopython_1_n/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,151 intel-2.7/Bio/PopGen/SimCoal/data/split_ssm_1d.par -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,151 copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/data/split_ssm_2d.par -> /galaxydir/gala/biopython/package_biopytoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,152 data/ssm_1d.par -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,152 intel-2.7/Bio/PopGen/SimCoal/data/split_island.par -> /galaxydir/galaxy/database/dependencies/biopyt67/a12f73c3b116/lib/pythocopying build/lib.macosx-10.11-xy/database/dependencies/biopython/1.67hon_1_67/a12f73c3b116/lib/python/Bio/PopGen/SimCcopying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/abase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3n/SimCoal/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,152 copying build/lib.macosx-10.11-intel-2.7/Bio/PopGen/SimCoal/data/ssm_2d.par -> /galaxydir/galaxy/datb116/lib/python/Bio/PopGecopying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73cen/SimCoal tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,152 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Restricopying build/lib.macosx-10.11-intel-2.7/Bio/Restriction/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Restriction tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,152 intel-2.7/Bio/PopGen/SimCoal/Template.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/PopGcreating /galaxydir/galaxy/dataction tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,152 copying build/lib.macosx-10.11-intel-2.7/Bio/Restriction/PrintFormat.py -> /galaxydir/galaxy/databason tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,152 e/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Restricticopying build/lib.macosx-.67/biopython/package_biopythonthon/Bio/Restriction tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,152 10.11-intel-2.7/Bio/Restriction/RanaConfig.py -> /galaxydir/galaxy/database/dependencies/biopython/1_1_67/a12f73c3b116/lib/pycopying build/lib.macosx-10.11-iopython/package_biopython_1_67/a12f73criction tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,152 intel-2.7/Bio/Restriction/Restriction.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/b3b116/lib/python/Bio/Restcopying build/lib.macosx-10.11-thon/1.67/biopython/package_biopython_1on/Bio/Restriction tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,152 intel-2.7/Bio/Restriction/Restriction_Dictionary.py -> /galaxydir/galaxy/database/dependencies/biopy_67/a12f73c3b116/lib/pythcreating /galaxydir/galaxy/datacopying build/lib.macosx-10.11-intel-2.7/Bio/SCOP/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,152 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,152 biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,152 10.11-intel-2.7/Bio/SCOP/Des.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/b116/lib/python/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,153 copying build/lib.macosx-10.11-intel-2.7/Bio/SCOP/Cla.py -> /galaxydir/galaxy/database/dependencies/copying build/lib.macosx-package_biopython_1_67/a12f73c3copying build/lib.macosx-10.11-intel-2.hon_1_67/a12f73c3b116/lib/python/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,153 10.11-intel-2.7/Bio/SCOP/Hie.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/b116/lib/python/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,153 7/Bio/SCOP/Dom.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopytcopying build/lib.macosx-package_biopython_1_67/a12f73c3copying build/lib.macosx-10.11-intel-2.hon_1_67/a12f73c3b116/lib/python/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,153 10.11-intel-2.7/Bio/SCOP/Residues.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SCOP tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,153 7/Bio/SCOP/Raf.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopytcopying build/lib.macosx-f73c3b116/lib/python/Bio/Searchcopying build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,153 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12IO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,153 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,153 copying build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/_index.py -> /galaxydir/galaxy/database/dependcreating /galaxydir/galaxSearchIO/_model tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,153 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-/1.67/biopython/package_biopythpython/Bio/SearchIO/_model tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,153 10.11-intel-2.7/Bio/SearchIO/_model/__init__.py -> /galaxydir/galaxy/database/dependencies/biopythonon_1_67/a12f73c3b116/lib/copying build/lib.macosx-10.11-python/package_biopython_1_67/a12f73c3bIO/_model tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,153 intel-2.7/Bio/SearchIO/_model/_base.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio116/lib/python/Bio/Searchcopying build/lib.macosx-10.11-thon/package_biopython_1_67/a12f73c3b11/_model tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,153 intel-2.7/Bio/SearchIO/_model/hsp.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/_model tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,154 7/Bio/SearchIO/_model/query.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/po/SearchIO/_model tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,154 intel-2.7/Bio/SearchIO/_model/hit.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopy6/lib/python/Bio/SearchIOcopying build/lib.macosx-10.11-copying build/lib.macosx-10.11-intel-2.ackage_biopython_1_67/a12f73c3b116/lib/python/Bicopying build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/_utils3c3b116/lib/python/Bio/SearchIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,154 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/BlastIO/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/BlastIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,155 .py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f7creating /galaxydir/galaxSearchIO/BlastIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,155 copying build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/BlastIO/blast_tab.py -> /galaxydir/galaxy/dataIO/BlastIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,155 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Searchcopying build/lib.macosx-hon/1.67/biopython/package_biopib/python/Bio/SearchIO/BlastIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,155 10.11-intel-2.7/Bio/SearchIO/BlastIO/blast_text.py -> /galaxydir/galaxy/database/dependencies/biopytython_1_67/a12f73c3b116/lcopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12fearchIO/BlastIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,155 intel-2.7/Bio/SearchIO/BlatIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythonb/python/Bio/SearchIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,155 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/ExonerateIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,155 intel-2.7/Bio/SearchIO/BlastIO/blast_xml.py -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Scopying build/lib.macosx-10.11-/package_biopython_1_67/a12f73c3b116/licreating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/Exonerhon_1_67/a12f73c3b116/lib/python/Bio/SearchIO/ExonerateIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,155 ateIO/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopytcopying build/lib.macosx-on/1.67/biopython/package_biopyb/python/Bio/SearchIO/ExonerateIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,155 10.11-intel-2.7/Bio/SearchIO/ExonerateIO/_base.py -> /galaxydir/galaxy/database/dependencies/biopyththon_1_67/a12f73c3b116/licopying build/lib.macosx-10.11-python/1.67/biopython/package_biopythonthon/Bio/SearchIO/ExonerateIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,155 intel-2.7/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /galaxydir/galaxy/database/dependencies/bio_1_67/a12f73c3b116/lib/pycopying build/lib.macosx-10.11-ython/1.67/biopython/package_biopython_hon/Bio/SearchIO/ExonerateIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,156 intel-2.7/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /galaxydir/galaxy/database/dependencies/biop1_67/a12f73c3b116/lib/pytcopying build/lib.macosx-10.11-opython/1.67/biopython/package_biopythoython/Bio/SearchIO/ExonerateIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,156 intel-2.7/Bio/SearchIO/FastaIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythoib/python/Bio/SearchIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,156 intel-2.7/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /galaxydir/galaxy/database/dependencies/bin_1_67/a12f73c3b116/lib/pcopying build/lib.macosx-10.11-n/package_biopython_1_67/a12f73c3b116/lcreating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/HmmerIO/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/HmmerIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,156 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/HmmerIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,156 copying build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/HmmerIO/_base.py -> /galaxydir/galaxy/databasemmerIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,156 10.11-intel-2.7/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /galaxydir/galaxy/database/dependencies/biopypython_1_67/a12f73c3b116/copying build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/HmmerIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,156 /dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/Hcopying build/lib.macosx-thon/1.67/biopython/package_biolib/python/Bio/SearchIO/HmmerIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,156 copying build/lib.macosx-10.11-intel-2.7/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /galaxydir/galaxy/dathIO/HmmerIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,156 10.11-intel-2.7/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/HmmerIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,156 copying build/lib.macosx-10.11-intel-2.7/Bio/Seq.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,156 copying build/lib.macosx-10.11-intel-2.7/Bio/SeqFeature.py -> /galaxydir/galaxy/database/dependencieage_biopython_1_67/a12f73c3b116/lib/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,156 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,157 copying build/lib.macosx-10.11-intel-2.7/Bio/SeqIO/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,157 abase/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Searccopying build/lib.macosx-s/biopython/1.67/biopython/packncies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,157 copying build/lib.macosx-10.11-intel-2.7/Bio/SeqIO/_convert.py -> /galaxydir/galaxy/database/dependecopying build/lib.macosx-eqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,157 7/Bio/SeqIO/AbiIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,157 copying build/lib.macosx-10.11-intel-2.7/Bio/SeqIO/AceIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,157 10.11-intel-2.7/Bio/SeqIO/_index.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Scopying build/lib.macosx-10.11-intel-2.cies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,157 copying build/lib.macosx-10.11-intel-2.7/Bio/SeqIO/FastaIO.py -> /galaxydir/galaxy/database/dependencopying build/lib.macosx-n/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,157 copying build/lib.macosx-10.11-intel-2.7/Bio/SeqIO/InsdcIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,157 copying build/lib.macosx-10.11-intel-2.7/Bio/SeqIO/Interfaces.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,157 copying build/lib.macosx-10.11-intel-2.7/Bio/SeqIO/PdbIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,157 10.11-intel-2.7/Bio/SeqIO/IgIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythoes/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,157 copying build/lib.macosx-10.11-intel-2.7/Bio/SeqIO/PhdIO.py -> /galaxydir/galaxy/database/dependencicopying build/lib.macosx-on/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,157 10.11-intel-2.7/Bio/SeqIO/PirIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopythencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,158 copying build/lib.macosx-10.11-intel-2.7/Bio/SeqIO/QualityIO.py -> /galaxydir/galaxy/database/dependcopying build/lib.macosx-ython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,158 copying build/lib.macosx-10.11-intel-2.7/Bio/SeqIO/SffIO.py -> /galaxydir/galaxy/database/dependencicopying build/lib.macosx-10.11-intel-2.7/Bio/SeqIO/SwissIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,158 10.11-intel-2.7/Bio/SeqIO/SeqXmlIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopes/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,158 es/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,158 copying build/lib.macosx-10.11-intel-2.7/Bio/SeqIO/TabIO.py -> /galaxydir/galaxy/database/dependencicopying build/lib.macosx-python/package_biopython_1_67/ao/SeqIO install_environment.STDOUT DEBUG 2017-11-18 17:04:08,160 10.11-intel-2.7/Bio/SeqIO/UniprotIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio12f73c3b116/lib/python/Bif73c3b116/lib/python/Bio/Sequencopying build/lib.macosx-10.11-intel-2.ncies/biopython/1.67/biopython/package_biopythonthon/Bio/Sequencing install_environment.STDOUT DEBUG 2017-11-18 17:04:08,163 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Sequencopying build/lib.macosx-tabase/dependencies/biopython/1python_1_67/a12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-intel-2.7/Bio/Seqxy/database/dependencies/biopython/1.67/biopython/package_bi/lib/python/Bio/Sequencing/Applications install_environment.STDOUT DEBUG 2017-11-18 17:04:08,164 intel-2.7/Bio/Sequencing/Phd.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython//python/Bio/Sequencing install_environment.STDOUT DEBUG 2017-11-18 17:04:08,166 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqUtils install_environment.STDOUT DEBUG 2017-11-18 17:04:08,166 ndencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqUtils install_environment.STDOUT DEBUG 2017-11-18 17:04:08,167 10.11-intel-2.7/Bio/SeqUtils/CodonUsage.py -> /galaxydir/galaxy/database/dependencies/biopython/1.6767/a12f73c3b116/lib/pythocopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12feqUtils install_environment.STDOUT DEBUG 2017-11-18 17:04:08,169 intel-2.7/Bio/SeqUtils/IsoelectricPoint.py -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Secopying build/lib.macosx-10.11-ckage_biopython_1_67/a12f73c3b116/lib/pcopying build/lib.macosx-10.11-intel-2.7/Bio/Seqpython_1_67/a12f73c3b116/lib/python/Bio/SeqUtils install_environment.STDOUT DEBUG 2017-11-18 17:04:08,170 10.11-intel-2.7/Bio/SeqUtils/ProtParam.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/7/a12f73c3b116/lib/pythoncopying build/lib.macosx-10.11-opython/package_biopython_1_67/a12f73c3ils install_environment.STDOUT DEBUG 2017-11-18 17:04:08,171 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Statiscopying build/lib.macosx-/biopython/package_biopython_1_n/Bio/Statistics install_environment.STDOUT DEBUG 2017-11-18 17:04:08,171 f73c3b116/lib/python/Bio/SubsMat install_environment.STDOUT DEBUG 2017-11-18 17:04:08,172 ndencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SubsMat install_environment.STDOUT DEBUG 2017-11-18 17:04:08,174 10.11-intel-2.7/Bio/SubsMat/MatrixInfo.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/7/a12f73c3b116/lib/pythoncreating /galaxydir/galaxy/dataerimposer install_environment.STDOUT DEBUG 2017-11-18 17:04:08,174 f73c3b116/lib/python/Bio/SwissProt install_environment.STDOUT DEBUG 2017-11-18 17:04:08,174 10.11-intel-2.7/Bio/SwissProt/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SwissProt install_environment.STDOUT DEBUG 2017-11-18 17:04:08,176 intel-2.7/Bio/SwissProt/KeyWList.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt/lib/python/Bio/SwissProtcreating /galaxydir/galaxy/data install_environment.STDOUT DEBUG 2017-11-18 17:04:08,176 ython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio install_environment.STDOUT DEBUG 2017-11-18 17:04:08,177 10.11-intel-2.7/Bio/triefind.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/b116/lib/python/Bio install_environment.STDOUT DEBUG 2017-11-18 17:04:08,177 endencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/UniGene install_environment.STDOUT DEBUG 2017-11-18 17:04:08,179 Gene/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythcreating /galaxydir/galaxUniProt install_environment.STDOUT DEBUG 2017-11-18 17:04:08,180 f73c3b116/lib/python/Bio/Wise install_environment.STDOUT DEBUG 2017-11-18 17:04:08,180 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Wise install_environment.STDOUT DEBUG 2017-11-18 17:04:08,181 10.11-intel-2.7/Bio/Wise/psw.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/b116/lib/python/Bio/Wise install_environment.STDOUT DEBUG 2017-11-18 17:04:08,182 endencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/BioSQL install_environment.STDOUT DEBUG 2017-11-18 17:04:08,187 __init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-intel-2.7/BioSQL/7/a12f73c3b116/lib/python/BioSQL install_environment.STDOUT DEBUG 2017-11-18 17:04:08,189 67/a12f73c3b116/lib/python/Bio/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,193 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoit__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,198 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/_py3k/_o67/a12f73c3b116/lib/python/Bio/_utils.py to _utils.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,199 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythot__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,207 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Affy/Celbyte-compiling /galaxydirn/Bio/Align/__init__.py to __inbyte-compiling /galaxydir/galaxy/databaignInfo.py to AlignInfo.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,213 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,215 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Align/Ap install_environment.STDOUT DEBUG 2017-11-18 17:04:08,227 thon/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Align/Applications/_Clustalw.byte-compiling /galaxydirn/Bio/Align/Applications/_Dialibyte-compiling /galaxydir/galaxy/databaplications/_Mafft.py to _Mafft.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,230 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoobs.py to _MSAProbs.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,240 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Align/Apbyte-compiling /galaxydirn/Bio/Align/Applications/_Prankbyte-compiling /galaxydir/galaxy/databaplications/_Probcons.py to _Probcons.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,240 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoee.py to _TCoffee.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,249 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Align/Gebyte-compiling /galaxydirn/Bio/AlignIO/__init__.py to __byte-compiling /galaxydir/galaxy/databaClustalIO.py to ClustalIO.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,254 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobossIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,261 copying build/lib.macosx-10.11-intel-2.7/Bio/SeqRecord.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,261 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12cing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,262 7/Bio/Sequencing/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Sequencing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,262 10.11-intel-2.7/Bio/SeqIO/UniprotIO.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bio12f73c3b116/lib/python/Bif73c3b116/lib/python/Bio/Sequencopying build/lib.macosx-10.11-intel-2.ncies/biopython/1.67/biopython/package_biopythonthon/Bio/Sequencing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,262 copying build/lib.macosx-10.11-intel-2.7/Bio/Sequencing/Ace.py -> /galaxydir/galaxy/database/depende_1_67/a12f73c3b116/lib/pycreating /galaxydir/galaxy/datacing/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,262 10.11-intel-2.7/Bio/Sequencing/Applications/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Sequencing/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,262 copying build/lib.macosx-10.11-intel-2.7/Bio/Sequencing/Applications/_bwa.py -> /galaxydir/galaxy/da.67/biopython/package_bio/Sequencing/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,262 uencing/Applications/_Novoalign.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Sequencing/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,262 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Sequencopying build/lib.macosx-tabase/dependencies/biopython/1python_1_67/a12f73c3b116/lib/python/Biocopying build/lib.macosx-10.11-intel-2.7/Bio/Seqxy/database/dependencies/biopython/1.67/biopython/package_bi/lib/python/Bio/Sequencing/Applications tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,262 intel-2.7/Bio/Sequencing/Phd.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython//python/Bio/Sequencing tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,262 copying build/lib.macosx-10.11-intel-2.7/Bio/Sequencing/Applications/_samtools.py -> /galaxydir/galaopython_1_67/a12f73c3b116copying build/lib.macosx-10.11-package_biopython_1_67/a12f73c3b116/libcreating /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,262 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,263 ndencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,263 copying build/lib.macosx-10.11-intel-2.7/Bio/SeqUtils/CheckSum.py -> /galaxydir/galaxy/database/depecopying build/lib.macosx-/biopython/package_biopython_1_n/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,263 10.11-intel-2.7/Bio/SeqUtils/CodonUsage.py -> /galaxydir/galaxy/database/dependencies/biopython/1.6767/a12f73c3b116/lib/pythocopying build/lib.macosx-10.11-7/biopython/package_biopython_1_67/a12feqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,263 intel-2.7/Bio/SeqUtils/CodonUsageIndices.py -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Scopying build/lib.macosx-10.11-/biopython/package_biopython_1_67/a12f7qUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,263 intel-2.7/Bio/SeqUtils/lcc.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/paython/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,263 intel-2.7/Bio/SeqUtils/IsoelectricPoint.py -> /galaxydir/galaxy/database/dependencies/biopython/1.673c3b116/lib/python/Bio/Secopying build/lib.macosx-10.11-ckage_biopython_1_67/a12f73c3b116/lib/pcopying build/lib.macosx-10.11-intel-2.7/Bio/Seqpython_1_67/a12f73c3b116/lib/python/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,263 Utils/MeltingTemp.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biocopying build/lib.macosx-biopython/package_biopython_1_6/Bio/SeqUtils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,263 10.11-intel-2.7/Bio/SeqUtils/ProtParam.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/7/a12f73c3b116/lib/pythoncopying build/lib.macosx-10.11-opython/package_biopython_1_67/a12f73c3ils tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,263 intel-2.7/Bio/SeqUtils/ProtParamData.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/bib116/lib/python/Bio/SeqUtcreating /galaxydir/galaxy/datatics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,263 10.11-intel-2.7/Bio/Statistics/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.6767/a12f73c3b116/lib/pythocopying build/lib.macosx-10.11-intel-2.7/Bio/Statistics/lowess.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Statistics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,264 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Statiscopying build/lib.macosx-/biopython/package_biopython_1_n/Bio/Statistics tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,264 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12copying build/lib.macosx-10.11-intel-2.7/Bio/SubsMat/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SubsMat tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,264 f73c3b116/lib/python/Bio/SubsMat tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,264 ndencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SubsMat tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,264 copying build/lib.macosx-10.11-intel-2.7/Bio/SubsMat/FreqTable.py -> /galaxydir/galaxy/database/depecopying build/lib.macosx-biopython/package_biopython_1_6/Bio/SubsMat tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,264 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SVDSupcopying build/lib.macosx-10.11-intel-2.7/Bio/SVDSuperimposer/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SVDSuperimposer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,264 10.11-intel-2.7/Bio/SubsMat/MatrixInfo.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/7/a12f73c3b116/lib/pythoncreating /galaxydir/galaxy/dataerimposer tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,264 f73c3b116/lib/python/Bio/SwissProt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,264 10.11-intel-2.7/Bio/SwissProt/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SwissProt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,264 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12copying build/lib.macosx-copying build/lib.macosx-10.11-hon/package_biopython_1_67/a12f73c3b116 tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,264 base/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/TogoWScopying build/lib.macosx-10.11-intel-2.7/Bio/TogoWS/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/TogoWS tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,265 intel-2.7/Bio/SwissProt/KeyWList.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopyt/lib/python/Bio/SwissProtcreating /galaxydir/galaxy/data tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,265 ython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,265 10.11-intel-2.7/Bio/triefind.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/b116/lib/python/Bio tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,265 endencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/UniGene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,265 copying build/lib.macosx-10.11-intel-2.7/Bio/trie.so -> /galaxydir/galaxy/database/dependencies/biopcopying build/lib.macosx-package_biopython_1_67/a12f73c3creating /galaxydir/galaxy/database/depcopying build/lib.macosx-10.11-intel-2.7/Bio/Union_1_67/a12f73c3b116/lib/python/Bio/UniGene tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,265 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/copying build/lib.macosx-10.11-intel-2.7/Bio/UniProt/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/UniProt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,265 copying build/lib.macosx-10.11-intel-2.7/Bio/UniProt/GOA.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/UniProt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,265 Gene/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopythcreating /galaxydir/galaxUniProt tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,265 creating /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12copying build/lib.macosx-10.11-intel-2.7/Bio/Wise/__init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Wise tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,265 f73c3b116/lib/python/Bio/Wise tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,265 /biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Wise tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,265 10.11-intel-2.7/Bio/Wise/psw.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/b116/lib/python/Bio/Wise tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,266 endencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/BioSQL tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,266 copying build/lib.macosx-10.11-intel-2.7/Bio/Wise/dnal.py -> /galaxydir/galaxy/database/dependenciescopying build/lib.macosx-package_biopython_1_67/a12f73c3creating /galaxydir/galaxy/database/depcopying build/lib.macosx-10.11-intel-2.7/BioSQL/n/BioSQL tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,266 copying build/lib.macosx-10.11-intel-2.7/BioSQL/BioSeq.py -> /galaxydir/galaxy/database/dependencieson/BioSQL tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,266 copying build/lib.macosx-10.11-intel-2.7/BioSQL/BioSeqDatabase.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/BioSQL tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,266 DBUtils.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_6copying build/lib.macosx-10.11-intel-2.7/BioSQL/Loader.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/BioSQL tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,266 __init__.py -> /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythcopying build/lib.macosx-10.11-intel-2.7/BioSQL/7/a12f73c3b116/lib/python/BioSQL tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,266 67/a12f73c3b116/lib/python/Bio/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,266 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoit__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,266 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_byte-compiling /galaxydirn/Bio/_py3k/__init__.py to __inbyte-compiling /galaxydir/galaxy/databardereddict.py to _ordereddict.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,266 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/_py3k/_o67/a12f73c3b116/lib/python/Bio/_utils.py to _utils.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,266 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythot__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,266 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_byte-compiling /galaxydirn/Bio/Affy/__init__.py to __inibyte-compiling /galaxydir/galaxy/databaFile.py to CelFile.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,266 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoit__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,267 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Affy/Celbyte-compiling /galaxydirn/Bio/Align/__init__.py to __inbyte-compiling /galaxydir/galaxy/databaignInfo.py to AlignInfo.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,267 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,267 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Align/Ap tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,267 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Align/Albyte-compiling /galaxydirn/Bio/Align/Applications/__initbyte-compiling /galaxydir/galaxy/databaplications/_ClustalOmega.py to _ClustalOmega.pycbyte-compiling /galaxydir/galaxy/database/dependencies/biopypy to _Clustalw.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,267 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythogn.py to _Dialign.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,267 thon/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Align/Applications/_Clustalw.byte-compiling /galaxydirn/Bio/Align/Applications/_Dialibyte-compiling /galaxydir/galaxy/databaplications/_Mafft.py to _Mafft.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,267 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoobs.py to _MSAProbs.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,267 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Align/Apbyte-compiling /galaxydirn/Bio/Align/Applications/_MSAPrbyte-compiling /galaxydir/galaxy/databaplications/_Muscle.py to _Muscle.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,267 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho.py to _Prank.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,267 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Align/Apbyte-compiling /galaxydirn/Bio/Align/Applications/_Prankbyte-compiling /galaxydir/galaxy/databaplications/_Probcons.py to _Probcons.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,267 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoee.py to _TCoffee.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,267 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Align/Apbyte-compiling /galaxydirn/Bio/Align/Applications/_TCoffbyte-compiling /galaxydir/galaxy/databaneric.py to Generic.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,267 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoinit__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,268 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Align/Gebyte-compiling /galaxydirn/Bio/AlignIO/__init__.py to __byte-compiling /galaxydir/galaxy/databaClustalIO.py to ClustalIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,268 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobossIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,268 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/AlignIO/byte-compiling /galaxydirn/Bio/AlignIO/EmbossIO.py to Embyte-compiling /galaxydir/galaxy/databaFastaIO.py to FastaIO.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,282 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/AlignIO/byte-compiling /galaxydirn/Bio/AlignIO/Interfaces.py to byte-compiling /galaxydir/galaxy/databa67/a12f73c3b116/lib/python/Bio/AlignIO/PhylipIO.67/a12f73c3b116/lib/python/Bio/AlignIO/StockholmIO.py to StockholmIO.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,287 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho_init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,297 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Alphabet/IUPAC.py to IUPAC.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,298 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Alphabet/Reduced.py to Reduced.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,306 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_t__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,310 thon/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/bgzf.py to bgzf.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,316 thon/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Blast/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,317 hon_1_67/a12f73c3b116/lib/python/Bio/Blast/Applications.py to Applications.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,325 b/python/Bio/Blast/NCBIStandalone.py to NCBIStandalone.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,341 to NCBIWWW.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,356 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_byte-compiling /galaxydir67/a12f73c3b116/lib/python/Bio/t__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,371 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoInterfaces.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,371 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/AlignIO/NexusIO.py to NexusIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,371 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_py to PhylipIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,371 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/AlignIO/byte-compiling /galaxydirn/Bio/AlignIO/Interfaces.py to byte-compiling /galaxydir/galaxy/databa67/a12f73c3b116/lib/python/Bio/AlignIO/PhylipIO.67/a12f73c3b116/lib/python/Bio/AlignIO/StockholmIO.py to StockholmIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,371 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho_init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,371 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Alphabet/IUPAC.py to IUPAC.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,371 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Alphabet/Reduced.py to Reduced.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,371 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_t__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,371 thon/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/bgzf.py to bgzf.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,371 thon/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Blast/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,372 hon_1_67/a12f73c3b116/lib/python/Bio/Blast/Applications.py to Applications.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,372 b/python/Bio/Blast/NCBIStandalone.py to NCBIStandalone.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,372 to NCBIWWW.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,372 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_byte-compiling /galaxydirn/Bio/Alphabet/__init__.py to _byte-compiling /galaxydir/galaxy/databa67/a12f73c3b116/lib/python/Bio/Application/__inibyte-compiling /galaxydir/galaxy/database/dependencies/biopybyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopybyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopytbyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/libyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Blast/NCBIWWW.pybyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Blast/NCBIXML.py to NCBIXML.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,372 67/a12f73c3b116/lib/python/Bio/Blast/ParseBlastTable.py to ParseBlastTable.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,372 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Blast/Record.py to Record.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,372 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_byte-compiling /galaxydir67/a12f73c3b116/lib/python/Bio/t__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,372 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_CAPS/__init__.py to __inibyte-compiling /galaxydir/galaxCluster/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,372 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,372 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydirn/Bio/codonalign/__init__.py tobyte-compiling /galaxydir/galaxy/databagn/chisq.py to chisq.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,381 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho.py to codonalignment.pyc67/a12f73c3b116/lib/python/Bio/py to codonalphabet.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,404 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydirn/Bio/Compass/__init__.py to __byte-compiling /galaxydir/galaxy/databa__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,407 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythot__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,432 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Data/Codbyte-compiling /galaxydirn/Bio/Data/IUPACData.py to IUPAbyte-compiling /galaxydir/galaxy/databa67/a12f73c3b116/lib/python/Bio/DocSQL.py to DocSbyte-compiling /galaxydir/galaxy/database/dependencies/biopy_.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,432 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho Applications.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,458 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Emboss/Pbyte-compiling /galaxydirn/Bio/Emboss/PrimerSearch.py tobyte-compiling /galaxydir/galaxy/databa67/a12f73c3b116/lib/python/Bio/Entrez/Parser.py byte-compiling /galaxydir/galaxy/database/dependencies/biopy_.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,459 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoe.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,465 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/ExPASy/Pbyte-compiling /galaxydir67/a12f73c3b116/lib/python/Bio/ScanProsite.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,473 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydirn/Bio/codonalign/__init__.py tobyte-compiling /galaxydir/galaxy/databagn/chisq.py to chisq.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,473 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/codonalibyte-compiling /galaxydirn/Bio/codonalign/codonalignment tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,473 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho.py to codonalignment.pyc67/a12f73c3b116/lib/python/Bio/py to codonalphabet.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,473 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_codonalign/codonalphabet.byte-compiling /galaxydir/galaxcodonalign/codonseq.py to codonseq.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,474 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoinit__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,474 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydirn/Bio/Compass/__init__.py to __byte-compiling /galaxydir/galaxy/databa__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,474 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythot__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,474 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Crystal/byte-compiling /galaxydirn/Bio/Data/__init__.py to __inibyte-compiling /galaxydir/galaxy/databaonTable.py to CodonTable.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,474 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoCData.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,474 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Data/SCOPData.py to SCOPData.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,475 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_QL.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,475 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Data/Codbyte-compiling /galaxydirn/Bio/Data/IUPACData.py to IUPAbyte-compiling /galaxydir/galaxy/databa67/a12f73c3b116/lib/python/Bio/DocSQL.py to DocSbyte-compiling /galaxydir/galaxy/database/dependencies/biopy_.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,475 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho Applications.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,475 thon/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Emboss/__init__.py to __init_byte-compiling /galaxydirn/Bio/Emboss/Applications.py tobyte-compiling /galaxydir/galaxy/databarimer3.py to Primer3.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,475 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho PrimerSearch.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,475 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Entrez/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,475 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_to Parser.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,475 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Emboss/Pbyte-compiling /galaxydirn/Bio/Emboss/PrimerSearch.py tobyte-compiling /galaxydir/galaxy/databa67/a12f73c3b116/lib/python/Bio/Entrez/Parser.py byte-compiling /galaxydir/galaxy/database/dependencies/biopy_.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,475 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoe.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,475 thon/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/ExPASy/__init__.py to __init_byte-compiling /galaxydirn/Bio/ExPASy/Enzyme.py to Enzymbyte-compiling /galaxydir/galaxy/databarodoc.py to Prodoc.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,475 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/ExPASy/Prosite.py to Prosite.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,475 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/ExPASy/Pbyte-compiling /galaxydir67/a12f73c3b116/lib/python/Bio/ScanProsite.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,476 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_ExPASy/ScanProsite.py to byte-compiling /galaxydir/galaxFile.py to File.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,476 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/FSSP/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,476 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydir67/a12f73c3b116/lib/python/Bio/rec.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,479 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydirn/Bio/GA/__init__.py to __init_67/a12f73c3b116/lib/python/Bio/GA/Crosst__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,483 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydirn/Bio/GA/Crossover/GeneralPointbyte-compiling /galaxydir/galaxy/databaover/Point.py to Point.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,484 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoto TwoPoint.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,487 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Crossbyte-compiling /galaxydirn/Bio/GA/Evolver.py to Evolver.byte-compiling /galaxydir/galaxy/databaion/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,488 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho General.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,492 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Mutatbyte-compiling /galaxydirn/Bio/GA/Organism.py to Organisbyte-compiling /galaxydir/galaxy/databar/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,492 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoto Stabilizing.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,495 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Selecbyte-compiling /galaxydirn/Bio/GA/Selection/Abstract.py byte-compiling /galaxydir/galaxy/databation/Diversity.py to Diversity.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,500 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythol.py to RouletteWheel.pycbyte-compiling /galaxydir/galaxGA/Selection/Tournament.py to Tournamenbyte-compiling /galaxydir/galaxy/database/dependpy to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,511 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythord.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,528 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GenBank/byte-compiling /galaxydirn/Bio/GenBank/utils.py to utilsbyte-compiling /galaxydir/galaxy/databait__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,529 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,532 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphicsbyte-compiling /galaxydirn/Bio/Graphics/BasicChromosome. install_environment.STDOUT DEBUG 2017-11-18 17:04:08,540 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,544 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/Comparatbyte-compiling /galaxydirn/Bio/Graphics/DisplayRepresententation.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,547 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/n.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,550 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDiagram/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,554 thon/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDiagram/_Abstrbyte-compiling /galaxydirn/Bio/Graphics/GenomeDiagram/_CularDrawer.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,569 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/olors.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,573 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDibyte-compiling /galaxydirn/Bio/Graphics/GenomeDiagram/_D install_environment.STDOUT DEBUG 2017-11-18 17:04:08,575 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Feature.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,578 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydir67/a12f73c3b116/lib/python/Bio/rec.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,578 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_FSSP/fssp_rec.py to fssp_byte-compiling /galaxydir/galaxFSSP/FSSPTools.py to FSSPTools.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,578 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho_.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,578 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydirn/Bio/GA/__init__.py to __init_67/a12f73c3b116/lib/python/Bio/GA/Crosst__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,579 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_over/__init__.py to __inibyte-compiling /galaxydir/galaxGA/Crossover/General.py to General.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,579 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho.py to GeneralPoint.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,579 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydirn/Bio/GA/Crossover/GeneralPointbyte-compiling /galaxydir/galaxy/databaover/Point.py to Point.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,579 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoto TwoPoint.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,579 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Crossbyte-compiling /galaxydirn/Bio/GA/Crossover/TwoPoint.py byte-compiling /galaxydir/galaxy/databaover/Uniform.py to Uniform.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,579 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythopyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,579 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Crossbyte-compiling /galaxydirn/Bio/GA/Evolver.py to Evolver.byte-compiling /galaxydir/galaxy/databaion/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,579 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho General.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,579 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Mutatbyte-compiling /galaxydirn/Bio/GA/Mutation/General.py tobyte-compiling /galaxydir/galaxy/databaion/Simple.py to Simple.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,579 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythom.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,579 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Mutatbyte-compiling /galaxydirn/Bio/GA/Organism.py to Organisbyte-compiling /galaxydir/galaxy/databar/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,580 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDibyte-compiling /galaxydirram/_Graph.py to _Graph.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,580 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoto Stabilizing.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,580 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Repaibyte-compiling /galaxydirn/Bio/GA/Repair/Stabilizing.py byte-compiling /galaxydir/galaxy/databation/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,580 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoto Abstract.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,580 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Selecbyte-compiling /galaxydirn/Bio/GA/Selection/Abstract.py byte-compiling /galaxydir/galaxy/databation/Diversity.py to Diversity.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,580 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GA/Selecbyte-compiling /galaxydirn/Bio/GA/Selection/RouletteWhee tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,580 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/t.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,580 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythol.py to RouletteWheel.pycbyte-compiling /galaxydir/galaxGA/Selection/Tournament.py to Tournamenbyte-compiling /galaxydir/galaxy/database/dependpy to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,580 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythord.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,580 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GenBank/__init__.byte-compiling /galaxydirn/Bio/GenBank/Record.py to Recobyte-compiling /galaxydir/galaxy/databaScanner.py to Scanner.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,580 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,581 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/GenBank/byte-compiling /galaxydirn/Bio/GenBank/utils.py to utilsbyte-compiling /galaxydir/galaxy/databait__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,581 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,581 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Geo/__inbyte-compiling /galaxydirn/Bio/Geo/Record.py to Record.pbyte-compiling /galaxydir/galaxy/databa/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,581 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphicsbyte-compiling /galaxydirn/Bio/Graphics/BasicChromosome. tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,581 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,581 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythopy to BasicChromosome.pycbyte-compiling /galaxydir/galaxGraphics/ColorSpiral.py to ColorSpiral.byte-compiling /galaxydir/galaxy/database/dependive.py to Comparative.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,581 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/Comparatbyte-compiling /galaxydirn/Bio/Graphics/DisplayRepresententation.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,581 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/n.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,581 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDiagram/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,581 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoation.py to DisplayRepresbyte-compiling /galaxydir/galaxGraphics/Distribution.py to Distributiobyte-compiling /galaxydir/galaxy/database/dependbyte-compiling /galaxydir/galaxy/database/dependencies/biopyactDrawer.py to _AbstractDrawer.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,581 thon/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDiagram/_Abstrbyte-compiling /galaxydirn/Bio/Graphics/GenomeDiagram/_CularDrawer.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,582 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/olors.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,582 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoircularDrawer.py to _Circbyte-compiling /galaxydir/galaxGraphics/GenomeDiagram/_Colors.py to _Cbyte-compiling /galaxydir/galaxy/database/dependagram/_CrossLink.py to _CrossLink.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,582 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDibyte-compiling /galaxydirn/Bio/Graphics/GenomeDiagram/_D tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,582 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Feature.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,582 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoiagram.py to _Diagram.pycbyte-compiling /galaxydir/galaxGraphics/GenomeDiagram/_Feature.py to _byte-compiling /galaxydir/galaxy/database/dependagram/_FeatureSet.py to _FeatureSet.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,582 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDibyte-compiling /galaxydirram/_Graph.py to _Graph.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,582 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/_GraphSet.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,598 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDibyte-compiling /galaxydirn/Bio/Graphics/GenomeDiagram/_Tbyte-compiling /galaxydir/galaxy/databa/KGML_vis.py to KGML_vis.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,602 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,610 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/HMM/Dynabyte-compiling /galaxydirn/Bio/HMM/MarkovModel.py to Marbyte-compiling /galaxydir/galaxy/databaner.py to Trainer.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,613 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoties.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,618 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Index.pybyte-compiling /galaxydirn/Bio/KDTree/__init__.py to __ibyte-compiling /galaxydir/galaxy/databaDTree.py to KDTree.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,620 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythot__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,627 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KEGG/Combyte-compiling /galaxydirn/Bio/KEGG/Enzyme/__init__.py tbyte-compiling /galaxydir/galaxy/databaL/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,628 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoto KGML_parser.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,638 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KEGG/KGMbyte-compiling /galaxydirn/Bio/KEGG/Map/__init__.py to _byte-compiling /galaxydir/galaxy/databaT.py to REST.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,641 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/kNN.py to kNN.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,643 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/67/a12f73c3b116/lib/python/Bio/MarkovModel.py to MarkovModel.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,649 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythopy.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,660 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Medline/byte-compiling /galaxydirn/Bio/motifs/__init__.py to __ibyte-compiling /galaxydir/galaxy/databalignace.py to alignace.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,661 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythot__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,669 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/abyte-compiling /galaxydirn/Bio/motifs/jaspar/__init__.pybyte-compiling /galaxydir/galaxy/databaaspar/db.py to db.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,674 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,686 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/_GraphSet.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,688 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDiagbyte-compiling /galaxydir/galaxGraphics/GenomeDiagram/_GraphSet.py to byte-compiling /galaxydir/galaxy/database/dependagram/_LinearDrawer.py to _LinearDrawer.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,689 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythorack.py to _Track.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,689 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/mbyte-compiling /galaxydirbyte-compiling /galaxydir/galaxmotifs/thresholds.py to thresholds.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,693 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphics/GenomeDibyte-compiling /galaxydirn/Bio/Graphics/GenomeDiagram/_Tbyte-compiling /galaxydir/galaxy/databa/KGML_vis.py to KGML_vis.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,693 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,693 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Graphicsbyte-compiling /galaxydirn/Bio/HMM/__init__.py to __initbyte-compiling /galaxydir/galaxy/databamicProgramming.py to DynamicProgramming.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,693 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythokovModel.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,694 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/HMM/Dynabyte-compiling /galaxydirn/Bio/HMM/MarkovModel.py to Marbyte-compiling /galaxydir/galaxy/databaner.py to Trainer.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,694 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoties.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,694 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/HMM/Traibyte-compiling /galaxydirn/Bio/HMM/Utilities.py to Utilibyte-compiling /galaxydir/galaxy/databa to Index.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,694 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythonit__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,694 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Index.pybyte-compiling /galaxydirn/Bio/KDTree/__init__.py to __ibyte-compiling /galaxydir/galaxy/databaDTree.py to KDTree.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,694 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythot__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,694 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KDTree/Kbyte-compiling /galaxydirn/Bio/KEGG/__init__.py to __inibyte-compiling /galaxydir/galaxy/databapound/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,694 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoo __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,694 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KEGG/Combyte-compiling /galaxydirn/Bio/KEGG/Enzyme/__init__.py tbyte-compiling /galaxydir/galaxy/databaL/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,695 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoto KGML_parser.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,695 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KEGG/KGMbyte-compiling /galaxydirn/Bio/KEGG/KGML/KGML_parser.py byte-compiling /galaxydir/galaxy/databaL/KGML_pathway.py to KGML_pathway.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,695 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho_init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,695 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KEGG/KGMbyte-compiling /galaxydirn/Bio/KEGG/Map/__init__.py to _byte-compiling /galaxydir/galaxy/databaT.py to REST.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,695 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/kNN.py to kNN.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,695 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/KEGG/RESbyte-compiling /galaxydirbyte-compiling /galaxydir/galaxLogisticRegression.py to LogisticRegression.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,695 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/67/a12f73c3b116/lib/python/Bio/MarkovModel.py to MarkovModel.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,695 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythopy.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,695 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_byte-compiling /galaxydirn/Bio/MaxEntropy.py to MaxEntrobyte-compiling /galaxydir/galaxy/databa__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,695 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythonit__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,695 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Medline/byte-compiling /galaxydirn/Bio/motifs/__init__.py to __ibyte-compiling /galaxydir/galaxy/databalignace.py to alignace.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,695 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythot__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,696 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/abyte-compiling /galaxydirn/Bio/motifs/applications/__inibyte-compiling /galaxydir/galaxy/databapplications/_xxmotif.py to _xxmotif.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,696 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,696 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/abyte-compiling /galaxydirn/Bio/motifs/jaspar/__init__.pybyte-compiling /galaxydir/galaxy/databaaspar/db.py to db.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,696 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,696 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/jbyte-compiling /galaxydirn/Bio/motifs/mast.py to mast.pybyte-compiling /galaxydir/galaxy/databaatrix.py to matrix.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,696 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/meme.py to meme.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,696 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/mbyte-compiling /galaxydirbyte-compiling /galaxydir/galaxmotifs/thresholds.py to thresholds.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,696 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/motifs/transfac.py to transfac.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,696 67/a12f73c3b116/lib/python/Bio/NaiveBayes.py to NaiveBayes.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,698 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_byte-compiling /galaxydirn/Bio/NeuralNetwork/__init__.pybyte-compiling /galaxydir/galaxy/databatwork/BackPropagation/__init__.py to __init__.pybyte-compiling /galaxydir/galaxy/database/dependencies/biopy/Layer.py to Layer.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,706 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork/BackPropagation/Network.py to Network.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,713 67/a12f73c3b116/lib/python/Bio/NeuralNetwork/Gene/Signature.py to Signature.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,716 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork/StopTraining.py to StopTraining.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,724 67/a12f73c3b116/lib/python/Bio/Nexus/__init__.py to __init__.pyc 127.0.0.1 - - [18/Nov/2017:17:04:08 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" install_environment.STDOUT DEBUG 2017-11-18 17:04:08,746 67/a12f73c3b116/lib/python/Bio/Nexus/Nodes.py to Nodes.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,748 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoStandardData.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,760 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Nexus/Trbyte-compiling /galaxydirn/Bio/NMR/__init__.py to __initbyte-compiling /galaxydir/galaxy/databaools.py to NOEtools.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,762 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythols.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,779 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/pairwisebyte-compiling /galaxydirn/Bio/ParserSupport.py to Parsebyte-compiling /galaxydir/galaxy/databa__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,782 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoo __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,788 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Pathway/byte-compiling /galaxydirn/Bio/Pathway/Rep/MultiGraph.pybyte-compiling /galaxydir/galaxy/databait__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,790 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoy to AbstractPropertyMap.byte-compiling /galaxydir/galaxPDB/Atom.py to Atom.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,792 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho install_environment.STDOUT DEBUG 2017-11-18 17:04:08,794 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/Dicebyte-compiling /galaxydirn/Bio/PDB/DSSP.py to DSSP.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,797 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,797 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNec tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,797 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_byte-compiling /galaxydirn/Bio/NeuralNetwork/__init__.pybyte-compiling /galaxydir/galaxy/databatwork/BackPropagation/__init__.py to __init__.pybyte-compiling /galaxydir/galaxy/database/dependencies/biopy/Layer.py to Layer.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,797 thon/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork/BackPropagationbyte-compiling /galaxydirbyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork/Gene/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,797 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork/Gene/Motif.py to Motif.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,797 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork/Gene/Pattern.py to Pattern.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,798 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/Entity.py to Entity.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,797 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork/Gene/Schema.py to Schema.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,798 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork/BackPropagation/Network.py to Network.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,798 67/a12f73c3b116/lib/python/Bio/NeuralNetwork/Gene/Signature.py to Signature.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,798 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_byte-compiling /galaxydirbyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork/Training.py to Training.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,798 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NeuralNetwork/StopTraining.py to StopTraining.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,798 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Nexus/Nexus.py to Nexus.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,798 67/a12f73c3b116/lib/python/Bio/Nexus/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,798 67/a12f73c3b116/lib/python/Bio/Nexus/Nodes.py to Nodes.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,799 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoStandardData.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,799 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_byte-compiling /galaxydirn/Bio/Nexus/StandardData.py to byte-compiling /galaxydir/galaxy/databaees.py to Trees.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,799 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,799 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Nexus/Trbyte-compiling /galaxydirn/Bio/NMR/__init__.py to __initbyte-compiling /galaxydir/galaxy/databaools.py to NOEtools.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,799 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythols.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,799 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/NMR/NOEtbyte-compiling /galaxydirn/Bio/NMR/xpktools.py to xpktoobyte-compiling /galaxydir/galaxy/databa2.py to pairwise2.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,799 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythorSupport.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,799 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/pairwisebyte-compiling /galaxydirn/Bio/ParserSupport.py to Parsebyte-compiling /galaxydir/galaxy/databa__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,799 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoo __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,799 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Pathway/byte-compiling /galaxydirn/Bio/Pathway/Rep/__init__.py tbyte-compiling /galaxydir/galaxy/databaRep/Graph.py to Graph.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,799 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho to MultiGraph.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,800 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Pathway/byte-compiling /galaxydirn/Bio/Pathway/Rep/MultiGraph.pybyte-compiling /galaxydir/galaxy/databait__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,800 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/__inbyte-compiling /galaxydirn/Bio/PDB/AbstractPropertyMap.ppyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,800 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoy to AbstractPropertyMap.byte-compiling /galaxydir/galaxPDB/Atom.py to Atom.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,800 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,800 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydirn/Bio/PDB/Chain.py to Chain.pycbyte-compiling /galaxydir/galaxy/databa.py to Dice.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,800 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/Dicebyte-compiling /galaxydirn/Bio/PDB/DSSP.py to DSSP.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,800 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/Entity.py to Entity.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,801 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,808 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/HSExposure.pybyte-compiling /galaxydirn/Bio/PDB/MMCIF2Dict.py to MMCIbyte-compiling /galaxydir/galaxy/databaFParser.py to MMCIFParser.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,811 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho install_environment.STDOUT DEBUG 2017-11-18 17:04:08,818 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/NACCbyte-compiling /galaxydirn/Bio/PDB/NeighborSearch.py to byte-compiling /galaxydir/galaxy/databae_pdb_header.py to parse_pdb_header.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,822 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoDBExceptions.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,830 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/PDBIbyte-compiling /galaxydirn/Bio/PDB/PDBList.py to PDBListbyte-compiling /galaxydir/galaxy/databaarser.py to PDBParser.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,834 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoypeptide.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,842 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/PSEAbyte-compiling /galaxydirn/Bio/PDB/QCPSuperimposer/__inibyte-compiling /galaxydir/galaxy/databadue.py to Residue.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,844 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythosidueDepth.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,847 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/Selebyte-compiling /galaxydirn/Bio/PDB/Structure.py to Strucbyte-compiling /galaxydir/galaxy/databactureAlignment.py to StructureAlignment.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,850 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoo StructureBuilder.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,859 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/Supebyte-compiling /galaxydirn/Bio/PDB/Vector.py to Vector.pbyte-compiling /galaxydir/galaxy/databae/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,860 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoo phen_micro.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,874 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/phenotypbyte-compiling /galaxydirn/Bio/Phylo/__init__.py to __inbyte-compiling /galaxydir/galaxy/databadao_owl.py to _cdao_owl.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,887 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirn/Bio/Phylo/_utils.py to _utilsbyte-compiling /galaxydir/galaxy/databa67/a12f73c3b116/lib/python/Bio/Phylo/Applicationee.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,889 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,902 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,902 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirbyte-compiling /galaxydir/galaxPDB/FragmentMapper.py to FragmentMapperbyte-compiling /galaxydir/galaxy/database/depend to HSExposure.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,902 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoF2Dict.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,902 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/HSExposure.pybyte-compiling /galaxydirn/Bio/PDB/MMCIF2Dict.py to MMCIbyte-compiling /galaxydir/galaxy/databaFParser.py to MMCIFParser.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,902 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,902 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/MMCIbyte-compiling /galaxydirn/Bio/PDB/Model.py to Model.pycbyte-compiling /galaxydir/galaxy/databaESS.py to NACCESS.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,903 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoNeighborSearch.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,903 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/NACCbyte-compiling /galaxydirn/Bio/PDB/NeighborSearch.py to byte-compiling /galaxydir/galaxy/databae_pdb_header.py to parse_pdb_header.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,903 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoDBExceptions.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,903 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/parsbyte-compiling /galaxydirn/Bio/PDB/PDBExceptions.py to Pbyte-compiling /galaxydir/galaxy/databaO.py to PDBIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,903 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,903 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/PDBIbyte-compiling /galaxydirn/Bio/PDB/PDBList.py to PDBListbyte-compiling /galaxydir/galaxy/databaarser.py to PDBParser.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,903 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoypeptide.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,903 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/PDBPbyte-compiling /galaxydirn/Bio/PDB/Polypeptide.py to Polbyte-compiling /galaxydir/galaxy/databa.py to PSEA.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,903 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythot__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,903 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/PSEAbyte-compiling /galaxydirn/Bio/PDB/QCPSuperimposer/__inibyte-compiling /galaxydir/galaxy/databadue.py to Residue.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,904 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythosidueDepth.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,904 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/Resibyte-compiling /galaxydirn/Bio/PDB/ResidueDepth.py to Rebyte-compiling /galaxydir/galaxy/databaction.py to Selection.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,904 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoture.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,904 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/Selebyte-compiling /galaxydirn/Bio/PDB/Structure.py to Strucbyte-compiling /galaxydir/galaxy/databactureAlignment.py to StructureAlignment.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,904 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoo StructureBuilder.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,904 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/Strubyte-compiling /galaxydirn/Bio/PDB/StructureBuilder.py tbyte-compiling /galaxydir/galaxy/databarimposer.py to Superimposer.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,904 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,904 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PDB/Supebyte-compiling /galaxydirn/Bio/PDB/Vector.py to Vector.pbyte-compiling /galaxydir/galaxy/databae/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,905 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoo phen_micro.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,905 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/phenotypbyte-compiling /galaxydirn/Bio/phenotype/phen_micro.py tbyte-compiling /galaxydir/galaxy/databae/pm_fitting.py to pm_fitting.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,905 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoit__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,905 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/phenotypbyte-compiling /galaxydirn/Bio/Phylo/__init__.py to __inbyte-compiling /galaxydir/galaxy/databadao_owl.py to _cdao_owl.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,905 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/_cbyte-compiling /galaxydirn/Bio/Phylo/_io.py to _io.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,905 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,905 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/Applications/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,905 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirn/Bio/Phylo/_utils.py to _utilsbyte-compiling /galaxydir/galaxy/databa67/a12f73c3b116/lib/python/Bio/Phylo/Applicationee.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,905 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,905 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_s/_Fasttree.py to _Fasttrbyte-compiling /galaxydir/galaxPhylo/Applications/_Phyml.py to _Phyml.byte-compiling /galaxydir/galaxy/database/depends/_Raxml.py to _Raxml.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,905 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoTree.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,906 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/CDAO.py to CDAO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:08,906 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_o CDAOIO.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,931 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/Applicationbyte-compiling /galaxydirn/Bio/Phylo/BaseTree.py to Basebyte-compiling /galaxydir/galaxy/databa67/a12f73c3b116/lib/python/Bio/Phylo/CDAOIO.py t67/a12f73c3b116/lib/python/Bio/Phylo/Consensus.py to Consensbyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopybyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopytbyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/libyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/NeXMLIO.pybyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/NexusIO.py to NexusIO.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,932 67/a12f73c3b116/lib/python/Bio/Phylo/PAML/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,937 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho67/a12f73c3b116/lib/pythoaseml.py to _parse_baseml.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,940 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/odeml.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,951 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/PAML/_parsebyte-compiling /galaxydirn/Bio/Phylo/PAML/baseml.py to bbyte-compiling /galaxydir/galaxy/databaML/chi2.py to chi2.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,953 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoodeml.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,973 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/PAbyte-compiling /galaxydirn/Bio/Phylo/PhyloXML.py to Phylbyte-compiling /galaxydir/galaxy/databayloXMLIO.py to PhyloXMLIO.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:08,986 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho to TreeConstruction.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,000 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/_byte-compiling /galaxydirn/Bio/PopGen/Async/__init__.py byte-compiling /galaxydir/galaxy/databasync/Local.py to Local.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,002 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoto __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,011 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_us.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,011 thon/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/Newick.py to Newick.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,011 hon_1_67/a12f73c3b116/lib/python/Bio/Phylo/NewickIO.py to NewickIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,011 b/python/Bio/Phylo/NeXML.py to NeXML.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,011 to NeXMLIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,012 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/Applicationbyte-compiling /galaxydirn/Bio/Phylo/BaseTree.py to Basebyte-compiling /galaxydir/galaxy/databa67/a12f73c3b116/lib/python/Bio/Phylo/CDAOIO.py t67/a12f73c3b116/lib/python/Bio/Phylo/Consensus.py to Consensbyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopybyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopytbyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/libyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/NeXMLIO.pybyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/NexusIO.py to NexusIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,012 67/a12f73c3b116/lib/python/Bio/Phylo/PAML/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,012 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_byte-compiling /galaxydirn/Bio/Phylo/PAML/_paml.py to _paml.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,012 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho67/a12f73c3b116/lib/pythoaseml.py to _parse_baseml.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,012 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/odeml.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,012 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_n/Bio/Phylo/PAML/_parse_bbyte-compiling /galaxydir/galaxPhylo/PAML/_parse_codeml.py to _parse_cbyte-compiling /galaxydir/galaxy/database/depend_yn00.py to _parse_yn00.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,012 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoaseml.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,012 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/PAML/_parsebyte-compiling /galaxydirn/Bio/Phylo/PAML/baseml.py to bbyte-compiling /galaxydir/galaxy/databaML/chi2.py to chi2.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,012 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoodeml.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,012 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/PAbyte-compiling /galaxydirn/Bio/Phylo/PAML/codeml.py to cbyte-compiling /galaxydir/galaxy/databaML/yn00.py to yn00.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,012 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythooXML.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,013 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/PAbyte-compiling /galaxydirn/Bio/Phylo/PhyloXML.py to Phylbyte-compiling /galaxydir/galaxy/databayloXMLIO.py to PhyloXMLIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,013 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho to TreeConstruction.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,013 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Phylo/Phbyte-compiling /galaxydirn/Bio/Phylo/TreeConstruction.pybyte-compiling /galaxydir/galaxy/databa_init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,013 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoto __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,013 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/_byte-compiling /galaxydirn/Bio/PopGen/Async/__init__.py byte-compiling /galaxydir/galaxy/databasync/Local.py to Local.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,013 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoto __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,013 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/Abyte-compiling /galaxydirn/Bio/PopGen/FDist/__init__.py byte-compiling /galaxydir/galaxy/databaDist/Async.py to Async.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,013 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoy to Controller.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,014 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/Fbyte-compiling /galaxydirn/Bio/PopGen/FDist/Controller.pbyte-compiling /galaxydir/galaxy/databaDist/Utils.py to Utils.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,017 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoy to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,060 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/Gbyte-compiling /galaxydirn/Bio/PopGen/GenePop/EasyContro.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,063 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/ser.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,069 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/GenePop/Labyte-compiling /galaxydirn/Bio/PopGen/GenePop/Utils.py tbyte-compiling /galaxydir/galaxy/databaimCoal/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,069 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoo Async.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,076 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/Sbyte-compiling /galaxydirn/Bio/PopGen/SimCoal/Controllerbyte-compiling /galaxydir/galaxy/databaimCoal/Template.py to Template.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,079 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoo __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,087 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Restrictbyte-compiling /galaxydirn/Bio/Restriction/RanaConfig.pybyte-compiling /galaxydir/galaxy/databaion/Restriction.py to Restriction.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,116 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/Fbyte-compiling /galaxydirn/Bio/PopGen/FDist/Controller.pbyte-compiling /galaxydir/galaxy/databaDist/Utils.py to Utils.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,116 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoy to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,116 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/Fbyte-compiling /galaxydirn/Bio/PopGen/GenePop/__init__.pbyte-compiling /galaxydir/galaxy/databaenePop/Controller.py to Controller.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,116 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/Gbyte-compiling /galaxydirn/Bio/PopGen/GenePop/EasyContro.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,116 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/ser.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,116 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytholler.py to EasyControllerbyte-compiling /galaxydir/galaxPopGen/GenePop/FileParser.py to FileParbyte-compiling /galaxydir/galaxy/database/dependrgeFileParser.py to LargeFileParser.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,116 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoo Utils.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,116 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/GenePop/Labyte-compiling /galaxydirn/Bio/PopGen/GenePop/Utils.py tbyte-compiling /galaxydir/galaxy/databaimCoal/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,117 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoo Async.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,117 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/Sbyte-compiling /galaxydirn/Bio/PopGen/SimCoal/Async.py tbyte-compiling /galaxydir/galaxy/databaimCoal/Cache.py to Cache.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,117 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho.py to Controller.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,117 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/Sbyte-compiling /galaxydirn/Bio/PopGen/SimCoal/Controllerbyte-compiling /galaxydir/galaxy/databaimCoal/Template.py to Template.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,117 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoo __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,117 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/PopGen/Sbyte-compiling /galaxydirn/Bio/Restriction/__init__.py tbyte-compiling /galaxydir/galaxy/databaion/PrintFormat.py to PrintFormat.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,117 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho to RanaConfig.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,117 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Restrictbyte-compiling /galaxydirn/Bio/Restriction/RanaConfig.pybyte-compiling /galaxydir/galaxy/databaion/Restriction.py to Restriction.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,219 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Restrictbyte-compiling /galaxydirn/Bio/Restriction/Restriction_Don_Dictionary.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,336 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoictionary.py to Restrictibyte-compiling /galaxydir/galaxSCOP/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,344 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirn/Bio/SCOP/Des.py to Des.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,346 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirn/Bio/SCOP/Hie.py to Hie.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,352 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirn/Bio/SCOP/Residues.py to Residbyte-compiling /galaxydir/galaxy/databa/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,354 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythodex.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,356 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/_model/_base.py byte-compiling /galaxydir/galaxy/databa/_model/hit.py to hit.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,359 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho hsp.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,373 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/_utils.py to _utbyte-compiling /galaxydir/galaxy/databa/BlastIO/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,374 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythob.py to blast_tab.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,392 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/BlastIO/blast_xmbyte-compiling /galaxydir/galaxy/databa/BlatIO.py to BlatIO.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,397 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoit__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,402 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/ExonerateIO/exonte_cigar.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,404 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/to exonerate_text.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,419 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/Exoneratbyte-compiling /galaxydirn/Bio/SearchIO/FastaIO.py to Fabyte-compiling /galaxydir/galaxy/databa/HmmerIO/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,420 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho to _base.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,426 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoictionary.py to Restrictibyte-compiling /galaxydir/galaxSCOP/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,427 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydirn/Bio/SCOP/Cla.py to Cla.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,427 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirn/Bio/SCOP/Des.py to Des.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,427 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirn/Bio/SCOP/Dom.py to Dom.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,427 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirn/Bio/SCOP/Hie.py to Hie.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,427 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirn/Bio/SCOP/Raf.py to Raf.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,427 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoues.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,427 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirn/Bio/SCOP/Residues.py to Residbyte-compiling /galaxydir/galaxy/databa/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,427 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythodex.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,427 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/_index.py to _inbyte-compiling /galaxydir/galaxy/databa/_model/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,427 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoto _base.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,427 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/_model/_base.py byte-compiling /galaxydir/galaxy/databa/_model/hit.py to hit.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,428 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho hsp.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,428 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/_model/hsp.py tobyte-compiling /galaxydir/galaxy/databa/_model/query.py to query.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,428 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoils.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,428 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/_utils.py to _utbyte-compiling /galaxydir/galaxy/databa/BlastIO/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,428 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythob.py to blast_tab.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,428 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/BlastIO/blast_tabyte-compiling /galaxydir/galaxy/databa/BlastIO/blast_text.py to blast_text.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,428 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythol.py to blast_xml.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,428 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/BlastIO/blast_xmbyte-compiling /galaxydir/galaxy/databa/BlatIO.py to BlatIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,428 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoit__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,428 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/ExonerateIO/__inbyte-compiling /galaxydir/galaxy/databa/ExonerateIO/_base.py to _base.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,428 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/ExonerateIO/exonte_cigar.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,428 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/to exonerate_text.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,429 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoerate_cigar.py to exonerabyte-compiling /galaxydir/galaxSearchIO/ExonerateIO/exonerate_text.py byte-compiling /galaxydir/galaxy/database/dependeIO/exonerate_vulgar.py to exonerate_vulgar.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,429 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythostaIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,429 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/Exoneratbyte-compiling /galaxydirn/Bio/SearchIO/FastaIO.py to Fabyte-compiling /galaxydir/galaxy/databa/HmmerIO/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,429 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho to _base.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,429 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/HmmerIO/_base.pybyte-compiling /galaxydir/galaxy/databa/HmmerIO/hmmer2_text.py to hmmer2_text.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,430 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/HmmerIO/hmmer3_d.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,435 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/3_tab.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,442 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/HmmerIO/byte-compiling /galaxydirn/Bio/Seq.py to Seq.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,454 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythore.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,477 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO/__byte-compiling /galaxydirn/Bio/SeqIO/_convert.py to _conbyte-compiling /galaxydir/galaxy/databandex.py to _index.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,482 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,489 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO/Acbyte-compiling /galaxydirn/Bio/SeqIO/FastaIO.py to Fastabyte-compiling /galaxydir/galaxy/databaIO.py to IgIO.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,490 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoIO.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,501 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO/Inbyte-compiling /galaxydirn/Bio/SeqIO/PdbIO.py to PdbIO.pbyte-compiling /galaxydir/galaxy/databadIO.py to PhdIO.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,502 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,512 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO/Qubyte-compiling /galaxydirn/Bio/SeqIO/SeqXmlIO.py to SeqXbyte-compiling /galaxydir/galaxy/databafIO.py to SffIO.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,525 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,531 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIObyte-compiling /galaxydirn/Bio/SearchIO/HmmerIO/hmmer3_d.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,531 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/3_tab.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,531 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoomtab.py to hmmer3_domtabbyte-compiling /galaxydir/galaxSearchIO/HmmerIO/hmmer3_tab.py to hmmerbyte-compiling /galaxydir/galaxy/database/dependhmmer3_text.py to hmmer3_text.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,531 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SearchIO/HmmerIO/byte-compiling /galaxydirn/Bio/Seq.py to Seq.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,531 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythore.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,531 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirn/Bio/SeqFeature.py to SeqFeatubyte-compiling /galaxydir/galaxy/databainit__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,531 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythovert.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,531 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO/__byte-compiling /galaxydirn/Bio/SeqIO/_convert.py to _conbyte-compiling /galaxydir/galaxy/databandex.py to _index.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,532 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,532 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO/_ibyte-compiling /galaxydirn/Bio/SeqIO/AbiIO.py to AbiIO.pbyte-compiling /galaxydir/galaxy/databaeIO.py to AceIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,532 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,532 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO/Acbyte-compiling /galaxydirn/Bio/SeqIO/FastaIO.py to Fastabyte-compiling /galaxydir/galaxy/databaIO.py to IgIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,532 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,532 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO/Igbyte-compiling /galaxydirn/Bio/SeqIO/InsdcIO.py to Insdcbyte-compiling /galaxydir/galaxy/databaterfaces.py to Interfaces.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,532 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,532 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO/Inbyte-compiling /galaxydirn/Bio/SeqIO/PdbIO.py to PdbIO.pbyte-compiling /galaxydir/galaxy/databadIO.py to PhdIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,532 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,532 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO/Phbyte-compiling /galaxydirn/Bio/SeqIO/PirIO.py to PirIO.pbyte-compiling /galaxydir/galaxy/databaalityIO.py to QualityIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,532 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythomlIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,533 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO/Qubyte-compiling /galaxydirn/Bio/SeqIO/SeqXmlIO.py to SeqXbyte-compiling /galaxydir/galaxy/databafIO.py to SffIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,533 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,533 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO/Sfbyte-compiling /galaxydirn/Bio/SeqIO/SwissIO.py to Swissbyte-compiling /galaxydir/galaxy/datababIO.py to TabIO.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,533 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoprotIO.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,538 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO/Tabyte-compiling /galaxydirn/Bio/SeqIO/UniprotIO.py to Unibyte-compiling /galaxydir/galaxy/databad.py to SeqRecord.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,544 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,548 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Sequencibyte-compiling /galaxydirn/Bio/Sequencing/Applications/_c install_environment.STDOUT DEBUG 2017-11-18 17:04:09,549 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,556 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Sequencing/Applicbyte-compiling /galaxydirn/Bio/Sequencing/Applications/_pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,572 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydirn/Bio/SeqUtils/__init__.py to _67/a12f73c3b116/lib/python/Bio/SeqUtilspyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,574 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/c install_environment.STDOUT DEBUG 2017-11-18 17:04:09,577 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqUtils/CodonUsabyte-compiling /galaxydirn/Bio/SeqUtils/IsoelectricPointyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,589 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydirn/Bio/SeqUtils/MeltingTemp.py tbyte-compiling /galaxydir/galaxy/databa/ProtParam.py to ProtParam.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,591 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho to ProtParamData.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,598 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Statistibyte-compiling /galaxydirn/Bio/Statistics/lowess.py to lbyte-compiling /galaxydir/galaxy/databa__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,599 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoreqTable.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,634 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqIO/Tabyte-compiling /galaxydirn/Bio/SeqIO/UniprotIO.py to Unibyte-compiling /galaxydir/galaxy/databad.py to SeqRecord.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,634 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,634 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqRecorbyte-compiling /galaxydirn/Bio/Sequencing/__init__.py tobyte-compiling /galaxydir/galaxy/databang/Ace.py to Ace.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,634 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Sequencibyte-compiling /galaxydirn/Bio/Sequencing/Applications/_c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,634 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,634 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho_init__.py to __init__.pybyte-compiling /galaxydir/galaxSequencing/Applications/_bwa.py to _bwabyte-compiling /galaxydir/galaxy/database/dependations/_Novoalign.py to _Novoalign.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,634 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Sequencing/Applicbyte-compiling /galaxydirn/Bio/Sequencing/Applications/_pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,634 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythosamtools.py to _samtools.byte-compiling /galaxydir/galaxSequencing/Phd.py to Phd.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,634 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho_init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,634 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydirn/Bio/SeqUtils/__init__.py to _67/a12f73c3b116/lib/python/Bio/SeqUtilspyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,635 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/c tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,635 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_/CheckSum.py to CheckSum.byte-compiling /galaxydir/galaxSeqUtils/CodonUsage.py to CodonUsage.pybyte-compiling /galaxydir/galaxy/database/dependgeIndices.py to CodonUsageIndices.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,635 encies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqUtils/CodonUsabyte-compiling /galaxydirn/Bio/SeqUtils/IsoelectricPointyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,635 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho.py to IsoelectricPoint.pbyte-compiling /galaxydir/galaxSeqUtils/lcc.py to lcc.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,635 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoo MeltingTemp.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,635 y/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/byte-compiling /galaxydirn/Bio/SeqUtils/MeltingTemp.py tbyte-compiling /galaxydir/galaxy/databa/ProtParam.py to ProtParam.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,635 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho to ProtParamData.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,635 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SeqUtilsbyte-compiling /galaxydirn/Bio/SeqUtils/ProtParamData.pybyte-compiling /galaxydir/galaxy/databacs/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,635 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoowess.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,636 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Statistibyte-compiling /galaxydirn/Bio/Statistics/lowess.py to lbyte-compiling /galaxydir/galaxy/databa__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,636 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoreqTable.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,636 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SubsMat/byte-compiling /galaxydirn/Bio/SubsMat/FreqTable.py to Fbyte-compiling /galaxydir/galaxy/databaMatrixInfo.py to MatrixInfo.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,725 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SubsMat/byte-compiling /galaxydirn/Bio/SVDSuperimposer/__init__.byte-compiling /galaxydir/galaxy/databat/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,731 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoKeyWList.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,738 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythopy to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,738 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/TogoWS/_67/a12f73c3b116/lib/pythofind.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,738 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SubsMat/byte-compiling /galaxydirn/Bio/SVDSuperimposer/__init__.byte-compiling /galaxydir/galaxy/databat/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,739 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoKeyWList.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,739 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/SwissProbyte-compiling /galaxydirn/Bio/SwissProt/KeyWList.py to byte-compiling /galaxydir/galaxy/databa_init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,740 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_n/Bio/triefind.py to triebyte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/UniGene/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,740 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/TogoWS/_67/a12f73c3b116/lib/pythofind.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,741 67/a12f73c3b116/lib/python/Bio/UniProt/__init__.py to __init__.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,742 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho install_environment.STDOUT DEBUG 2017-11-18 17:04:09,748 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Wise/__ibyte-compiling /galaxydirn/Bio/Wise/dnal.py to dnal.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,751 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirn/BioSQL/__init__.py to __init_byte-compiling /galaxydir/galaxy/databaq.py to BioSeq.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,755 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoioSeqDatabase.pyc install_environment.STDOUT DEBUG 2017-11-18 17:04:09,775 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/BioSQL/DBUtibyte-compiling /galaxydirn/BioSQL/Loader.py to Loader.pyrunning install_egg_info install_environment.STDOUT DEBUG 2017-11-18 17:04:09,777 73c3b116/lib/python/biopython-1.67-py2.7.egg-info tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,845 67/a12f73c3b116/lib/python/Bio/UniProt/__init__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,845 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,845 byte-compiling /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_byte-compiling /galaxydirn/Bio/UniProt/GOA.py to GOA.pycbyte-compiling /galaxydir/galaxy/databanit__.py to __init__.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,845 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/Bio/Wise/__ibyte-compiling /galaxydirn/Bio/Wise/dnal.py to dnal.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,845 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirn/Bio/Wise/psw.py to psw.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,845 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pytho_.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,846 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythobyte-compiling /galaxydirn/BioSQL/__init__.py to __init_byte-compiling /galaxydir/galaxy/databaq.py to BioSeq.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,846 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoioSeqDatabase.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,846 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/BioSQL/BioSebyte-compiling /galaxydirn/BioSQL/BioSeqDatabase.py to Bbyte-compiling /galaxydir/galaxy/databals.py to DBUtils.pyc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,846 /galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/pythoc tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,846 se/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116/lib/python/BioSQL/DBUtibyte-compiling /galaxydirn/BioSQL/Loader.py to Loader.pyrunning install_egg_info tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,846 73c3b116/lib/python/biopython-1.67-py2.7.egg-info tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:biopython DEBUG 2017-11-18 17:04:09,846 Writing /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f tool_shed.galaxy_install.tool_dependencies.recipe.install_environment WARNING 2017-11-18 17:04:09,952 Length of stdout > 32K, so only a portion will be saved in the database. tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 17:04:09,953 Environment variable PYTHONPATH_NUMPY not found, removing from set_environment. tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 17:04:09,954 Environment variable PATH_NUMPY not found, removing from set_environment. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 17:04:10,298 Changing status for tool dependency biopython from Installing to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:04:10,298 Updating an existing record for version 1.67 of tool dependency biopython for revision a12f73c3b116 of repository package_biopython_1_67 by updating the status from Installing to Installed. tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 17:04:10,376 Tool dependency biopython version 1.67 has been installed in /galaxydir/galaxy/database/dependencies/biopython/1.67/biopython/package_biopython_1_67/a12f73c3b116. 127.0.0.1 - - [18/Nov/2017:16:55:01 -0400] "POST /admin_toolshed/manage_repositories HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 63747) Traceback (most recent call last): File "/galaxydir/galaxy/.venv/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 657, in __init__ self.finish() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 716, in finish self.wfile.close() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 283, in close self.flush() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- 127.0.0.1 - - [18/Nov/2017:17:04:11 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/monitor_repository_installation?installing_repository_ids=a799d38679e985db" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:31 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:32 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:32 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:32 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:32 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:32 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:32 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:32 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:32 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:32 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:32 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:34 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:38 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=8smmls4u50w&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:38 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:38 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:43 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 17:13:44,181 Validated and populated state for tool request (46.502 ms) galaxy.tools.actions INFO 2017-11-18 17:13:44,519 Handled output named html_file for tool seq_sero_reads_multiple (44.674 ms) galaxy.tools.actions INFO 2017-11-18 17:13:44,572 Handled output named text_file for tool seq_sero_reads_multiple (53.051 ms) galaxy.tools.actions INFO 2017-11-18 17:13:44,598 Added output datasets to history (25.781 ms) galaxy.tools.actions INFO 2017-11-18 17:13:44,669 Verified access to datasets for Job[unflushed,tool_id=seq_sero_reads_multiple] (29.495 ms) galaxy.tools.actions INFO 2017-11-18 17:13:44,669 Setup for job Job[unflushed,tool_id=seq_sero_reads_multiple] complete, ready to flush (70.722 ms) galaxy.tools.actions INFO 2017-11-18 17:13:44,714 Flushed transaction for job Job[id=5,tool_id=seq_sero_reads_multiple] (45.052 ms) galaxy.tools.execute DEBUG 2017-11-18 17:13:44,715 Tool [seq_sero_reads_multiple] created job [5] (259.682 ms) galaxy.tools.execute DEBUG 2017-11-18 17:13:44,739 Executed 1 job(s) for tool seq_sero_reads_multiple request: (557.621 ms) 127.0.0.1 - - [18/Nov/2017:17:13:44 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:44 -0400] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:44 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A13%3A32.337Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 17:13:45,600 (5) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/5 galaxy.jobs.handler DEBUG 2017-11-18 17:13:45,615 (5) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 17:13:45,671 (5) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 17:13:45,683 Job [5] queued (67.357 ms) galaxy.jobs.handler INFO 2017-11-18 17:13:45,702 (5) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 17:13:46,021 Built script [/galaxydir/galaxy/database/jobs_directory/000/5/tool_script.sh] for tool command [/galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/files/000/dataset_2.dat /galaxydir/galaxy/tools/GalaxySeqsero/] galaxy.jobs.runners DEBUG 2017-11-18 17:13:46,294 (5) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/5/tool_script.sh; return_code=$?; if [ -f /galaxydir/galaxy/database/jobs_directory/000/5/working/Seqsero_result.html ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/5/working/Seqsero_result.html /galaxydir/galaxy/database/files/000/dataset_7.dat ; fi; if [ -f /galaxydir/galaxy/database/jobs_directory/000/5/working/Seqsero_result.txt ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/5/working/Seqsero_result.txt /galaxydir/galaxy/database/files/000/dataset_8.dat ; fi; cd '/galaxydir/galaxy/database/jobs_directory/000/5'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True python "/galaxydir/galaxy/database/jobs_directory/000/5/set_metadata_7GCMIj.py" "/galaxydir/galaxy/database/jobs_directory/000/5/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/5/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/5/metadata_in_HistoryDatasetAssociation_7_mUQ_3o,/galaxydir/galaxy/database/jobs_directory/000/5/metadata_kwds_HistoryDatasetAssociation_7_dTuW8X,/galaxydir/galaxy/database/jobs_directory/000/5/metadata_out_HistoryDatasetAssociation_7_Qldxlf,/galaxydir/galaxy/database/jobs_directory/000/5/metadata_results_HistoryDatasetAssociation_7_DqFmjJ,/galaxydir/galaxy/database/files/000/dataset_7.dat,/galaxydir/galaxy/database/jobs_directory/000/5/metadata_override_HistoryDatasetAssociation_7_JRvPxh" "/galaxydir/galaxy/database/jobs_directory/000/5/metadata_in_HistoryDatasetAssociation_8_SjZsZB,/galaxydir/galaxy/database/jobs_directory/000/5/metadata_kwds_HistoryDatasetAssociation_8_O1wCt4,/galaxydir/galaxy/database/jobs_directory/000/5/metadata_out_HistoryDatasetAssociation_8_pbYd4K,/galaxydir/galaxy/database/jobs_directory/000/5/metadata_results_HistoryDatasetAssociation_8_jBXaXT,/galaxydir/galaxy/database/files/000/dataset_8.dat,/galaxydir/galaxy/database/jobs_directory/000/5/metadata_override_HistoryDatasetAssociation_8_ELt0_n" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 17:13:46,309 (5) executing job script: /galaxydir/galaxy/database/jobs_directory/000/5/galaxy_5.sh galaxy.jobs DEBUG 2017-11-18 17:13:46,318 (5) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:17:13:48 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A13%3A44.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:49 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:49 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:53 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A13%3A49.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 17:13:53,420 execution finished: /galaxydir/galaxy/database/jobs_directory/000/5/galaxy_5.sh galaxy.jobs.output_checker INFO 2017-11-18 17:13:53,430 Job 5: Warning: Exit code 0 () galaxy.jobs.output_checker INFO 2017-11-18 17:13:53,430 Job 5: Fatal error: Matched on Error: galaxy.jobs.output_checker DEBUG 2017-11-18 17:13:53,430 Tool exit code indicates an error, failing job. galaxy.jobs DEBUG 2017-11-18 17:13:53,505 (5) setting dataset 7 state to ERROR galaxy.jobs DEBUG 2017-11-18 17:13:53,542 (5) setting dataset 8 state to ERROR galaxy.jobs INFO 2017-11-18 17:13:53,753 Collecting metrics for Job 5 galaxy.jobs DEBUG 2017-11-18 17:13:53,777 job 5 ended (finish() executed in (356.995 ms)) galaxy.tools.error_reports DEBUG 2017-11-18 17:13:53,808 Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x107a71710> generated response None galaxy.tools.error_reports DEBUG 2017-11-18 17:13:53,808 Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x107a71710> generated response None galaxy.model.metadata DEBUG 2017-11-18 17:13:53,809 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:17:13:57 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A13%3A53.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:57 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:57 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:57 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:13:57 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:14:24 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/df7a1f0c02a5b08e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=8smmls4u50w" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:14:27 -0400] "GET /api/datasets/df7a1f0c02a5b08e HTTP/1.1" 200 - "http://localhost:8080/datasets/error?dataset_id=df7a1f0c02a5b08e&__identifer=xcpp7yu5zf" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:14:27 -0400] "GET /api/jobs/33b43b4e7093c91f?full=True HTTP/1.1" 200 - "http://localhost:8080/datasets/error?dataset_id=df7a1f0c02a5b08e&__identifer=xcpp7yu5zf" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:27 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/datasets/error?dataset_id=df7a1f0c02a5b08e&__identifer=xcpp7yu5zf" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:28 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:28 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:28 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:28 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:28 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:28 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:28 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:28 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:28 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:28 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:30 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:32 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=3vvuzc401d4&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:32 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:32 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:35 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 17:31:35,883 Validated and populated state for tool request (45.082 ms) galaxy.tools.actions INFO 2017-11-18 17:31:35,957 Handled output named html_file for tool seq_sero_reads_multiple (30.789 ms) galaxy.tools.actions INFO 2017-11-18 17:31:35,997 Handled output named text_file for tool seq_sero_reads_multiple (39.571 ms) galaxy.tools.actions INFO 2017-11-18 17:31:36,019 Added output datasets to history (22.078 ms) galaxy.tools.actions INFO 2017-11-18 17:31:36,084 Verified access to datasets for Job[unflushed,tool_id=seq_sero_reads_multiple] (28.127 ms) galaxy.tools.actions INFO 2017-11-18 17:31:36,085 Setup for job Job[unflushed,tool_id=seq_sero_reads_multiple] complete, ready to flush (65.533 ms) galaxy.tools.actions INFO 2017-11-18 17:31:36,115 Flushed transaction for job Job[id=6,tool_id=seq_sero_reads_multiple] (29.604 ms) galaxy.tools.execute DEBUG 2017-11-18 17:31:36,115 Tool [seq_sero_reads_multiple] created job [6] (210.627 ms) galaxy.tools.execute DEBUG 2017-11-18 17:31:36,131 Executed 1 job(s) for tool seq_sero_reads_multiple request: (248.015 ms) 127.0.0.1 - - [18/Nov/2017:17:31:35 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:36 -0400] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:36 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A31%3A28.623Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 17:31:36,363 (6) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/6 galaxy.jobs.handler DEBUG 2017-11-18 17:31:36,379 (6) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 17:31:36,426 (6) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 17:31:36,439 Job [6] queued (59.748 ms) galaxy.jobs.handler INFO 2017-11-18 17:31:36,453 (6) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 17:31:36,737 Built script [/galaxydir/galaxy/database/jobs_directory/000/6/tool_script.sh] for tool command [/galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/files/000/dataset_2.dat /galaxydir/galaxy/tools/GalaxySeqsero/] galaxy.jobs.runners DEBUG 2017-11-18 17:31:37,020 (6) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/6/tool_script.sh; return_code=$?; if [ -f /galaxydir/galaxy/database/jobs_directory/000/6/working/Seqsero_result.html ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/6/working/Seqsero_result.html /galaxydir/galaxy/database/files/000/dataset_9.dat ; fi; if [ -f /galaxydir/galaxy/database/jobs_directory/000/6/working/Seqsero_result.txt ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/6/working/Seqsero_result.txt /galaxydir/galaxy/database/files/000/dataset_10.dat ; fi; cd '/galaxydir/galaxy/database/jobs_directory/000/6'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True python "/galaxydir/galaxy/database/jobs_directory/000/6/set_metadata_KhbGy2.py" "/galaxydir/galaxy/database/jobs_directory/000/6/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/6/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/6/metadata_in_HistoryDatasetAssociation_9_eeDl5t,/galaxydir/galaxy/database/jobs_directory/000/6/metadata_kwds_HistoryDatasetAssociation_9_88b73i,/galaxydir/galaxy/database/jobs_directory/000/6/metadata_out_HistoryDatasetAssociation_9_Nvf24o,/galaxydir/galaxy/database/jobs_directory/000/6/metadata_results_HistoryDatasetAssociation_9_PofTtd,/galaxydir/galaxy/database/files/000/dataset_9.dat,/galaxydir/galaxy/database/jobs_directory/000/6/metadata_override_HistoryDatasetAssociation_9_xXODc5" "/galaxydir/galaxy/database/jobs_directory/000/6/metadata_in_HistoryDatasetAssociation_10_wJr3y4,/galaxydir/galaxy/database/jobs_directory/000/6/metadata_kwds_HistoryDatasetAssociation_10_DDD5N6,/galaxydir/galaxy/database/jobs_directory/000/6/metadata_out_HistoryDatasetAssociation_10_hvY5tX,/galaxydir/galaxy/database/jobs_directory/000/6/metadata_results_HistoryDatasetAssociation_10_zPRX_q,/galaxydir/galaxy/database/files/000/dataset_10.dat,/galaxydir/galaxy/database/jobs_directory/000/6/metadata_override_HistoryDatasetAssociation_10_CCkNub" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 17:31:37,036 (6) executing job script: /galaxydir/galaxy/database/jobs_directory/000/6/galaxy_6.sh galaxy.jobs DEBUG 2017-11-18 17:31:37,044 (6) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:17:31:40 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A31%3A36.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:40 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:40 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:41 -0400] "GET /?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4 HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:41 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:41 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:42 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:42 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:42 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:42 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:42 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=3vvuzc401d4&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:42 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:42 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:42 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:42 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 17:31:44,063 execution finished: /galaxydir/galaxy/database/jobs_directory/000/6/galaxy_6.sh galaxy.jobs.output_checker INFO 2017-11-18 17:31:44,075 Job 6: Warning: Exit code 0 () galaxy.model.metadata DEBUG 2017-11-18 17:31:44,214 loading metadata from file for: HistoryDatasetAssociation 9 galaxy.model.metadata DEBUG 2017-11-18 17:31:44,322 loading metadata from file for: HistoryDatasetAssociation 10 galaxy.jobs INFO 2017-11-18 17:31:44,516 Collecting metrics for Job 6 galaxy.jobs DEBUG 2017-11-18 17:31:44,534 job 6 ended (finish() executed in (470.830 ms)) galaxy.model.metadata DEBUG 2017-11-18 17:31:44,543 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:17:31:45 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:47 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A31%3A42.638Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:47 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:47 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:47 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:47 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:31:58 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/03501d7626bd192f HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:32:01 -0400] "GET /datasets/03501d7626bd192f/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:32:01 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/03501d7626bd192f/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:32:07 -0400] "GET /datasets/03501d7626bd192f/stdout HTTP/1.1" 200 - "http://localhost:8080/datasets/03501d7626bd192f/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:32:15 -0400] "GET /datasets/03501d7626bd192f/display/?preview=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:32:19 -0400] "GET /datasets/0a248a1f62a0cc04/display/?preview=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:33:23 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/03501d7626bd192f HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:33:30 -0400] "GET /datasets/03501d7626bd192f/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:33:30 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/03501d7626bd192f/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:33:32 -0400] "GET /datasets/03501d7626bd192f/stderr HTTP/1.1" 200 - "http://localhost:8080/datasets/03501d7626bd192f/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:33:47 -0400] "GET /datasets/03501d7626bd192f/display/?preview=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:33:52 -0400] "GET /datasets/0a248a1f62a0cc04/display/?preview=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:33:57 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/03501d7626bd192f HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:33:58 -0400] "GET /datasets/03501d7626bd192f/display/?preview=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:34:01 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/03501d7626bd192f HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:34:03 -0400] "GET /datasets/03501d7626bd192f/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:34:03 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/03501d7626bd192f/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:34:12 -0400] "GET /datasets/03501d7626bd192f/stdout HTTP/1.1" 200 - "http://localhost:8080/datasets/03501d7626bd192f/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:34:18 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/03501d7626bd192f HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:34:20 -0400] "GET /datasets/03501d7626bd192f/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:34:20 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/03501d7626bd192f/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:35:15 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/0a248a1f62a0cc04 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:35:18 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/03501d7626bd192f HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:35:26 -0400] "GET /datasets/0a248a1f62a0cc04/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:35:26 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/0a248a1f62a0cc04/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:35:28 -0400] "GET /datasets/0a248a1f62a0cc04/stderr HTTP/1.1" 200 - "http://localhost:8080/datasets/0a248a1f62a0cc04/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:06 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:06 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:06 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:06 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:06 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:20 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:20 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:25 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=3vvuzc401d4" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:25 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:25 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:25 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:25 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:27 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:27 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:30 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=a799d38679e985db HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:30 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=a799d38679e985db&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:37:30 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=a799d38679e985db&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.queue_worker DEBUG 2017-11-18 17:38:18,479 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 17:38:18,495 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:38:18,506 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:38:18,508 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:38:18,512 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:38:18,517 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,518 Reading tools from config files finshed (23.419 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,519 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,521 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,521 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,522 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,522 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,522 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,524 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,524 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,524 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,525 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,526 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,526 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,526 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,526 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,527 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,529 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,529 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,529 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,529 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,529 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,530 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,530 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:38:18,531 Loading tool panel finished (12.316 ms) galaxy.tools.deps DEBUG 2017-11-18 17:38:18,533 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 17:38:18,561 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 17:38:18,564 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 17:38:18,567 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 17:38:18,567 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 17:38:18,575 Toolbox reload (95.982 ms) galaxy.queue_worker INFO 2017-11-18 17:38:19,490 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 17:38:19,491 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 17:38:19,536 Toolbox index finished (45.666 ms) 127.0.0.1 - - [18/Nov/2017:17:38:21 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:21 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:21 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:21 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:22 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:22 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:22 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:22 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:22 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:22 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:22 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:24 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:28 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=10nwczanasrq&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:29 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:29 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:31 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 17:38:32,719 Validated and populated state for tool request (45.040 ms) galaxy.tools.actions INFO 2017-11-18 17:38:32,799 Handled output named html_file for tool seq_sero_reads_multiple (31.986 ms) galaxy.tools.actions INFO 2017-11-18 17:38:32,837 Handled output named text_file for tool seq_sero_reads_multiple (38.252 ms) galaxy.tools.actions INFO 2017-11-18 17:38:32,863 Added output datasets to history (25.377 ms) galaxy.tools.actions INFO 2017-11-18 17:38:32,920 Verified access to datasets for Job[unflushed,tool_id=seq_sero_reads_multiple] (26.456 ms) galaxy.tools.actions INFO 2017-11-18 17:38:32,921 Setup for job Job[unflushed,tool_id=seq_sero_reads_multiple] complete, ready to flush (58.181 ms) galaxy.tools.actions INFO 2017-11-18 17:38:32,954 Flushed transaction for job Job[id=7,tool_id=seq_sero_reads_multiple] (33.096 ms) galaxy.tools.execute DEBUG 2017-11-18 17:38:32,955 Tool [seq_sero_reads_multiple] created job [7] (211.683 ms) galaxy.tools.execute DEBUG 2017-11-18 17:38:32,972 Executed 1 job(s) for tool seq_sero_reads_multiple request: (252.532 ms) 127.0.0.1 - - [18/Nov/2017:17:38:32 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:33 -0400] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:33 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A38%3A22.215Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 17:38:33,214 (7) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/7 galaxy.jobs.handler DEBUG 2017-11-18 17:38:33,234 (7) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 17:38:33,283 (7) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 17:38:33,296 Job [7] queued (61.805 ms) galaxy.jobs.handler INFO 2017-11-18 17:38:33,308 (7) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 17:38:33,623 Built script [/galaxydir/galaxy/database/jobs_directory/000/7/tool_script.sh] for tool command [/galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/files/000/dataset_2.dat /galaxydir/galaxy/tools/GalaxySeqsero/] galaxy.jobs.runners DEBUG 2017-11-18 17:38:33,917 (7) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/7/tool_script.sh; return_code=$?; if [ -f /galaxydir/galaxy/database/jobs_directory/000/7/working/Seqsero_result.html ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/7/working/Seqsero_result.html /galaxydir/galaxy/database/files/000/dataset_11.dat ; fi; if [ -f /galaxydir/galaxy/database/jobs_directory/000/7/working/Seqsero_result.txt ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/7/working/Seqsero_result.txt /galaxydir/galaxy/database/files/000/dataset_12.dat ; fi; cd '/galaxydir/galaxy/database/jobs_directory/000/7'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True python "/galaxydir/galaxy/database/jobs_directory/000/7/set_metadata_diiu_5.py" "/galaxydir/galaxy/database/jobs_directory/000/7/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/7/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/7/metadata_in_HistoryDatasetAssociation_11_4nk_6T,/galaxydir/galaxy/database/jobs_directory/000/7/metadata_kwds_HistoryDatasetAssociation_11_prV4hd,/galaxydir/galaxy/database/jobs_directory/000/7/metadata_out_HistoryDatasetAssociation_11_MWchHK,/galaxydir/galaxy/database/jobs_directory/000/7/metadata_results_HistoryDatasetAssociation_11_l9mC3x,/galaxydir/galaxy/database/files/000/dataset_11.dat,/galaxydir/galaxy/database/jobs_directory/000/7/metadata_override_HistoryDatasetAssociation_11_13QAT5" "/galaxydir/galaxy/database/jobs_directory/000/7/metadata_in_HistoryDatasetAssociation_12_VOsyDX,/galaxydir/galaxy/database/jobs_directory/000/7/metadata_kwds_HistoryDatasetAssociation_12_FWwLn0,/galaxydir/galaxy/database/jobs_directory/000/7/metadata_out_HistoryDatasetAssociation_12_OBCmgX,/galaxydir/galaxy/database/jobs_directory/000/7/metadata_results_HistoryDatasetAssociation_12_ctimf5,/galaxydir/galaxy/database/files/000/dataset_12.dat,/galaxydir/galaxy/database/jobs_directory/000/7/metadata_override_HistoryDatasetAssociation_12_PvyCrA" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 17:38:33,932 (7) executing job script: /galaxydir/galaxy/database/jobs_directory/000/7/galaxy_7.sh galaxy.jobs DEBUG 2017-11-18 17:38:33,941 (7) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:17:38:36 -0400] "GET /?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:36 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:36 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:36 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:36 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:36 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:36 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:36 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=10nwczanasrq&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:36 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:36 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:36 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:36 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:39 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 17:38:40,297 execution finished: /galaxydir/galaxy/database/jobs_directory/000/7/galaxy_7.sh galaxy.jobs.output_checker INFO 2017-11-18 17:38:40,307 Job 7: Warning: Exit code 0 () galaxy.model.metadata DEBUG 2017-11-18 17:38:40,467 loading metadata from file for: HistoryDatasetAssociation 11 galaxy.model.metadata DEBUG 2017-11-18 17:38:40,588 loading metadata from file for: HistoryDatasetAssociation 12 galaxy.jobs INFO 2017-11-18 17:38:40,775 Collecting metrics for Job 7 galaxy.jobs DEBUG 2017-11-18 17:38:40,802 job 7 ended (finish() executed in (504.967 ms)) galaxy.model.metadata DEBUG 2017-11-18 17:38:40,809 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:17:38:41 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A38%3A36.719Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:41 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:41 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:41 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:41 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:44 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/e85a3be143d5905b HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:46 -0400] "GET /datasets/e85a3be143d5905b/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:47 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/e85a3be143d5905b/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:38:48 -0400] "GET /datasets/e85a3be143d5905b/stderr HTTP/1.1" 200 - "http://localhost:8080/datasets/e85a3be143d5905b/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:04 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=10nwczanasrq" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:04 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:04 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:04 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:04 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:06 -0400] "GET /admin_toolshed/browse_tool_sheds HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:06 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:08 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:08 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:08 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:08 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:08 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:08 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:09 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:09 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:09 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:09 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:09 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:11 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:11 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:12 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:12 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:12 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:12 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:13 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:13 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:41 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=f2db41e1fa331b3e HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:41 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:41 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.queue_worker DEBUG 2017-11-18 17:39:56,805 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 17:39:56,827 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:39:56,838 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:39:56,840 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:39:56,843 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:39:56,848 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,850 Reading tools from config files finshed (22.289 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,850 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,852 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,852 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,853 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,853 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,853 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,855 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,855 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,855 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,856 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,857 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,857 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,857 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,857 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,858 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,860 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,860 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,860 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,860 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,860 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,861 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,861 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:39:56,862 Loading tool panel finished (12.091 ms) galaxy.tools.deps DEBUG 2017-11-18 17:39:56,864 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 17:39:56,887 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 17:39:56,889 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 17:39:56,891 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 17:39:56,891 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 17:39:56,899 Toolbox reload (93.464 ms) galaxy.queue_worker INFO 2017-11-18 17:39:57,310 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 17:39:57,311 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 17:39:57,344 Toolbox index finished (33.475 ms) 127.0.0.1 - - [18/Nov/2017:17:39:58 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:58 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:58 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:58 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:58 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:58 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:58 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:58 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:58 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:58 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:39:59 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:01 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:05 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=j7xclppnsa&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:05 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:05 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:06 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 17:40:07,803 Validated and populated state for tool request (40.820 ms) galaxy.tools.actions INFO 2017-11-18 17:40:07,892 Handled output named html_file for tool seq_sero_reads_multiple (33.581 ms) galaxy.tools.actions INFO 2017-11-18 17:40:07,931 Handled output named text_file for tool seq_sero_reads_multiple (38.359 ms) galaxy.tools.actions INFO 2017-11-18 17:40:07,956 Added output datasets to history (24.557 ms) galaxy.tools.actions INFO 2017-11-18 17:40:08,015 Verified access to datasets for Job[unflushed,tool_id=seq_sero_reads_multiple] (25.901 ms) galaxy.tools.actions INFO 2017-11-18 17:40:08,016 Setup for job Job[unflushed,tool_id=seq_sero_reads_multiple] complete, ready to flush (60.543 ms) galaxy.tools.actions INFO 2017-11-18 17:40:08,047 Flushed transaction for job Job[id=8,tool_id=seq_sero_reads_multiple] (29.876 ms) galaxy.tools.execute DEBUG 2017-11-18 17:40:08,047 Tool [seq_sero_reads_multiple] created job [8] (220.551 ms) galaxy.tools.execute DEBUG 2017-11-18 17:40:08,063 Executed 1 job(s) for tool seq_sero_reads_multiple request: (259.468 ms) 127.0.0.1 - - [18/Nov/2017:17:40:07 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:08 -0400] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 17:40:08,183 (8) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/8 galaxy.jobs.handler DEBUG 2017-11-18 17:40:08,220 (8) Dispatching to local runner 127.0.0.1 - - [18/Nov/2017:17:40:08 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A39%3A58.899Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 17:40:08,276 (8) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 17:40:08,288 Job [8] queued (68.654 ms) galaxy.jobs.handler INFO 2017-11-18 17:40:08,311 (8) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 17:40:08,626 Built script [/galaxydir/galaxy/database/jobs_directory/000/8/tool_script.sh] for tool command [/galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/files/000/dataset_2.dat /galaxydir/galaxy/tools/GalaxySeqsero/] galaxy.jobs.runners DEBUG 2017-11-18 17:40:08,909 (8) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/8/tool_script.sh; return_code=$?; if [ -f /galaxydir/galaxy/database/jobs_directory/000/8/working/Seqsero_result.html ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/8/working/Seqsero_result.html /galaxydir/galaxy/database/files/000/dataset_13.dat ; fi; if [ -f /galaxydir/galaxy/database/jobs_directory/000/8/working/Seqsero_result.txt ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/8/working/Seqsero_result.txt /galaxydir/galaxy/database/files/000/dataset_14.dat ; fi; cd '/galaxydir/galaxy/database/jobs_directory/000/8'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True python "/galaxydir/galaxy/database/jobs_directory/000/8/set_metadata_V4Himv.py" "/galaxydir/galaxy/database/jobs_directory/000/8/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/8/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/8/metadata_in_HistoryDatasetAssociation_13_aCdIZe,/galaxydir/galaxy/database/jobs_directory/000/8/metadata_kwds_HistoryDatasetAssociation_13_aKRO7I,/galaxydir/galaxy/database/jobs_directory/000/8/metadata_out_HistoryDatasetAssociation_13_C1fmK5,/galaxydir/galaxy/database/jobs_directory/000/8/metadata_results_HistoryDatasetAssociation_13_WLehIj,/galaxydir/galaxy/database/files/000/dataset_13.dat,/galaxydir/galaxy/database/jobs_directory/000/8/metadata_override_HistoryDatasetAssociation_13_luM9z3" "/galaxydir/galaxy/database/jobs_directory/000/8/metadata_in_HistoryDatasetAssociation_14_9QxJ4m,/galaxydir/galaxy/database/jobs_directory/000/8/metadata_kwds_HistoryDatasetAssociation_14_bvYHK6,/galaxydir/galaxy/database/jobs_directory/000/8/metadata_out_HistoryDatasetAssociation_14_BUBcnz,/galaxydir/galaxy/database/jobs_directory/000/8/metadata_results_HistoryDatasetAssociation_14_Weipem,/galaxydir/galaxy/database/files/000/dataset_14.dat,/galaxydir/galaxy/database/jobs_directory/000/8/metadata_override_HistoryDatasetAssociation_14_6peKPz" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 17:40:08,923 (8) executing job script: /galaxydir/galaxy/database/jobs_directory/000/8/galaxy_8.sh galaxy.jobs DEBUG 2017-11-18 17:40:08,933 (8) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:17:40:10 -0400] "GET /?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:10 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:10 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:10 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:10 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:10 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:10 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:11 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:11 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=j7xclppnsa&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:11 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:11 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:11 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:13 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 17:40:15,573 execution finished: /galaxydir/galaxy/database/jobs_directory/000/8/galaxy_8.sh galaxy.jobs.output_checker INFO 2017-11-18 17:40:15,583 Job 8: Warning: Exit code 0 () galaxy.model.metadata DEBUG 2017-11-18 17:40:15,735 loading metadata from file for: HistoryDatasetAssociation 13 127.0.0.1 - - [18/Nov/2017:17:40:15 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A40%3A11.186Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.model.metadata DEBUG 2017-11-18 17:40:15,896 loading metadata from file for: HistoryDatasetAssociation 14 galaxy.jobs INFO 2017-11-18 17:40:16,083 Collecting metrics for Job 8 galaxy.jobs DEBUG 2017-11-18 17:40:16,114 job 8 ended (finish() executed in (540.193 ms)) galaxy.model.metadata DEBUG 2017-11-18 17:40:16,123 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:17:40:19 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A40%3A15.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:20 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:20 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:20 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:20 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:22 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/2a56795cad3c7db3 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:24 -0400] "GET /datasets/2a56795cad3c7db3/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:24 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/2a56795cad3c7db3/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:26 -0400] "GET /datasets/2a56795cad3c7db3/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:26 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/2a56795cad3c7db3/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:28 -0400] "GET /datasets/2a56795cad3c7db3/stderr HTTP/1.1" 200 - "http://localhost:8080/datasets/2a56795cad3c7db3/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:35 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:35 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:36 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:36 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:36 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:38 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:38 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:59 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=a799d38679e985db HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:40:59 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=a799d38679e985db&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:41:00 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=a799d38679e985db&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:41:05 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:41:06 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.deps DEBUG 2017-11-18 17:41:10,189 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,189 Dependency samtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,189 Dependency bedtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,190 Dependency ucsc-fatotwobit not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,190 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,191 Dependency bowtie not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,194 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,194 Dependency gnuplot not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,195 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,195 Dependency bedtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,196 Dependency samtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,197 Dependency biom-format not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,197 Dependency python not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,218 Using dependency sra-tools version 2.8.1 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:41:10,218 Dependency rpy2 not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,219 Dependency bcftools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,219 Dependency openbabel not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,220 Dependency gnuplot-py not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,220 Dependency samtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,221 Dependency samtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,221 Dependency bcftools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,228 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 17:41:10,240 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,240 Dependency samtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,240 Dependency bedtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,241 Dependency ucsc-fatotwobit not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,241 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,242 Dependency bowtie not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,243 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,243 Dependency gnuplot not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,244 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,244 Dependency bedtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,245 Dependency samtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,246 Dependency biom-format not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,246 Dependency python not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,246 Using dependency sra-tools version 2.8.1 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:41:10,247 Dependency rpy2 not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,247 Dependency bcftools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,248 Dependency openbabel not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,248 Dependency gnuplot-py not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,249 Dependency samtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,250 Dependency samtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,250 Dependency bcftools not found. galaxy.tools.deps DEBUG 2017-11-18 17:41:10,250 Using dependency blast version 2.5.0 of type tool_shed_package 127.0.0.1 - - [18/Nov/2017:17:41:10 -0400] "GET /admin/manage_tool_dependencies HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:41:10 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/manage_tool_dependencies" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.deps.conda_util DEBUG 2017-11-18 17:42:19,072 Executing command: /galaxydir/galaxy/database/dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --channel r --name mulled-v1-455f1740bc23f7b621a4cf1a40c9900eef81a592ab5ff7feec0224bfc897189f ucsc_tools=332 samtools=1.3.1 bedtools=2.26.0gx Fetching package metadata ................. Solving package specifications: . Package plan for installation in environment /galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-455f1740bc23f7b621a4cf1a40c9900eef81a592ab5ff7feec0224bfc897189f: The following NEW packages will be INSTALLED: bedtools: 2.26.0gx-0 bioconda ca-certificates: 2017.11.5-0 conda-forge curl: 7.55.1-0 conda-forge krb5: 1.14.2-0 conda-forge libssh2: 1.8.0-2 conda-forge openssl: 1.0.2l-0 conda-forge samtools: 1.3.1-5 bioconda ucsc-bedgraphtobigwig: 332-0 bioconda ucsc-bedtobigbed: 332-0 bioconda ucsc-fatotwobit: 332-0 bioconda ucsc-liftover: 332-0 bioconda ucsc-nibfrag: 332-0 bioconda ucsc-twobittofa: 332-0 bioconda ucsc-wigtobigwig: 332-0 bioconda ucsc_tools: 332-1 iuc zlib: 1.2.11-0 conda-forge ca-certificate 100% |##########################################################################################################################################################| Time: 0:00:00 3.21 MB/s krb5-1.14.2-0. 100% |##########################################################################################################################################################| Time: 0:00:00 7.76 MB/s ucsc-bedgrapht 100% |##########################################################################################################################################################| Time: 0:00:00 8.54 MB/s ucsc-bedtobigb 100% |##########################################################################################################################################################| Time: 0:00:00 8.39 MB/s ucsc-fatotwobi 100% |##########################################################################################################################################################| Time: 0:00:00 8.57 MB/s ucsc-liftover- 100% |##########################################################################################################################################################| Time: 0:00:00 4.39 MB/s ucsc-nibfrag-3 100% |##########################################################################################################################################################| Time: 0:00:00 5.43 MB/s ucsc-twobittof 100% |##########################################################################################################################################################| Time: 0:00:00 7.87 MB/s ucsc-wigtobigw 100% |##########################################################################################################################################################| Time: 0:00:00 8.14 MB/s zlib-1.2.11-0. 100% |##########################################################################################################################################################| Time: 0:00:00 9.40 MB/s bedtools-2.26. 100% |##########################################################################################################################################################| Time: 0:00:00 8.09 MB/s openssl-1.0.2l 100% |##########################################################################################################################################################| Time: 0:00:00 6.55 MB/s ucsc_tools-332 100% |##########################################################################################################################################################| Time: 0:00:00 1.56 MB/s libssh2-1.8.0- 100% |##########################################################################################################################################################| Time: 0:00:00 8.59 MB/s curl-7.55.1-0. 100% |##########################################################################################################################################################| Time: 0:00:00 8.13 MB/s samtools-1.3.1 100% |##########################################################################################################################################################| Time: 0:00:00 8.36 MB/s # # To activate this environment, use: # > source activate mulled-v1-455f1740bc23f7b621a4cf1a40c9900eef81a592ab5ff7feec0224bfc897189f # # To deactivate an active environment, use: # > source deactivate # galaxy.tools.deps DEBUG 2017-11-18 17:42:50,281 Using dependency ucsc_tools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:42:50,281 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:42:50,281 Using dependency bedtools version None of type conda galaxy.tools.deps.conda_util DEBUG 2017-11-18 17:42:50,282 Executing command: /galaxydir/galaxy/database/dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --channel r --name __samtools@1.3.1 samtools=1.3.1 Fetching package metadata ...............127.0.0.1 - - [18/Nov/2017:17:42:54 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:42:55 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" .. 127.0.0.1 - - [18/Nov/2017:17:42:57 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=j7xclppnsa" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:42:58 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:42:58 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:42:58 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" Solving package specifications: 127.0.0.1 - - [18/Nov/2017:17:42:58 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" . Package plan for installation in environment /galaxydir/galaxy/database/dependencies/_conda/envs/__samtools@1.3.1: The following NEW packages will be INSTALLED: ca-certificates: 2017.11.5-0 conda-forge curl: 7.55.1-0 conda-forge krb5: 1.14.2-0 conda-forge libssh2: 1.8.0-2 conda-forge openssl: 1.0.2l-0 conda-forge samtools: 1.3.1-5 bioconda zlib: 1.2.11-0 conda-forge # # To activate this environment, use: # > source activate __samtools@1.3.1 # # To deactivate an active environment, use: # > source deactivate # galaxy.tools.deps DEBUG 2017-11-18 17:43:01,510 Using dependency samtools version None of type conda galaxy.tools.deps.conda_util DEBUG 2017-11-18 17:43:01,511 Executing command: /galaxydir/galaxy/database/dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --channel r --name __samtools@0.1.19 samtools=0.1.19 127.0.0.1 - - [18/Nov/2017:17:43:01 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" Fetching package metadata .........127.0.0.1 - - [18/Nov/2017:17:43:04 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:05 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ........ Solving package specifications: . Package plan for installation in environment /galaxydir/galaxy/database/dependencies/_conda/envs/__samtools@0.1.19: The following NEW packages will be INSTALLED: ncurses: 5.9-10 conda-forge samtools: 0.1.19-2 bioconda zlib: 1.2.11-0 conda-forge ncurses-5.9-10 100% |##########################################################################################################################################################| Time: 0:00:00 6.23 MB/s 127.0.0.1 - - [18/Nov/2017:17:43:08 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=5969b1f7201f12ae HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" samtools-0.1.1 100% |##########################################################################################################################################################| Time: 0:00:00 5.16 MB/s 127.0.0.1 - - [18/Nov/2017:17:43:08 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=5969b1f7201f12ae&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:09 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=5969b1f7201f12ae&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:12 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:13 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" # # To activate this environment, use: # > source activate __samtools@0.1.19 # # To deactivate an active environment, use: # > source deactivate # galaxy.tools.deps DEBUG 2017-11-18 17:43:14,914 Using dependency samtools version 0.1.19 of type conda galaxy.tools.deps.conda_util DEBUG 2017-11-18 17:43:14,915 Executing command: /galaxydir/galaxy/database/dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --channel r --name mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397 samtools=1.3.1 bcftools=1.5 Fetching package metadata .......galaxy.tools.deps DEBUG 2017-11-18 17:43:17,098 Using dependency ucsc_tools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:17,098 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:17,098 Using dependency bedtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:17,100 Dependency ucsc-fatotwobit not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,100 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,101 Dependency bowtie not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,102 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,103 Dependency gnuplot not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,104 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,105 Dependency bedtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,105 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:17,106 Dependency biom-format not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,107 Dependency python not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,164 Using dependency sra-tools version 2.8.1 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:17,165 Dependency rpy2 not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,166 Dependency bcftools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,167 Dependency openbabel not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,168 Dependency gnuplot-py not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,168 Using dependency samtools version 0.1.19 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:17,169 Using dependency samtools version 1.3.1 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:17,170 Dependency bcftools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,181 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 17:43:17,209 Using dependency ucsc_tools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:17,209 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:17,209 Using dependency bedtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:17,211 Dependency ucsc-fatotwobit not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,211 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,212 Dependency bowtie not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,213 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,214 Dependency gnuplot not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,216 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,216 Dependency bedtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,217 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:17,218 Dependency biom-format not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,218 Dependency python not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,219 Using dependency sra-tools version 2.8.1 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:17,220 Dependency rpy2 not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,221 Dependency bcftools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,221 Dependency openbabel not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,222 Dependency gnuplot-py not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,224 Using dependency samtools version 0.1.19 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:17,225 Using dependency samtools version 1.3.1 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:17,226 Dependency bcftools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:17,226 Using dependency blast version 2.5.0 of type tool_shed_package 127.0.0.1 - - [18/Nov/2017:17:43:17 -0400] "GET /admin/manage_tool_dependencies HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:17 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/manage_tool_dependencies" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" .......... Solving package specifications: . Package plan for installation in environment /galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397: The following NEW packages will be INSTALLED: bcftools: 1.5-3 bioconda bzip2: 1.0.6-1 conda-forge ca-certificates: 2017.11.5-0 conda-forge curl: 7.55.1-0 conda-forge krb5: 1.14.2-0 conda-forge libssh2: 1.8.0-2 conda-forge openssl: 1.0.2l-0 conda-forge samtools: 1.3.1-5 bioconda xz: 5.2.3-0 conda-forge zlib: 1.2.11-0 conda-forge bzip2-1.0.6-1. 100% |##########################################################################################################################################################| Time: 0:00:00 1.90 MB/s xz-5.2.3-0.tar 100% |##########################################################################################################################################################| Time: 0:00:00 6.55 MB/s bcftools-1.5-3 100% |##########################################################################################################################################################| Time: 0:00:00 8.18 MB/s # # To activate this environment, use: # > source activate mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397 # # To deactivate an active environment, use: # > source deactivate # galaxy.tools.deps DEBUG 2017-11-18 17:43:28,871 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,871 Using dependency bcftools version 1.5 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,883 Using dependency ucsc_tools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,883 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,883 Using dependency bedtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,884 Dependency ucsc-fatotwobit not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,884 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,886 Dependency bowtie not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,887 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,888 Dependency gnuplot not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,890 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,890 Dependency bedtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,891 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,891 Dependency biom-format not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,892 Dependency python not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,922 Using dependency sra-tools version 2.8.1 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,923 Dependency rpy2 not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,924 Dependency bcftools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,925 Dependency openbabel not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,925 Dependency gnuplot-py not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,926 Using dependency samtools version 0.1.19 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,926 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,926 Using dependency bcftools version 1.5 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,934 Using dependency blast version 2.5.0 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 17:43:28,950 Using dependency ucsc_tools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,950 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,950 Using dependency bedtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,951 Dependency ucsc-fatotwobit not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,951 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,952 Dependency bowtie not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,953 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,953 Dependency gnuplot not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,954 Dependency ucsc_tools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,955 Dependency bedtools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,955 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,956 Dependency biom-format not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,957 Dependency python not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,957 Using dependency sra-tools version 2.8.1 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,958 Dependency rpy2 not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,958 Dependency bcftools not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,959 Dependency openbabel not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,960 Dependency gnuplot-py not found. galaxy.tools.deps DEBUG 2017-11-18 17:43:28,960 Using dependency samtools version 0.1.19 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,961 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,961 Using dependency bcftools version 1.5 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:28,961 Using dependency blast version 2.5.0 of type tool_shed_package 127.0.0.1 - - [18/Nov/2017:17:42:19 -0400] "GET /admin/manage_tool_dependencies?selected_tool_ids=upload1&selected_tool_ids=__SET_METADATA__&selected_tool_ids=CONVERTER_sam_to_bigwig_0&selected_tool_ids=CONVERTER_fasta_to_fai&install_dependencies=Install+checked+dependencies+using+Conda HTTP/1.1" 200 - "http://localhost:8080/admin/manage_tool_dependencies" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 64993) Traceback (most recent call last): File "/galaxydir/galaxy/.venv/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 657, in __init__ self.finish() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 716, in finish self.wfile.close() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 283, in close self.flush() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- 127.0.0.1 - - [18/Nov/2017:17:43:36 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:37 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:37 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:37 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:37 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:37 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:37 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:37 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:37 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:37 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C2a56795cad3c7db3&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:38 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:40 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C2a56795cad3c7db3&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:47 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=001oul3m244a&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:47 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:47 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:50 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 17:43:51,235 Validated and populated state for tool request (59.839 ms) galaxy.tools.actions INFO 2017-11-18 17:43:51,367 Handled output named html_file for tool seq_sero_reads_multiple (51.460 ms) galaxy.tools.actions INFO 2017-11-18 17:43:51,461 Handled output named text_file for tool seq_sero_reads_multiple (93.587 ms) galaxy.tools.actions INFO 2017-11-18 17:43:51,498 Added output datasets to history (36.647 ms) galaxy.tools.actions INFO 2017-11-18 17:43:51,610 Verified access to datasets for Job[unflushed,tool_id=seq_sero_reads_multiple] (54.746 ms) galaxy.tools.actions INFO 2017-11-18 17:43:51,611 Setup for job Job[unflushed,tool_id=seq_sero_reads_multiple] complete, ready to flush (113.196 ms) galaxy.tools.actions INFO 2017-11-18 17:43:51,668 Flushed transaction for job Job[id=9,tool_id=seq_sero_reads_multiple] (55.956 ms) galaxy.tools.execute DEBUG 2017-11-18 17:43:51,668 Tool [seq_sero_reads_multiple] created job [9] (389.589 ms) galaxy.tools.execute DEBUG 2017-11-18 17:43:51,699 Executed 1 job(s) for tool seq_sero_reads_multiple request: (463.709 ms) 127.0.0.1 - - [18/Nov/2017:17:43:51 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:51 -0400] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:51 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A43%3A37.955Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 17:43:52,473 (9) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/9 galaxy.jobs.handler DEBUG 2017-11-18 17:43:52,488 (9) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 17:43:52,533 (9) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 17:43:52,546 Job [9] queued (58.094 ms) galaxy.jobs.handler INFO 2017-11-18 17:43:52,557 (9) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 17:43:52,875 Built script [/galaxydir/galaxy/database/jobs_directory/000/9/tool_script.sh] for tool command [/galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/files/000/dataset_2.dat /galaxydir/galaxy/tools/GalaxySeqsero/] galaxy.tools.deps DEBUG 2017-11-18 17:43:53,184 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:43:53,184 Using dependency bcftools version 1.5 of type conda galaxy.jobs.runners DEBUG 2017-11-18 17:43:53,193 (9) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/9/tool_script.sh; return_code=$?; if [ -f /galaxydir/galaxy/database/jobs_directory/000/9/working/Seqsero_result.html ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/9/working/Seqsero_result.html /galaxydir/galaxy/database/files/000/dataset_15.dat ; fi; if [ -f /galaxydir/galaxy/database/jobs_directory/000/9/working/Seqsero_result.txt ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/9/working/Seqsero_result.txt /galaxydir/galaxy/database/files/000/dataset_16.dat ; fi; cd '/galaxydir/galaxy/database/jobs_directory/000/9'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; python "/galaxydir/galaxy/database/jobs_directory/000/9/set_metadata_tk0oY2.py" "/galaxydir/galaxy/database/jobs_directory/000/9/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/9/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/9/metadata_in_HistoryDatasetAssociation_15_3ZnuYg,/galaxydir/galaxy/database/jobs_directory/000/9/metadata_kwds_HistoryDatasetAssociation_15_KaOPBr,/galaxydir/galaxy/database/jobs_directory/000/9/metadata_out_HistoryDatasetAssociation_15_TjGB_C,/galaxydir/galaxy/database/jobs_directory/000/9/metadata_results_HistoryDatasetAssociation_15_hVPsen,/galaxydir/galaxy/database/files/000/dataset_15.dat,/galaxydir/galaxy/database/jobs_directory/000/9/metadata_override_HistoryDatasetAssociation_15_pKj9uz" "/galaxydir/galaxy/database/jobs_directory/000/9/metadata_in_HistoryDatasetAssociation_16_EMLLq5,/galaxydir/galaxy/database/jobs_directory/000/9/metadata_kwds_HistoryDatasetAssociation_16_hWgV8F,/galaxydir/galaxy/database/jobs_directory/000/9/metadata_out_HistoryDatasetAssociation_16_xXGKIl,/galaxydir/galaxy/database/jobs_directory/000/9/metadata_results_HistoryDatasetAssociation_16_3ZJt0y,/galaxydir/galaxy/database/files/000/dataset_16.dat,/galaxydir/galaxy/database/jobs_directory/000/9/metadata_override_HistoryDatasetAssociation_16_IlRyVt" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 17:43:53,211 (9) executing job script: /galaxydir/galaxy/database/jobs_directory/000/9/galaxy_9.sh galaxy.jobs DEBUG 2017-11-18 17:43:53,221 (9) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:17:43:54 -0400] "GET /?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:54 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:54 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:55 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:55 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:55 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:55 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:55 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=001oul3m244a&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:55 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:55 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:55 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:55 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:43:58 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:00 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A43%3A55.336Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 17:44:00,366 execution finished: /galaxydir/galaxy/database/jobs_directory/000/9/galaxy_9.sh galaxy.jobs.output_checker INFO 2017-11-18 17:44:00,377 Job 9: Warning: Exit code 0 () galaxy.model.metadata DEBUG 2017-11-18 17:44:00,526 loading metadata from file for: HistoryDatasetAssociation 15 galaxy.model.metadata DEBUG 2017-11-18 17:44:00,651 loading metadata from file for: HistoryDatasetAssociation 16 galaxy.jobs INFO 2017-11-18 17:44:00,856 Collecting metrics for Job 9 galaxy.jobs DEBUG 2017-11-18 17:44:00,886 job 9 ended (finish() executed in (519.258 ms)) galaxy.model.metadata DEBUG 2017-11-18 17:44:00,895 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:17:44:04 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A44%3A00.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:04 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:04 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:04 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:04 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:06 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/1e8ab44153008be8 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:12 -0400] "GET /datasets/1e8ab44153008be8/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:12 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/1e8ab44153008be8/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:14 -0400] "GET /datasets/1e8ab44153008be8/stderr HTTP/1.1" 200 - "http://localhost:8080/datasets/1e8ab44153008be8/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:34 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=001oul3m244a" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:34 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:34 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:34 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:34 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:35 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:36 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:40 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=33b43b4e7093c91f HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.deps DEBUG 2017-11-18 17:44:40,896 Using dependency sra-tools version 2.8.1 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:44:40,897 Using dependency sra-tools version 2.8.1 of type conda galaxy.tools.deps DEBUG 2017-11-18 17:44:40,897 Using dependency sra-tools version 2.8.1 of type conda 127.0.0.1 - - [18/Nov/2017:17:44:40 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=33b43b4e7093c91f&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:44:41 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=33b43b4e7093c91f&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.queue_worker DEBUG 2017-11-18 17:45:19,866 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 17:45:19,886 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:45:19,894 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:45:19,897 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:45:19,900 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:45:19,907 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,908 Reading tools from config files finshed (22.830 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,909 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,912 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,912 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,912 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,913 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,913 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,914 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,915 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,915 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,915 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,916 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,917 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,917 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,917 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,918 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,919 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,919 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,920 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,920 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,920 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,921 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,921 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:45:19,922 Loading tool panel finished (13.121 ms) galaxy.tools.deps DEBUG 2017-11-18 17:45:19,924 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 17:45:19,952 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 17:45:19,955 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 17:45:19,958 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 17:45:19,958 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 17:45:19,965 Toolbox reload (99.559 ms) galaxy.queue_worker INFO 2017-11-18 17:45:20,883 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 17:45:20,883 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 17:45:20,916 Toolbox index finished (32.704 ms) galaxy.queue_worker DEBUG 2017-11-18 17:46:29,619 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 17:46:29,641 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:46:29,647 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:46:29,650 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:46:29,655 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:46:29,658 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,659 Reading tools from config files finshed (18.083 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,659 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,661 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,661 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,662 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,663 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,663 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,664 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,664 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,665 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,666 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,667 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,667 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,667 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,668 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,668 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,670 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,670 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,671 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,673 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,673 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,674 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,674 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:46:29,675 Loading tool panel finished (16.066 ms) galaxy.tools.deps DEBUG 2017-11-18 17:46:29,677 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 17:46:29,701 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 17:46:29,703 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 17:46:29,704 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 17:46:29,704 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 17:46:29,711 Toolbox reload (91.574 ms) galaxy.queue_worker INFO 2017-11-18 17:46:30,024 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 17:46:30,024 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 17:46:30,063 Toolbox index finished (38.483 ms) 127.0.0.1 - - [18/Nov/2017:17:46:32 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:46:33 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:46:44 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=f2db41e1fa331b3e HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:46:44 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:46:44 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:46:49 -0400] "GET /admin_toolshed/browse_tool_dependency?id=f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:46:49 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_dependency?id=f2db41e1fa331b3e" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.shed_util_common WARNING 2017-11-18 17:46:49,355 Request tries to access a folder outside of the allowed locations. Folder path: ./database/dependencies/bwa/0.5.9/devteam/package_bwa_0_5_9/ec2595e4d313 127.0.0.1 - - [18/Nov/2017:17:46:49 -0400] "GET /admin_toolshed/open_folder?folder_path=.%2Fdatabase%2Fdependencies%2Fbwa%2F0.5.9%2Fdevteam%2Fpackage_bwa_0_5_9%2Fec2595e4d313&repository_id=f2db41e1fa331b3e&_=1511045209264 HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_dependency?id=f2db41e1fa331b3e" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:46:52 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:47:40 -0400] "GET /admin_toolshed/browse_tool_dependency?id=f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:47:41 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_dependency?id=f2db41e1fa331b3e" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.shed_util_common WARNING 2017-11-18 17:47:41,122 Request tries to access a folder outside of the allowed locations. Folder path: ./database/dependencies/bwa/0.5.9/devteam/package_bwa_0_5_9/ec2595e4d313 127.0.0.1 - - [18/Nov/2017:17:47:41 -0400] "GET /admin_toolshed/open_folder?folder_path=.%2Fdatabase%2Fdependencies%2Fbwa%2F0.5.9%2Fdevteam%2Fpackage_bwa_0_5_9%2Fec2595e4d313&repository_id=f2db41e1fa331b3e&_=1511045261028 HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_dependency?id=f2db41e1fa331b3e" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.queue_worker DEBUG 2017-11-18 17:47:58,486 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 17:47:58,505 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:47:58,511 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:47:58,513 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:47:58,515 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:47:58,519 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,519 Reading tools from config files finshed (14.281 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,519 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,522 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,522 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,522 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,523 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,523 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,524 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,525 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,525 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,525 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,526 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,526 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,527 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,527 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,527 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,529 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,529 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,529 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,529 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,529 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,531 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,531 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:47:58,531 Loading tool panel finished (12.105 ms) galaxy.tools.deps DEBUG 2017-11-18 17:47:58,533 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 17:47:58,555 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 17:47:58,557 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 17:47:58,558 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 17:47:58,558 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 17:47:58,564 Toolbox reload (78.842 ms) galaxy.queue_worker INFO 2017-11-18 17:47:59,501 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 17:47:59,502 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 17:47:59,539 Toolbox index finished (37.009 ms) 127.0.0.1 - - [18/Nov/2017:17:48:02 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:02 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:02 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:02 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:02 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:02 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:02 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:03 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:03 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:03 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:03 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:05 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:07 -0400] "PUT /api/histories/f597429621d6eb2b/contents/datasets/1e8ab44153008be8 HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:08 -0400] "PUT /api/histories/f597429621d6eb2b/contents/datasets/4b187121143038ff HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:09 -0400] "PUT /api/histories/f597429621d6eb2b/contents/datasets/2a56795cad3c7db3 HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:10 -0400] "PUT /api/histories/f597429621d6eb2b/contents/datasets/c9468fdb6dc5c5f1 HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:10 -0400] "PUT /api/histories/f597429621d6eb2b/contents/datasets/e85a3be143d5905b HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:11 -0400] "PUT /api/histories/f597429621d6eb2b/contents/datasets/3f5830403180d620 HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:12 -0400] "PUT /api/histories/f597429621d6eb2b/contents/datasets/03501d7626bd192f HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:15 -0400] "PUT /api/histories/f597429621d6eb2b/contents/datasets/0a248a1f62a0cc04 HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:21 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=7keoeuqvfpc&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:21 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:21 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:23 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 17:48:24,454 Validated and populated state for tool request (52.064 ms) galaxy.tools.actions INFO 2017-11-18 17:48:24,536 Handled output named html_file for tool seq_sero_reads_multiple (33.299 ms) galaxy.tools.actions INFO 2017-11-18 17:48:24,575 Handled output named text_file for tool seq_sero_reads_multiple (38.834 ms) galaxy.tools.actions INFO 2017-11-18 17:48:24,598 Added output datasets to history (22.795 ms) galaxy.tools.actions INFO 2017-11-18 17:48:24,653 Verified access to datasets for Job[unflushed,tool_id=seq_sero_reads_multiple] (26.680 ms) galaxy.tools.actions INFO 2017-11-18 17:48:24,653 Setup for job Job[unflushed,tool_id=seq_sero_reads_multiple] complete, ready to flush (55.181 ms) galaxy.tools.actions INFO 2017-11-18 17:48:24,683 Flushed transaction for job Job[id=10,tool_id=seq_sero_reads_multiple] (29.529 ms) galaxy.tools.execute DEBUG 2017-11-18 17:48:24,683 Tool [seq_sero_reads_multiple] created job [10] (200.283 ms) galaxy.tools.execute DEBUG 2017-11-18 17:48:24,700 Executed 1 job(s) for tool seq_sero_reads_multiple request: (245.374 ms) 127.0.0.1 - - [18/Nov/2017:17:48:24 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:24 -0400] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:24 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A48%3A03.064Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 17:48:25,476 (10) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/10 galaxy.jobs.handler DEBUG 2017-11-18 17:48:25,489 (10) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 17:48:25,526 (10) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 17:48:25,538 Job [10] queued (48.501 ms) galaxy.jobs.handler INFO 2017-11-18 17:48:25,549 (10) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 17:48:25,852 Built script [/galaxydir/galaxy/database/jobs_directory/000/10/tool_script.sh] for tool command [/galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/files/000/dataset_2.dat /galaxydir/galaxy/tools/GalaxySeqsero/] galaxy.tools.deps DEBUG 2017-11-18 17:48:26,137 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:48:26,137 Using dependency bcftools version 1.5 of type conda galaxy.jobs.runners DEBUG 2017-11-18 17:48:26,144 (10) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/10/tool_script.sh; return_code=$?; if [ -f /galaxydir/galaxy/database/jobs_directory/000/10/working/Seqsero_result.html ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/10/working/Seqsero_result.html /galaxydir/galaxy/database/files/000/dataset_17.dat ; fi; if [ -f /galaxydir/galaxy/database/jobs_directory/000/10/working/Seqsero_result.txt ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/10/working/Seqsero_result.txt /galaxydir/galaxy/database/files/000/dataset_18.dat ; fi; cd '/galaxydir/galaxy/database/jobs_directory/000/10'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; python "/galaxydir/galaxy/database/jobs_directory/000/10/set_metadata_hNAKNn.py" "/galaxydir/galaxy/database/jobs_directory/000/10/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/10/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/10/metadata_in_HistoryDatasetAssociation_17_F9mVSv,/galaxydir/galaxy/database/jobs_directory/000/10/metadata_kwds_HistoryDatasetAssociation_17_vc2TcG,/galaxydir/galaxy/database/jobs_directory/000/10/metadata_out_HistoryDatasetAssociation_17_DotJ3U,/galaxydir/galaxy/database/jobs_directory/000/10/metadata_results_HistoryDatasetAssociation_17_yOp9je,/galaxydir/galaxy/database/files/000/dataset_17.dat,/galaxydir/galaxy/database/jobs_directory/000/10/metadata_override_HistoryDatasetAssociation_17_7GtQiy" "/galaxydir/galaxy/database/jobs_directory/000/10/metadata_in_HistoryDatasetAssociation_18_WZPDTw,/galaxydir/galaxy/database/jobs_directory/000/10/metadata_kwds_HistoryDatasetAssociation_18_kviBNm,/galaxydir/galaxy/database/jobs_directory/000/10/metadata_out_HistoryDatasetAssociation_18_2pHKbD,/galaxydir/galaxy/database/jobs_directory/000/10/metadata_results_HistoryDatasetAssociation_18_kKmrWS,/galaxydir/galaxy/database/files/000/dataset_18.dat,/galaxydir/galaxy/database/jobs_directory/000/10/metadata_override_HistoryDatasetAssociation_18_liRcak" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 17:48:26,159 (10) executing job script: /galaxydir/galaxy/database/jobs_directory/000/10/galaxy_10.sh galaxy.jobs DEBUG 2017-11-18 17:48:26,169 (10) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:17:48:27 -0400] "GET /?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:28 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:28 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:28 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:28 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:28 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:28 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:28 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=7keoeuqvfpc&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:28 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:28 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:28 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:28 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:31 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 17:48:33,114 execution finished: /galaxydir/galaxy/database/jobs_directory/000/10/galaxy_10.sh galaxy.jobs.output_checker INFO 2017-11-18 17:48:33,127 Job 10: Warning: Exit code 0 () galaxy.model.metadata DEBUG 2017-11-18 17:48:33,279 loading metadata from file for: HistoryDatasetAssociation 17 127.0.0.1 - - [18/Nov/2017:17:48:33 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A48%3A28.777Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.model.metadata DEBUG 2017-11-18 17:48:33,433 loading metadata from file for: HistoryDatasetAssociation 18 galaxy.jobs INFO 2017-11-18 17:48:33,644 Collecting metrics for Job 10 galaxy.jobs DEBUG 2017-11-18 17:48:33,678 job 10 ended (finish() executed in (563.788 ms)) galaxy.model.metadata DEBUG 2017-11-18 17:48:33,688 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:17:48:37 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A48%3A33.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:37 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:37 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:37 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:37 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:39 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/2d9035b3fc152403 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:41 -0400] "GET /datasets/2d9035b3fc152403/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:41 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/2d9035b3fc152403/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:48:43 -0400] "GET /datasets/2d9035b3fc152403/stderr HTTP/1.1" 200 - "http://localhost:8080/datasets/2d9035b3fc152403/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.queue_worker DEBUG 2017-11-18 17:49:19,353 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 17:49:19,381 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:49:19,393 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:49:19,398 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:49:19,403 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:49:19,408 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,409 Reading tools from config files finshed (28.275 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,409 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,411 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,411 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,412 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,412 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,412 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,414 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,414 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,415 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,415 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,416 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,416 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,416 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,417 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,417 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,419 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,419 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,419 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,419 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,419 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,420 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,421 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:49:19,421 Loading tool panel finished (12.469 ms) galaxy.tools.deps DEBUG 2017-11-18 17:49:19,424 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 17:49:19,448 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 17:49:19,449 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 17:49:19,451 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 17:49:19,451 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 17:49:19,457 Toolbox reload (103.932 ms) galaxy.queue_worker INFO 2017-11-18 17:49:19,934 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 17:49:19,934 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 17:49:20,041 Toolbox index finished (107.022 ms) 127.0.0.1 - - [18/Nov/2017:17:49:21 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=7keoeuqvfpc" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:22 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:22 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:22 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:22 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:22 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:22 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:22 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:22 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:22 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:22 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:24 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:26 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=st2e3cng4l&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:27 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:27 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:29 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 17:49:30,121 Validated and populated state for tool request (38.489 ms) galaxy.tools.actions INFO 2017-11-18 17:49:30,205 Handled output named html_file for tool seq_sero_reads_multiple (31.914 ms) galaxy.tools.actions INFO 2017-11-18 17:49:30,249 Handled output named text_file for tool seq_sero_reads_multiple (42.028 ms) galaxy.tools.actions INFO 2017-11-18 17:49:30,272 Added output datasets to history (23.415 ms) galaxy.tools.actions INFO 2017-11-18 17:49:30,332 Verified access to datasets for Job[unflushed,tool_id=seq_sero_reads_multiple] (29.320 ms) galaxy.tools.actions INFO 2017-11-18 17:49:30,333 Setup for job Job[unflushed,tool_id=seq_sero_reads_multiple] complete, ready to flush (60.422 ms) galaxy.tools.actions INFO 2017-11-18 17:49:30,363 Flushed transaction for job Job[id=11,tool_id=seq_sero_reads_multiple] (29.491 ms) galaxy.tools.execute DEBUG 2017-11-18 17:49:30,363 Tool [seq_sero_reads_multiple] created job [11] (214.940 ms) galaxy.tools.execute DEBUG 2017-11-18 17:49:30,379 Executed 1 job(s) for tool seq_sero_reads_multiple request: (257.938 ms) 127.0.0.1 - - [18/Nov/2017:17:49:30 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:30 -0400] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:30 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A49%3A22.394Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 17:49:30,568 (11) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/11 galaxy.jobs.handler DEBUG 2017-11-18 17:49:30,583 (11) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 17:49:30,635 (11) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 17:49:30,650 Job [11] queued (66.682 ms) galaxy.jobs.handler INFO 2017-11-18 17:49:30,686 (11) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 17:49:31,016 Built script [/galaxydir/galaxy/database/jobs_directory/000/11/tool_script.sh] for tool command [bwa /galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/files/000/dataset_2.dat /galaxydir/galaxy/tools/GalaxySeqsero/] galaxy.tools.deps DEBUG 2017-11-18 17:49:31,307 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:49:31,307 Using dependency bcftools version 1.5 of type conda galaxy.jobs.runners DEBUG 2017-11-18 17:49:31,317 (11) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/11/tool_script.sh; return_code=$?; if [ -f /galaxydir/galaxy/database/jobs_directory/000/11/working/Seqsero_result.html ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/11/working/Seqsero_result.html /galaxydir/galaxy/database/files/000/dataset_19.dat ; fi; if [ -f /galaxydir/galaxy/database/jobs_directory/000/11/working/Seqsero_result.txt ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/11/working/Seqsero_result.txt /galaxydir/galaxy/database/files/000/dataset_20.dat ; fi; cd '/galaxydir/galaxy/database/jobs_directory/000/11'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; python "/galaxydir/galaxy/database/jobs_directory/000/11/set_metadata_Ue7_O8.py" "/galaxydir/galaxy/database/jobs_directory/000/11/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/11/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/11/metadata_in_HistoryDatasetAssociation_19_SS8iaD,/galaxydir/galaxy/database/jobs_directory/000/11/metadata_kwds_HistoryDatasetAssociation_19_1_YnMA,/galaxydir/galaxy/database/jobs_directory/000/11/metadata_out_HistoryDatasetAssociation_19_r92ijq,/galaxydir/galaxy/database/jobs_directory/000/11/metadata_results_HistoryDatasetAssociation_19_XUYD0B,/galaxydir/galaxy/database/files/000/dataset_19.dat,/galaxydir/galaxy/database/jobs_directory/000/11/metadata_override_HistoryDatasetAssociation_19_PHiNAN" "/galaxydir/galaxy/database/jobs_directory/000/11/metadata_in_HistoryDatasetAssociation_20_qmMoBz,/galaxydir/galaxy/database/jobs_directory/000/11/metadata_kwds_HistoryDatasetAssociation_20_te96j1,/galaxydir/galaxy/database/jobs_directory/000/11/metadata_out_HistoryDatasetAssociation_20_vyPOGo,/galaxydir/galaxy/database/jobs_directory/000/11/metadata_results_HistoryDatasetAssociation_20_U4YfvK,/galaxydir/galaxy/database/files/000/dataset_20.dat,/galaxydir/galaxy/database/jobs_directory/000/11/metadata_override_HistoryDatasetAssociation_20_HbVUNf" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 17:49:31,333 (11) executing job script: /galaxydir/galaxy/database/jobs_directory/000/11/galaxy_11.sh galaxy.jobs DEBUG 2017-11-18 17:49:31,343 (11) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:17:49:32 -0400] "GET /?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:32 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:32 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:32 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:32 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:32 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:33 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:33 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=st2e3cng4l&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:33 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:33 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:33 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:33 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 17:49:35,354 execution finished: /galaxydir/galaxy/database/jobs_directory/000/11/galaxy_11.sh galaxy.jobs.output_checker INFO 2017-11-18 17:49:35,365 Job 11: Warning: Exit code 127 () galaxy.jobs INFO 2017-11-18 17:49:35,640 Collecting metrics for Job 11 galaxy.jobs DEBUG 2017-11-18 17:49:35,662 job 11 ended (finish() executed in (307.342 ms)) galaxy.model.metadata DEBUG 2017-11-18 17:49:35,672 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:17:49:35 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:37 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A49%3A33.217Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:37 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:37 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:38 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:49:39 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/d413a19dec13d11e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:52:44 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/5a1cff6882ddb5b2 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:53:18 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/5a1cff6882ddb5b2 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:53:23 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/5a1cff6882ddb5b2 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:53:26 -0400] "GET /datasets/5a1cff6882ddb5b2/display/?preview=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:53:28 -0400] "GET /datasets/5a1cff6882ddb5b2/display/?preview=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:53:50 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/417e33144b294c21 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.queue_worker DEBUG 2017-11-18 17:54:20,875 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 17:54:20,895 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:54:20,904 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:54:20,906 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:54:20,913 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:54:20,919 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,920 Reading tools from config files finshed (24.483 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,920 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,924 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,924 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,924 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,926 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,926 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,928 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,928 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,929 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,929 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,930 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,930 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,930 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,931 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,931 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,933 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,933 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,933 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,933 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,933 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,934 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,935 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:54:20,935 Loading tool panel finished (15.351 ms) galaxy.tools.deps DEBUG 2017-11-18 17:54:20,937 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 17:54:20,960 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 17:54:20,961 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 17:54:20,964 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 17:54:20,964 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 17:54:20,970 Toolbox reload (95.289 ms) galaxy.queue_worker INFO 2017-11-18 17:54:21,086 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 17:54:21,086 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 17:54:21,132 Toolbox index finished (46.193 ms) 127.0.0.1 - - [18/Nov/2017:17:55:16 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=st2e3cng4l" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:55:16 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:55:16 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:55:16 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:55:16 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:55:19 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:55:20 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:55:36 -0400] "GET /admin_toolshed/browse_tool_sheds HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:55:36 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:55:37 -0400] "GET /admin_toolshed/browse_tool_shed?tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:56:03 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:56:03 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:56:18 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=f2db41e1fa331b3e HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:56:18 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:56:18 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:56:21 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:56:47 -0400] "GET /admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&operation=deactivate+or+uninstall&id=f2db41e1fa331b3e&f-deleted=False HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:56:47 -0400] "GET /admin_toolshed/deactivate_or_uninstall_repository?sort=name&advanced_search=false&f-deleted=False&show_item_checkboxes=true&async=false&id=f2db41e1fa331b3e&page=1 HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:56:47 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/deactivate_or_uninstall_repository?sort=name&advanced_search=false&f-deleted=False&show_item_checkboxes=true&async=false&id=f2db41e1fa331b3e&page=1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.installed_repository_manager DEBUG 2017-11-18 17:56:49,535 Removed repository installation directory: /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/package_bwa_0_5_9/ec2595e4d313 tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:56:49,542 Removed tool dependency installation directory: ./database/dependencies/bwa/0.5.9/devteam/package_bwa_0_5_9/ec2595e4d313 127.0.0.1 - - [18/Nov/2017:17:56:49 -0400] "POST /admin_toolshed/deactivate_or_uninstall_repository HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/deactivate_or_uninstall_repository?sort=name&advanced_search=false&f-deleted=False&show_item_checkboxes=true&async=false&id=f2db41e1fa331b3e&page=1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:56:49 -0400] "GET /admin_toolshed/browse_repositories?status=done&message=The+repository+named+%3Cb%3Epackage_bwa_0_5_9%3C%2Fb%3E+has+been+uninstalled.++ HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/deactivate_or_uninstall_repository?sort=name&advanced_search=false&f-deleted=False&show_item_checkboxes=true&async=false&id=f2db41e1fa331b3e&page=1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:56:50 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories?status=done&message=The+repository+named+%3Cb%3Epackage_bwa_0_5_9%3C%2Fb%3E+has+been+uninstalled.++" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:56:57 -0400] "GET /admin_toolshed/browse_tool_sheds HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:56:57 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:56:58 -0400] "GET /admin_toolshed/browse_tool_shed?tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.deps DEBUG 2017-11-18 17:57:12,493 Dependency bwa not found. galaxy.tools.deps DEBUG 2017-11-18 17:57:12,494 Dependency bwa not found. 127.0.0.1 - - [18/Nov/2017:17:57:11 -0400] "GET /admin_toolshed/prepare_for_install?changeset_revisions=3a001705dc94&repository_ids=c07e587588ba3093&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:13 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=3a001705dc94&repository_ids=c07e587588ba3093&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 17:57:16,503 Creating repository dependency objects... galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:17,054 Appending to tool panel section: Get Data tool_shed.util.repository_util DEBUG 2017-11-18 17:57:17,067 Adding new row for repository 'bwa_wrappers' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_util DEBUG 2017-11-18 17:57:17,224 Updating an existing row for repository 'package_bwa_0_5_9' in the tool_shed_repository table, status set to 'New'. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 17:57:17,233 Building repository dependency relationships... tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-11-18 17:57:17,260 Creating new repository_dependency record for installed revision ec2595e4d313 of repository: package_bwa_0_5_9 owned by devteam. galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:17,291 Appending to tool panel section: Get Data 127.0.0.1 - - [18/Nov/2017:17:57:16 -0400] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install?changeset_revisions=3a001705dc94&repository_ids=c07e587588ba3093&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:17 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:57:20,413 Updating an existing record for version 0.5.9 of tool dependency bwa for revision ec2595e4d313 of repository package_bwa_0_5_9 by updating the status from Uninstalled to Never installed. 127.0.0.1 - - [18/Nov/2017:17:57:20 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:57:20,498 Updating an existing record for version 0.5.9 of tool dependency bwa for revision ec2595e4d313 of repository package_bwa_0_5_9 by updating the status from Never installed to Installing. tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 17:57:20,524 Attempting to download via url: http://depot.galaxyproject.org/package/darwin/x86_64/bwa/bwa-0.5.9-Darwin-x86_64.tgz tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2017-11-18 17:57:20,980 Successfully downloaded from url: http://depot.galaxyproject.org/package/darwin/x86_64/bwa/bwa-0.5.9-Darwin-x86_64.tgz tool_shed.galaxy_install.install_manager DEBUG 2017-11-18 17:57:20,988 Changing status for tool dependency bwa from Installing to Installed. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:57:20,988 Updating an existing record for version 0.5.9 of tool dependency bwa for revision ec2595e4d313 of repository package_bwa_0_5_9 by updating the status from Installing to Installed. galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:21,032 Appending to tool panel section: Get Data 127.0.0.1 - - [18/Nov/2017:17:57:23 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.data WARNING 2017-11-18 17:57:23,727 Cannot find index file './database/tmp/tmp-toolshed-gmfcrhrPts7/bwa_index.loc' for tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 17:57:23,727 Loading another instance of data table 'bwa_indexes' from file '../shed_tools/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/bwa_wrappers/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 17:57:23,727 Cannot find index file './database/tmp/tmp-toolshed-gmfcrhrPts7/bwa_index_color.loc' for tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 17:57:23,728 Loading another instance of data table 'bwa_indexes_color' from file '../shed_tools/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/bwa_wrappers/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 17:57:23,898 Cannot find index file '/galaxydir/galaxy/tool-data/bwa_index.loc' for tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 17:57:23,898 Loading another instance of data table 'bwa_indexes' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/bwa_wrappers/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 17:57:23,899 Cannot find index file '/galaxydir/galaxy/tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 17:57:23,899 Loading another instance of data table 'bwa_indexes_color' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/bwa_wrappers/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 17:57:23,916 Cannot find index file '/galaxydir/galaxy/tool-data/bwa_index.loc' for tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 17:57:23,916 Loading another instance of data table 'bwa_indexes' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/bwa_wrappers/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.data WARNING 2017-11-18 17:57:23,916 Cannot find index file '/galaxydir/galaxy/tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 17:57:23,916 Loading another instance of data table 'bwa_indexes_color' from file '/galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/bwa_wrappers/tool_data_table_conf.xml.sample', attempting to merge content. galaxy.tools.test INFO 2017-11-18 17:57:23,919 bwa_wrapper - Failed to find case matching value (preSet) for test parameter specification for conditional params. Remainder of test behavior is unspecified. tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:57:24,596 Creating a new record for version 0.5.9 of tool dependency bwa for revision 3a001705dc94 of repository bwa_wrappers. The status is being set to Never installed. galaxy.tools.data DEBUG 2017-11-18 17:57:24,617 Could not parse existing tool data table config, assume no existing elements: [Errno 2] No such file or directory: u'/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/tool_data_table_conf.xml' galaxy.tools.data DEBUG 2017-11-18 17:57:24,621 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/bwa_index.loc' for 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 17:57:24,621 Loading another instance of data table 'bwa_indexes' from file '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 17:57:24,621 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/bwa_index_color.loc' for 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 17:57:24,621 Loading another instance of data table 'bwa_indexes_color' from file '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/tool_data_table_conf.xml', attempting to merge content. galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:25,195 Loaded tool id: toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/bwa_color_wrapper/1.0.2, version: 1.0.2 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:25,208 Loaded tool id: toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/bwa_wrapper/1.2.3, version: 1.2.3 into tool panel.... galaxy.tools.toolbox.watcher DEBUG 2017-11-18 17:57:26,227 The file './config/shed_tool_conf.xml' has changes. galaxy.queue_worker DEBUG 2017-11-18 17:57:26,227 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 17:57:26,244 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:57:26,250 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 17:57:26,252 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:57:26,253 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 17:57:26,257 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,258 Reading tools from config files finshed (13.684 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,258 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,258 Loaded tool id: toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/bwa_color_wrapper/1.0.2, version: 1.0.2 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,259 Loaded tool id: toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/bwa_wrapper/1.2.3, version: 1.2.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,261 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,262 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,262 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,263 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,263 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,264 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,265 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,265 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,266 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,267 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,267 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,267 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,267 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,269 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,269 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,269 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,269 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,270 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,271 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,271 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 17:57:26,271 Loading tool panel finished (13.531 ms) galaxy.tools.deps DEBUG 2017-11-18 17:57:26,273 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 17:57:26,311 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 17:57:26,313 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 17:57:26,315 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 17:57:26,315 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 17:57:26,322 Toolbox reload (94.380 ms) galaxy.tools.deps.conda_util DEBUG 2017-11-18 17:57:26,386 Executing command: /galaxydir/galaxy/database/dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --channel r --name __bwa@0.5.9 bwa=0.5.9 127.0.0.1 - - [18/Nov/2017:17:57:26 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.queue_worker INFO 2017-11-18 17:57:27,240 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 17:57:27,240 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 17:57:27,502 Toolbox index finished (261.645 ms) Fetching package metadata .......127.0.0.1 - - [18/Nov/2017:17:57:29 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:32 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:35 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" .127.0.0.1 - - [18/Nov/2017:17:57:38 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ......... Solving package specifications: . Package plan for installation in environment /galaxydir/galaxy/database/dependencies/_conda/envs/__bwa@0.5.9: The following NEW packages will be INSTALLED: bwa: 0.5.9-0 bioconda libgcc: 4.8.5-1 zlib: 1.2.11-0 conda-forge 127.0.0.1 - - [18/Nov/2017:17:57:41 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" libgcc-4.8.5-1 100% |##########################################################################################################################################################| Time: 0:00:00 6.82 MB/s bwa-0.5.9-0.ta 100% |##########################################################################################################################################################| Time: 0:00:00 2.75 MB/s # # To activate this environment, use: # > source activate __bwa@0.5.9 # # To deactivate an active environment, use: # > source deactivate # galaxy.tools.deps DEBUG 2017-11-18 17:57:42,904 Using dependency bwa version 0.5.9 of type conda tool_shed.util.tool_dependency_util DEBUG 2017-11-18 17:57:43,354 Updating an existing record for version 0.5.9 of tool dependency bwa for revision 3a001705dc94 of repository bwa_wrappers by updating the status from Never installed to Installed. 127.0.0.1 - - [18/Nov/2017:17:57:17 -0400] "POST /admin_toolshed/manage_repositories HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:43 -0400] "GET /admin_toolshed/monitor_repository_installation?tool_shed_repository_ids=f2db41e1fa331b3e&tool_shed_repository_ids=2d9035b3fc152403 HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:44 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:51 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:51 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:52 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:52 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:52 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:52 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:52 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:52 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:52 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:52 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:52 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:54 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:56 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:56 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:56 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:56 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:56 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:57 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:57:58 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:58:05 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=2d9035b3fc152403 HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools.deps DEBUG 2017-11-18 17:58:05,641 Using dependency bwa version 0.5.9 of type tool_shed_package galaxy.tools.deps DEBUG 2017-11-18 17:58:05,641 Using dependency bwa version 0.5.9 of type tool_shed_package 127.0.0.1 - - [18/Nov/2017:17:58:05 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=2d9035b3fc152403&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:58:05 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=2d9035b3fc152403&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:29 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:29 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:29 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:29 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:29 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:29 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:29 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:29 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:29 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:29 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:30 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:32 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:34 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=ezn186zpc6b&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:34 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:34 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.queue_worker INFO 2017-11-18 17:59:37,210 Sending reload_tool control task. 127.0.0.1 - - [18/Nov/2017:17:59:37 -0400] "GET /api/tools/seq_sero_reads_multiple/reload HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:42 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 17:59:43,345 Validated and populated state for tool request (40.951 ms) galaxy.tools.actions INFO 2017-11-18 17:59:43,427 Handled output named html_file for tool seq_sero_reads_multiple (31.597 ms) galaxy.tools.actions INFO 2017-11-18 17:59:43,463 Handled output named text_file for tool seq_sero_reads_multiple (36.179 ms) galaxy.tools.actions INFO 2017-11-18 17:59:43,488 Added output datasets to history (25.021 ms) galaxy.tools.actions INFO 2017-11-18 17:59:43,556 Verified access to datasets for Job[unflushed,tool_id=seq_sero_reads_multiple] (33.384 ms) galaxy.tools.actions INFO 2017-11-18 17:59:43,560 Setup for job Job[unflushed,tool_id=seq_sero_reads_multiple] complete, ready to flush (71.992 ms) galaxy.tools.actions INFO 2017-11-18 17:59:43,596 Flushed transaction for job Job[id=12,tool_id=seq_sero_reads_multiple] (35.848 ms) galaxy.tools.execute DEBUG 2017-11-18 17:59:43,597 Tool [seq_sero_reads_multiple] created job [12] (222.301 ms) galaxy.tools.execute DEBUG 2017-11-18 17:59:43,618 Executed 1 job(s) for tool seq_sero_reads_multiple request: (273.516 ms) 127.0.0.1 - - [18/Nov/2017:17:59:43 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:43 -0400] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:43 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A59%3A29.837Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 17:59:44,613 (12) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/12 galaxy.jobs.handler DEBUG 2017-11-18 17:59:44,625 (12) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 17:59:44,663 (12) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 17:59:44,675 Job [12] queued (49.908 ms) galaxy.jobs.handler INFO 2017-11-18 17:59:44,686 (12) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 17:59:45,000 Built script [/galaxydir/galaxy/database/jobs_directory/000/12/tool_script.sh] for tool command [/galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/files/000/dataset_2.dat /galaxydir/galaxy/tools/GalaxySeqsero/] galaxy.tools.deps DEBUG 2017-11-18 17:59:45,302 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 17:59:45,303 Using dependency bcftools version 1.5 of type conda galaxy.jobs.runners DEBUG 2017-11-18 17:59:45,311 (12) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/12/tool_script.sh; return_code=$?; if [ -f /galaxydir/galaxy/database/jobs_directory/000/12/working/Seqsero_result.html ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/12/working/Seqsero_result.html /galaxydir/galaxy/database/files/000/dataset_21.dat ; fi; if [ -f /galaxydir/galaxy/database/jobs_directory/000/12/working/Seqsero_result.txt ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/12/working/Seqsero_result.txt /galaxydir/galaxy/database/files/000/dataset_22.dat ; fi; cd '/galaxydir/galaxy/database/jobs_directory/000/12'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; python "/galaxydir/galaxy/database/jobs_directory/000/12/set_metadata_EFgSgy.py" "/galaxydir/galaxy/database/jobs_directory/000/12/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/12/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/12/metadata_in_HistoryDatasetAssociation_21_9Gflym,/galaxydir/galaxy/database/jobs_directory/000/12/metadata_kwds_HistoryDatasetAssociation_21_wkD9ik,/galaxydir/galaxy/database/jobs_directory/000/12/metadata_out_HistoryDatasetAssociation_21_288MMp,/galaxydir/galaxy/database/jobs_directory/000/12/metadata_results_HistoryDatasetAssociation_21_JMvQ7G,/galaxydir/galaxy/database/files/000/dataset_21.dat,/galaxydir/galaxy/database/jobs_directory/000/12/metadata_override_HistoryDatasetAssociation_21_Ma02xb" "/galaxydir/galaxy/database/jobs_directory/000/12/metadata_in_HistoryDatasetAssociation_22_3K7PTy,/galaxydir/galaxy/database/jobs_directory/000/12/metadata_kwds_HistoryDatasetAssociation_22_FWtShF,/galaxydir/galaxy/database/jobs_directory/000/12/metadata_out_HistoryDatasetAssociation_22_DWIzfV,/galaxydir/galaxy/database/jobs_directory/000/12/metadata_results_HistoryDatasetAssociation_22_DIvQ5q,/galaxydir/galaxy/database/files/000/dataset_22.dat,/galaxydir/galaxy/database/jobs_directory/000/12/metadata_override_HistoryDatasetAssociation_22_pWimC3" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 17:59:45,325 (12) executing job script: /galaxydir/galaxy/database/jobs_directory/000/12/galaxy_12.sh galaxy.jobs DEBUG 2017-11-18 17:59:45,333 (12) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:17:59:47 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A59%3A43.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:47 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:48 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:51 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A59%3A47.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 17:59:52,284 execution finished: /galaxydir/galaxy/database/jobs_directory/000/12/galaxy_12.sh galaxy.jobs.output_checker INFO 2017-11-18 17:59:52,295 Job 12: Warning: Exit code 0 () galaxy.model.metadata DEBUG 2017-11-18 17:59:52,450 loading metadata from file for: HistoryDatasetAssociation 21 galaxy.model.metadata DEBUG 2017-11-18 17:59:52,570 loading metadata from file for: HistoryDatasetAssociation 22 galaxy.jobs INFO 2017-11-18 17:59:52,754 Collecting metrics for Job 12 galaxy.jobs DEBUG 2017-11-18 17:59:52,777 job 12 ended (finish() executed in (492.306 ms)) galaxy.model.metadata DEBUG 2017-11-18 17:59:52,784 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:17:59:56 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T22%3A59%3A52.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:56 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:56 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:56 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:56 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:17:59:59 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/8237ee2988567c1c HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:00:01 -0400] "GET /datasets/8237ee2988567c1c/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:00:01 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/8237ee2988567c1c/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:00:03 -0400] "GET /datasets/8237ee2988567c1c/stderr HTTP/1.1" 200 - "http://localhost:8080/datasets/8237ee2988567c1c/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:16 -0400] "GET /?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:16 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:17 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:17 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:17 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:17 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:17 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:17 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:17 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=ezn186zpc6b&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:17 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:17 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:17 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21%2C8237ee2988567c1c&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:17 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:19 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21%2C8237ee2988567c1c&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=ezn186zpc6b" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:21 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=fjqpexikggr&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:21 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:21 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:24 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 18:04:25,343 Validated and populated state for tool request (38.000 ms) galaxy.tools.actions INFO 2017-11-18 18:04:25,423 Handled output named html_file for tool seq_sero_reads_multiple (31.436 ms) galaxy.tools.actions INFO 2017-11-18 18:04:25,459 Handled output named text_file for tool seq_sero_reads_multiple (36.567 ms) galaxy.tools.actions INFO 2017-11-18 18:04:25,492 Added output datasets to history (32.075 ms) galaxy.tools.actions INFO 2017-11-18 18:04:25,560 Verified access to datasets for Job[unflushed,tool_id=seq_sero_reads_multiple] (30.718 ms) galaxy.tools.actions INFO 2017-11-18 18:04:25,561 Setup for job Job[unflushed,tool_id=seq_sero_reads_multiple] complete, ready to flush (68.887 ms) galaxy.tools.actions INFO 2017-11-18 18:04:25,592 Flushed transaction for job Job[id=13,tool_id=seq_sero_reads_multiple] (31.382 ms) galaxy.tools.execute DEBUG 2017-11-18 18:04:25,592 Tool [seq_sero_reads_multiple] created job [13] (221.824 ms) galaxy.tools.execute DEBUG 2017-11-18 18:04:25,611 Executed 1 job(s) for tool seq_sero_reads_multiple request: (268.073 ms) 127.0.0.1 - - [18/Nov/2017:18:04:25 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:25 -0400] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:25 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21%2C8237ee2988567c1c&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T23%3A04%3A17.322Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 18:04:26,540 (13) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/13 galaxy.jobs.handler DEBUG 2017-11-18 18:04:26,555 (13) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 18:04:26,602 (13) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 18:04:26,615 Job [13] queued (59.791 ms) galaxy.jobs.handler INFO 2017-11-18 18:04:26,637 (13) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 18:04:26,969 Built script [/galaxydir/galaxy/database/jobs_directory/000/13/tool_script.sh] for tool command [/galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/files/000/dataset_2.dat /galaxydir/galaxy/tools/GalaxySeqsero/] galaxy.tools.deps DEBUG 2017-11-18 18:04:27,254 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 18:04:27,254 Using dependency bcftools version 1.5 of type conda galaxy.jobs.runners DEBUG 2017-11-18 18:04:27,262 (13) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/13/tool_script.sh; return_code=$?; if [ -f /galaxydir/galaxy/database/jobs_directory/000/13/working/Seqsero_result.html ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/13/working/Seqsero_result.html /galaxydir/galaxy/database/files/000/dataset_23.dat ; fi; if [ -f /galaxydir/galaxy/database/jobs_directory/000/13/working/Seqsero_result.txt ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/13/working/Seqsero_result.txt /galaxydir/galaxy/database/files/000/dataset_24.dat ; fi; cd '/galaxydir/galaxy/database/jobs_directory/000/13'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; python "/galaxydir/galaxy/database/jobs_directory/000/13/set_metadata_zybGV3.py" "/galaxydir/galaxy/database/jobs_directory/000/13/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/13/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/13/metadata_in_HistoryDatasetAssociation_23_tXnre5,/galaxydir/galaxy/database/jobs_directory/000/13/metadata_kwds_HistoryDatasetAssociation_23_tT4D3W,/galaxydir/galaxy/database/jobs_directory/000/13/metadata_out_HistoryDatasetAssociation_23_e1QV8B,/galaxydir/galaxy/database/jobs_directory/000/13/metadata_results_HistoryDatasetAssociation_23_U2rAjO,/galaxydir/galaxy/database/files/000/dataset_23.dat,/galaxydir/galaxy/database/jobs_directory/000/13/metadata_override_HistoryDatasetAssociation_23_hupWYO" "/galaxydir/galaxy/database/jobs_directory/000/13/metadata_in_HistoryDatasetAssociation_24_7CeAXp,/galaxydir/galaxy/database/jobs_directory/000/13/metadata_kwds_HistoryDatasetAssociation_24_ESZKi3,/galaxydir/galaxy/database/jobs_directory/000/13/metadata_out_HistoryDatasetAssociation_24_iAPPFu,/galaxydir/galaxy/database/jobs_directory/000/13/metadata_results_HistoryDatasetAssociation_24_wnuQxe,/galaxydir/galaxy/database/files/000/dataset_24.dat,/galaxydir/galaxy/database/jobs_directory/000/13/metadata_override_HistoryDatasetAssociation_24_6jdT3E" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 18:04:27,279 (13) executing job script: /galaxydir/galaxy/database/jobs_directory/000/13/galaxy_13.sh galaxy.jobs DEBUG 2017-11-18 18:04:27,289 (13) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:18:04:29 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21%2C8237ee2988567c1c&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T23%3A04%3A25.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:29 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:30 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:30 -0400] "GET /?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:30 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:30 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:30 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:30 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:30 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:30 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:30 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:30 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=fjqpexikggr&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:31 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:31 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:31 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21%2C8237ee2988567c1c&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:33 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21%2C8237ee2988567c1c&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 18:04:34,218 execution finished: /galaxydir/galaxy/database/jobs_directory/000/13/galaxy_13.sh galaxy.jobs.output_checker INFO 2017-11-18 18:04:34,228 Job 13: Warning: Exit code 0 () galaxy.model.metadata DEBUG 2017-11-18 18:04:34,385 loading metadata from file for: HistoryDatasetAssociation 23 galaxy.model.metadata DEBUG 2017-11-18 18:04:34,497 loading metadata from file for: HistoryDatasetAssociation 24 galaxy.jobs INFO 2017-11-18 18:04:34,682 Collecting metrics for Job 13 galaxy.jobs DEBUG 2017-11-18 18:04:34,711 job 13 ended (finish() executed in (493.059 ms)) galaxy.model.metadata DEBUG 2017-11-18 18:04:34,719 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:18:04:35 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C2d9035b3fc152403%2Cd413a19dec13d11e%2C417e33144b294c21%2C8237ee2988567c1c&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T23%3A04%3A30.993Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:35 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:35 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:35 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:35 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:37 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/fb85969571388350 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:39 -0400] "GET /datasets/fb85969571388350/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:39 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/fb85969571388350/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:42 -0400] "GET /datasets/fb85969571388350/stderr HTTP/1.1" 200 - "http://localhost:8080/datasets/fb85969571388350/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:50 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/fb85969571388350/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:52 -0400] "GET /datasets/fb85969571388350/stdout HTTP/1.1" 200 - "http://localhost:8080/datasets/fb85969571388350/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:55 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/fb85969571388350/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:04:56 -0400] "GET /datasets/fb85969571388350/stderr HTTP/1.1" 200 - "http://localhost:8080/datasets/fb85969571388350/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:05:18 -0400] "PUT /api/histories/f597429621d6eb2b/contents/datasets/417e33144b294c21 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:05:19 -0400] "PUT /api/histories/f597429621d6eb2b/contents/datasets/2d9035b3fc152403 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:05:22 -0400] "PUT /api/histories/f597429621d6eb2b/contents/datasets/5a1cff6882ddb5b2 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:05:23 -0400] "PUT /api/histories/f597429621d6eb2b/contents/datasets/d413a19dec13d11e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:05:24 -0400] "PUT /api/histories/f597429621d6eb2b/contents/datasets/2f94e8ae9edff68a HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:05:25 -0400] "PUT /api/histories/f597429621d6eb2b/contents/datasets/8237ee2988567c1c HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:05:27 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/f09437b8822035f7 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:05:29 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/fb85969571388350 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:05:31 -0400] "GET /datasets/fb85969571388350/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:05:31 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/fb85969571388350/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:05:33 -0400] "GET /datasets/fb85969571388350/stderr HTTP/1.1" 200 - "http://localhost:8080/datasets/fb85969571388350/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:10:24 -0400] "GET /admin HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=fjqpexikggr" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:10:24 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:10:24 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:10:24 -0400] "GET /admin/center?message=&status=done HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:10:24 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin/center?message=&status=done" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:10:28 -0400] "GET /admin_toolshed/browse_repositories HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:10:28 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:10:35 -0400] "GET /admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=manage_repository&id=f2db41e1fa331b3e HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:10:35 -0400] "GET /admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:10:35 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:10:38 -0400] "GET /admin_toolshed/browse_tool_dependency?id=f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:10:38 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_dependency?id=f2db41e1fa331b3e" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" tool_shed.util.shed_util_common WARNING 2017-11-18 18:10:38,775 Request tries to access a folder outside of the allowed locations. Folder path: ./database/dependencies/bwa/0.5.9/devteam/package_bwa_0_5_9/ec2595e4d313 127.0.0.1 - - [18/Nov/2017:18:10:38 -0400] "GET /admin_toolshed/open_folder?folder_path=.%2Fdatabase%2Fdependencies%2Fbwa%2F0.5.9%2Fdevteam%2Fpackage_bwa_0_5_9%2Fec2595e4d313&repository_id=f2db41e1fa331b3e&_=1511046638667 HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_tool_dependency?id=f2db41e1fa331b3e" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:10:45 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.queue_worker DEBUG 2017-11-18 18:11:11,365 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 18:11:11,379 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 18:11:11,387 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 18:11:11,389 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 18:11:11,393 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 18:11:11,398 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,400 Reading tools from config files finshed (21.129 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,400 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,404 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,404 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,405 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,405 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,405 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,407 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,407 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,407 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,408 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,409 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,409 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,409 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,409 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,410 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,412 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,412 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,412 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,412 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,413 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,415 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,415 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:11,416 Loading tool panel finished (16.297 ms) galaxy.tools.deps DEBUG 2017-11-18 18:11:11,419 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:11,447 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 18:11:11,450 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 18:11:11,453 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 18:11:11,453 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 18:11:11,459 Toolbox reload (94.216 ms) galaxy.queue_worker INFO 2017-11-18 18:11:12,382 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 18:11:12,382 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 18:11:12,436 Toolbox index finished (53.627 ms) 127.0.0.1 - - [18/Nov/2017:18:11:32 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:11:32 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:11:32 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:11:32 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:11:32 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:11:32 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:11:32 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:11:32 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:11:32 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:11:32 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:11:33 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:11:35 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ^Cgalaxy.jobs.handler INFO 2017-11-18 18:11:43,837 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 18:11:43,837 job handler queue stopped galaxy.jobs.runners INFO 2017-11-18 18:11:43,837 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2017-11-18 18:11:43,838 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 18:11:43,838 job handler stop queue stopped CFM5081985:galaxy charles.strittmatter$ sh run.sh Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv galaxy.tools.deps DEBUG 2017-11-18 18:11:49,957 Unable to find config file './dependency_resolvers_conf.xml' DEBUG:galaxy.app:python path is: /galaxydir/galaxy/scripts, /galaxydir/galaxy/lib, /galaxydir/galaxy/.venv/lib/python27.zip, /galaxydir/galaxy/.venv/lib/python2.7, /galaxydir/galaxy/.venv/lib/python2.7/plat-darwin, /galaxydir/galaxy/.venv/lib/python2.7/plat-mac, /galaxydir/galaxy/.venv/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/Extras/lib/python, /galaxydir/galaxy/.venv/lib/python2.7/lib-tk, /galaxydir/galaxy/.venv/lib/python2.7/lib-old, /galaxydir/galaxy/.venv/lib/python2.7/lib-dynload, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/lib/python2.7/site-packages DEBUG:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config INFO:galaxy.config:Logging at '10' level to 'stdout' galaxy.queue_worker INFO 2017-11-18 18:11:52,284 Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE tool_shed.tool_shed_registry DEBUG 2017-11-18 18:11:52,365 Loading references to tool sheds from ./config/tool_sheds_conf.xml.sample tool_shed.tool_shed_registry DEBUG 2017-11-18 18:11:52,365 Loaded reference to tool shed: Galaxy Main Tool Shed galaxy.app DEBUG 2017-11-18 18:11:52,370 Using "galaxy.ini" config file: /galaxydir/galaxy/config/galaxy.ini migrate.versioning.repository DEBUG 2017-11-18 18:11:52,543 Loading repository lib/galaxy/model/migrate... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,545 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,546 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,546 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,546 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,546 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,546 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,547 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,547 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,547 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,547 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,547 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,547 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,547 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,547 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,548 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,548 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,548 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,548 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,548 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,548 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,548 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,549 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,549 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,549 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,549 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,549 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,549 Loading script lib/galaxy/model/migrate/versions/0014_pages.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,549 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,550 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,550 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully 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lib/galaxy/model/migrate/versions/0019_request_library_folder.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,551 Script lib/galaxy/model/migrate/versions/0019_request_library_folder.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,551 Loading script lib/galaxy/model/migrate/versions/0020_library_upload_job.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,551 Script lib/galaxy/model/migrate/versions/0020_library_upload_job.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,551 Loading script lib/galaxy/model/migrate/versions/0021_user_prefs.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,551 Script lib/galaxy/model/migrate/versions/0021_user_prefs.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,551 Loading script lib/galaxy/model/migrate/versions/0022_visualization_tables.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,551 Script lib/galaxy/model/migrate/versions/0022_visualization_tables.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,552 Loading script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,552 Script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,552 Loading script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,552 Script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,552 Loading script lib/galaxy/model/migrate/versions/0025_user_info.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,552 Script lib/galaxy/model/migrate/versions/0025_user_info.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,552 Loading script lib/galaxy/model/migrate/versions/0026_cloud_tables.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,552 Script lib/galaxy/model/migrate/versions/0026_cloud_tables.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,553 Loading script lib/galaxy/model/migrate/versions/0027_request_events.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,553 Script lib/galaxy/model/migrate/versions/0027_request_events.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,553 Loading script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,553 Script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,553 Loading script lib/galaxy/model/migrate/versions/0029_user_actions.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,553 Script lib/galaxy/model/migrate/versions/0029_user_actions.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,553 Loading script lib/galaxy/model/migrate/versions/0030_history_slug_column.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,553 Script lib/galaxy/model/migrate/versions/0030_history_slug_column.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,554 Loading script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,554 Script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,554 Loading script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py... migrate.versioning.script.base DEBUG 2017-11-18 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migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,579 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,579 Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,580 Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,580 Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,580 Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,580 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,580 Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,580 Loading script lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,580 Script lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,580 Loading script lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,580 Script lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,580 Loading script lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,580 Script lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,581 Loading script lib/galaxy/model/migrate/versions/0135_add_library_tags.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,581 Script lib/galaxy/model/migrate/versions/0135_add_library_tags.py loaded successfully migrate.versioning.repository DEBUG 2017-11-18 18:11:52,581 Repository lib/galaxy/model/migrate loaded successfully migrate.versioning.repository DEBUG 2017-11-18 18:11:52,581 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) galaxy.model.migrate.check INFO 2017-11-18 18:11:52,688 At database version 135 migrate.versioning.repository DEBUG 2017-11-18 18:11:52,691 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,693 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,693 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,693 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,694 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,694 Loading script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,694 Script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,694 Loading script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,694 Script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,694 Loading script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,695 Script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,695 Loading script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,695 Script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,695 Loading script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,695 Script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,695 Loading script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,696 Script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,696 Loading script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,696 Script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,696 Loading script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,696 Script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,696 Loading script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,696 Script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,697 Loading script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:11:52,697 Script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py loaded successfully migrate.versioning.repository DEBUG 2017-11-18 18:11:52,697 Repository lib/tool_shed/galaxy_install/migrate loaded successfully migrate.versioning.repository DEBUG 2017-11-18 18:11:52,697 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))]) tool_shed.galaxy_install.migrate.check INFO 2017-11-18 18:11:52,718 At migrate_tools version 12 galaxy.config INFO 2017-11-18 18:11:52,742 Install database targetting Galaxy's database configuration. /galaxydir/galaxy/lib/galaxy/datatypes/registry.py:98: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if root_dir and config: galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,835 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,836 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,836 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/binary: No module named binary galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,836 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,836 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,837 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,837 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,845 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,847 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,848 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,848 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,848 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,848 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,848 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,848 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,848 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,866 Loading datatypes from ./config/datatypes_conf.xml.sample galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,868 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,869 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,870 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,870 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,870 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,871 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,871 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,871 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,871 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,871 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,871 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,872 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,872 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,872 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,873 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,873 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,873 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,873 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,874 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,874 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,874 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,874 Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,874 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,875 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,879 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,879 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,879 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,879 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,880 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,880 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,880 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,880 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,881 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,881 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,881 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,881 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,881 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,882 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,882 Retrieved datatype module galaxy.datatypes.sequence:FastqGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,882 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,882 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,882 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,883 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,883 Retrieved datatype module galaxy.datatypes.sequence:FastqBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,883 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,883 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,883 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,883 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,883 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,884 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,884 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,884 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,884 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,884 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,884 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,884 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,885 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,885 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,885 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,885 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,885 Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,886 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,886 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,886 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,886 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,886 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,887 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,887 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,887 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,888 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,888 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,888 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,888 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,889 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,889 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,889 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,889 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,890 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,890 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,890 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,890 Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,890 Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,891 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,891 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,891 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,891 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,891 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,892 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,892 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,892 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,892 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,893 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,893 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,893 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,893 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,894 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,895 Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,895 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,900 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,901 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,901 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,901 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,902 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,902 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,902 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,902 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,902 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,903 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,903 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,903 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,903 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,903 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,903 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,904 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,904 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,904 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,904 Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,904 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,905 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,905 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,905 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,905 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,905 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,905 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,905 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,905 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,905 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,905 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,906 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,906 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,906 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,906 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,906 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,906 Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,906 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,906 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,907 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,907 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,907 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,907 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,907 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,908 Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,908 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,908 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,908 Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,908 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,908 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,909 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,909 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,909 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,909 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,910 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,910 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,910 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,910 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,910 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,911 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,911 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,911 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,911 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,911 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,912 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,912 Roadmaps is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,912 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,912 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,912 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,912 Sequences is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,912 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,913 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,913 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,913 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,913 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,913 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,913 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,914 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,914 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,914 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,915 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,915 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,915 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,916 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,916 Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,916 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,916 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,916 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,916 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,917 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,917 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,917 Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,917 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,917 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,918 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,918 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,918 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,919 Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,919 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,919 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,919 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,922 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,922 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,923 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,923 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,923 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,923 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,923 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,924 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,924 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,924 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,924 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,924 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,925 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,925 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,925 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,925 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,925 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,925 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,926 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,926 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,932 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,933 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,934 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,934 Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,934 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,934 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,934 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,935 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,935 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,935 Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,935 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,935 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,935 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,936 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,936 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,936 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:52,936 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,029 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,029 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,031 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,031 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,031 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,031 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,032 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,032 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,032 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,032 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,032 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,033 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,033 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,033 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,034 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,034 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,034 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,034 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,034 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,035 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,035 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,035 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,035 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,037 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,037 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,037 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,037 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,039 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,039 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,039 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,039 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,040 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,040 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,040 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,041 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,041 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,041 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,041 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,042 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,042 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,042 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,043 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,043 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,043 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,044 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,045 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,045 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,045 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,046 Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,046 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,046 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,046 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,047 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,047 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,047 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,047 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,050 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,050 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,050 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,050 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,052 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,052 Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,052 Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,054 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,054 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,054 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,054 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,054 Retrieved datatype module galaxy.datatypes.binary:Cel from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,055 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,055 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,055 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,055 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,055 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,055 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,055 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,057 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,057 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,057 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,057 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,058 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,058 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,058 Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,058 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,060 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,060 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,061 Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,061 Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,061 Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,061 Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,061 Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,062 Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,062 Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,062 Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,062 Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,062 Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,063 Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,063 Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,066 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,066 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,066 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,067 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,067 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,067 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,067 Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,068 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,068 Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,068 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,068 Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,069 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,069 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,069 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,069 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,070 Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,070 Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,070 Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,070 Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,070 Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,070 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,071 Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,071 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,071 Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,072 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,072 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,073 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,075 Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,075 Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,075 Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,075 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,076 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,076 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,077 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,077 Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,077 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,078 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,080 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,081 Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,083 Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,084 Overriding conflicting datatype with extension 'blastxml', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,084 Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,084 Overriding conflicting datatype with extension 'blastdbn', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,084 Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,084 Overriding conflicting datatype with extension 'blastdbp', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,085 Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,085 Overriding conflicting datatype with extension 'blastdbd', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,085 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,085 Overriding conflicting datatype with extension 'maskinfo-asn1', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,085 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,086 Overriding conflicting datatype with extension 'maskinfo-asn1-binary', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,086 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,086 Overriding conflicting datatype with extension 'pssm-asn1', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,088 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,088 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,088 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,088 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,088 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,089 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,089 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,089 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrtho from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,089 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,089 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylip from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,089 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,090 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,090 Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,090 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,090 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,090 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,091 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,091 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,091 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,091 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,091 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,091 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,091 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,092 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,092 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,092 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,092 Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,092 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,092 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,092 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,093 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,093 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,093 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,093 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,093 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,093 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,093 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,094 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,094 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,094 Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,094 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,094 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,094 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,095 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,095 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,095 Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,095 Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,095 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,095 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,096 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,096 Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,096 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,096 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,096 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,096 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,097 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,097 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,097 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,097 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,097 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,097 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,097 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,098 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,098 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,098 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,098 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,098 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,098 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,098 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,099 Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,099 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,099 Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,099 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,099 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,099 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,099 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,099 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,100 Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,100 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,100 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,100 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,100 Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,100 Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,100 Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,101 Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,101 Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,101 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,101 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,101 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerGz' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,101 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerBz2' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,101 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,102 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqGz' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,102 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqBz2' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,102 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,102 Loaded sniffer for datatype 'galaxy.datatypes.text:Html' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,102 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,102 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,102 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,103 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,103 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,103 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,104 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,104 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,104 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,104 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,104 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,104 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,105 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,106 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,106 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,106 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,106 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,106 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,107 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,107 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,107 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,107 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,107 Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,107 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,108 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,108 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,108 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,108 Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,108 Loaded sniffer for datatype 'galaxy.datatypes.binary:Cel' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,108 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,109 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,109 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,109 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,109 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,109 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,110 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,110 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,110 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,110 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,110 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,111 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,111 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,112 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,112 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,113 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,113 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,114 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,115 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,116 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,116 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,116 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,116 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,117 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,123 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,123 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,123 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,123 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,123 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,124 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,124 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,124 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:53,124 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.tools.data INFO 2017-11-18 18:11:53,953 Could not find tool data tool-data/all_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:11:53,955 Loaded 0 lines from 'tool-data/all_fasta.loc.sample' for 'all_fasta' galaxy.tools.data DEBUG 2017-11-18 18:11:53,955 Loaded tool data table 'all_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:11:53,956 Could not find tool data tool-data/bfast_indexes.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:11:53,957 Loaded 0 lines from 'tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' galaxy.tools.data DEBUG 2017-11-18 18:11:53,957 Loaded tool data table 'bfast_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 18:11:53,959 Loaded 0 lines from 'tool-data/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 18:11:53,960 Loaded tool data table 'blastdb' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 18:11:53,961 Loaded 0 lines from 'tool-data/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 18:11:53,962 Loaded tool data table 'blastdb_p' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 18:11:53,963 Loaded 0 lines from 'tool-data/blastdb_d.loc' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 18:11:53,964 Loaded tool data table 'blastdb_d' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 18:11:53,965 Loaded 0 lines from 'tool-data/bwa_index.loc' for 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 18:11:53,966 Loaded tool data table 'bwa_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 18:11:53,967 Loaded 0 lines from 'tool-data/bwa_index_color.loc' for 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 18:11:53,968 Loaded tool data table 'bwa_indexes_color' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:11:53,968 Could not find tool data tool-data/maf_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:11:53,970 Loaded 0 lines from 'tool-data/maf_index.loc.sample' for 'indexed_maf_files' galaxy.tools.data DEBUG 2017-11-18 18:11:53,970 Loaded tool data table 'indexed_maf_files' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:11:53,971 Could not find tool data tool-data/ngs_sim_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:11:53,972 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' galaxy.tools.data DEBUG 2017-11-18 18:11:53,973 Loaded tool data table 'ngs_sim_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:11:53,973 Could not find tool data tool-data/perm_base_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:11:53,975 Loaded 0 lines from 'tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' galaxy.tools.data DEBUG 2017-11-18 18:11:53,975 Loaded tool data table 'perm_base_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:11:53,975 Could not find tool data tool-data/perm_color_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:11:53,977 Loaded 0 lines from 'tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' galaxy.tools.data DEBUG 2017-11-18 18:11:53,977 Loaded tool data table 'perm_color_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:11:53,977 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:11:53,979 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'picard_indexes' galaxy.tools.data DEBUG 2017-11-18 18:11:53,979 Loaded tool data table 'picard_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:11:53,979 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:11:53,980 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'srma_indexes' galaxy.tools.data DEBUG 2017-11-18 18:11:53,980 Loaded tool data table 'srma_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:11:53,980 Could not find tool data tool-data/mosaik_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:11:53,982 Loaded 0 lines from 'tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' galaxy.tools.data DEBUG 2017-11-18 18:11:53,982 Loaded tool data table 'mosaik_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:11:53,983 Could not find tool data tool-data/twobit.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:11:53,984 Loaded 0 lines from 'tool-data/twobit.loc.sample' for 'twobit' galaxy.tools.data DEBUG 2017-11-18 18:11:53,984 Loaded tool data table 'twobit' from file './config/tool_data_table_conf.xml.sample' requests.packages.urllib3.connectionpool INFO 2017-11-18 18:11:53,999 Starting new HTTP connection (1): igv.broadinstitute.org requests.packages.urllib3.connectionpool DEBUG 2017-11-18 18:11:54,053 "GET /genomes/genomes.txt HTTP/1.1" 200 15681 galaxy.tools.data DEBUG 2017-11-18 18:11:54,066 Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-sX9gmc". galaxy.tools.data WARNING 2017-11-18 18:11:54,067 Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields): <Server-Side Genome List> galaxy.tools.data DEBUG 2017-11-18 18:11:54,071 Loaded 156 lines from '/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-sX9gmc' for 'igv_broad_genomes' galaxy.tools.data DEBUG 2017-11-18 18:11:54,073 Loaded tool data table 'igv_broad_genomes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:11:54,074 Could not find tool data tool-data/liftOver.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:11:54,075 Loaded 0 lines from 'tool-data/liftOver.loc.sample' for 'liftOver' galaxy.tools.data DEBUG 2017-11-18 18:11:54,076 Loaded tool data table 'liftOver' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:11:54,076 Could not find tool data tool-data/bam_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:11:54,078 Loaded 1 lines from 'tool-data/bam_iobio.loc.sample' for 'bam_iobio' galaxy.tools.data DEBUG 2017-11-18 18:11:54,078 Loaded tool data table 'bam_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:11:54,079 Could not find tool data tool-data/vcf_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:11:54,081 Loaded 1 lines from 'tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' galaxy.tools.data DEBUG 2017-11-18 18:11:54,081 Loaded tool data table 'vcf_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:11:54,081 Could not find tool data tool-data/biom_simple_display.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:11:54,083 Loaded 1 lines from 'tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' galaxy.tools.data DEBUG 2017-11-18 18:11:54,083 Loaded tool data table 'biom_simple_display' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 18:11:54,089 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 18:11:54,089 Loading another instance of data table 'blastdb' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 18:11:54,091 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 18:11:54,091 Loading another instance of data table 'blastdb_p' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 18:11:54,093 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb_d.loc' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 18:11:54,093 Loading another instance of data table 'blastdb_d' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 18:11:54,095 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/bwa_index.loc' for 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 18:11:54,095 Loading another instance of data table 'bwa_indexes' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 18:11:54,097 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/bwa_index_color.loc' for 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 18:11:54,097 Loading another instance of data table 'bwa_indexes_color' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.jobs WARNING 2017-11-18 18:11:54,204 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/galaxydir/galaxy/config/galaxy.ini" instead galaxy.jobs DEBUG 2017-11-18 18:11:54,204 Loading job configuration from /galaxydir/galaxy/config/galaxy.ini galaxy.jobs DEBUG 2017-11-18 18:11:54,204 Done loading job configuration beaker.container DEBUG 2017-11-18 18:11:54,443 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache galaxy.tools.toolbox.base INFO 2017-11-18 18:11:54,454 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 18:11:55,008 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 18:11:55,186 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 18:11:55,281 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 18:11:55,957 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,958 Reading tools from config files finshed (1504.334 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,958 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,959 Loaded tool id: toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/bwa_color_wrapper/1.0.2, version: 1.0.2 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,959 Loaded tool id: toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/bwa_wrapper/1.2.3, version: 1.2.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,959 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.8.1.2, version: 2.8.1.2 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,959 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,960 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,960 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,960 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,960 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,961 Loaded tool id: biomart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,961 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,961 Loaded tool id: gramenemart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,961 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,962 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,962 Loaded tool id: flymine_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,962 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,962 Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,962 Loaded tool id: flymine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,962 Loaded tool id: modmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,963 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,963 Loaded tool id: mousemine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,963 Loaded tool id: ratmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,963 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,963 Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,964 Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,964 Loaded tool id: hbvar, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,964 Loaded tool id: wormbase, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,964 Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,964 Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,965 Loaded tool id: genomespace_importer, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,965 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,965 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,965 Loaded tool id: genomespace_exporter, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,965 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,965 Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,966 Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,966 Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,966 Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,966 Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,966 Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,967 Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,967 Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,967 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,967 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,967 Loaded tool id: addValue, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,968 Loaded tool id: cat1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,968 Loaded tool id: Cut1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,968 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,968 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,969 Loaded tool id: createInterval, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,969 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,969 Loaded tool id: Paste1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,969 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,969 Loaded tool id: random_lines1, version: 2.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,970 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,970 Loaded tool id: Show tail1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,970 Loaded tool id: trimmer, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,970 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,970 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,971 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,971 Loaded tool id: Filter1, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,971 Loaded tool id: sort1, version: 1.0.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,971 Loaded tool id: Grep1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,971 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,972 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,972 Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,972 Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,972 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,972 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,973 Loaded tool id: join1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,973 Loaded tool id: comp1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,973 Loaded tool id: Grouping1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,973 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,973 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,974 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,974 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,974 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,974 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,974 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,974 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,975 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,975 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,975 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,975 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,975 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,976 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,976 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,976 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,976 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,976 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,977 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,977 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,977 Loaded tool id: Extract genomic DNA 1, version: 2.2.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,977 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,977 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,978 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,978 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,978 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_convert2blastmask_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,979 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,979 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,979 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,979 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,980 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_segmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,980 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,980 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,980 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,981 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,981 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,981 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,981 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,981 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,982 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,982 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,982 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,982 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,982 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,983 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,983 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,983 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,983 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,983 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,983 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,984 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,984 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,984 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,984 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,984 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,985 Loaded tool id: Summary_Statistics1, version: 1.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,985 Loaded tool id: Count1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,985 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,985 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,985 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,986 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:11:55,986 Loading tool panel finished (27.496 ms) galaxy.tools.deps DEBUG 2017-11-18 18:11:55,989 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.search DEBUG 2017-11-18 18:11:56,012 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 18:11:58,048 Toolbox index finished (2035.977 ms) galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,053 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,059 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,103 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,105 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,108 Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,111 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,114 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,117 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,120 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,124 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,126 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,130 Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,172 Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,181 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,216 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,218 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,226 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,237 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,241 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,286 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,290 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,296 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,349 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,351 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,354 Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,356 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,402 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,404 Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,406 Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,411 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,411 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,411 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,412 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,413 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,413 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,413 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,413 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,422 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,422 Adding inherited display application 'igv_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,431 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,431 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,432 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,432 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,434 Adding inherited display application 'igv_fasta' to datatype 'sequences' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,434 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,434 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,434 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,435 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,436 Adding inherited display application 'igv_fasta' to datatype 'mothur.align' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,439 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,440 Adding inherited display application 'igv_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,454 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,454 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,455 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,455 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,456 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,456 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,456 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,456 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,460 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,460 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,460 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,461 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,468 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,471 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,474 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,477 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,480 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,482 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,486 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,489 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,493 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,498 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,499 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,502 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,505 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,508 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,511 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,515 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,519 Loaded converter: CONVERTER_fasta_to_fai galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,525 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,528 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,529 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,530 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,531 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,534 Loaded converter: CONVERTER_fastqgz_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,537 Loaded converter: CONVERTER_fastqsangergz_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,540 Loaded converter: CONVERTER_fastqsolexagz_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,544 Loaded converter: CONVERTER_fastqcssangergz_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,548 Loaded converter: CONVERTER_fastqilluminagz_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,552 Loaded converter: CONVERTER_fastqbz2_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,555 Loaded converter: CONVERTER_fastqsangerbz2_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,558 Loaded converter: CONVERTER_fastqsolexabz2_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,562 Loaded converter: CONVERTER_fastqcssangerbz2_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,565 Loaded converter: CONVERTER_fastqilluminabz2_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,569 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,572 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,573 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,576 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,581 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,583 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,585 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,588 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,592 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,595 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,598 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,600 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,603 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,606 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,609 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,614 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,617 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,619 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,621 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,622 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,624 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,627 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,630 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,633 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,636 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,638 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,641 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,644 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,647 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,650 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,653 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,656 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,659 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,665 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,668 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,671 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,674 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,677 Loaded converter: CONVERTER_biom1_to_biom2 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,682 Loaded converter: CONVERTER_biom2_to_biom1 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,685 Loaded converter: CONVERTER_SMILES_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,687 Loaded converter: CONVERTER_SMILES_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,691 Loaded converter: CONVERTER_SMILES_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,699 Loaded converter: CONVERTER_SMILES_to_MOL galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,701 Loaded converter: CONVERTER_SMILES_to_MOL2 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,705 Loaded converter: CONVERTER_smiles_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,709 Loaded converter: CONVERTER_sdf_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,712 Loaded converter: CONVERTER_sdf_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,715 Loaded converter: CONVERTER_sdf_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,720 Loaded converter: CONVERTER_sdf_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,723 Loaded converter: CONVERTER_inchi_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,726 Loaded converter: CONVERTER_inchi_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,729 Loaded converter: CONVERTER_inchi_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,732 Loaded converter: CONVERTER_inchi_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,735 Loaded converter: CONVERTER_inchi_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,738 Loaded converter: CONVERTER_mol_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,741 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,746 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,750 Loaded converter: CONVERTER_mol_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,753 Loaded converter: CONVERTER_mol2_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,756 Loaded converter: CONVERTER_mol2_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,759 Loaded converter: CONVERTER_mol2_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,762 Loaded converter: CONVERTER_mol2_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,766 Loaded converter: CONVERTER_mol2_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,769 Loaded converter: CONVERTER_cml_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,772 Loaded converter: CONVERTER_cml_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,775 Loaded converter: CONVERTER_cml_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,782 Loaded converter: CONVERTER_cml_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,784 Loaded converter: CONVERTER_ref_to_seq_taxomony galaxy.datatypes.registry DEBUG 2017-11-18 18:11:58,788 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 18:11:58,795 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 18:11:58,797 Loaded history export tool: __EXPORT_HISTORY__ galaxy.web.base.pluginframework INFO 2017-11-18 18:11:58,801 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2017-11-18 18:11:58,803 Visualizations plugin disabled: Circster. Skipping... galaxy.visualization.plugins.config_parser INFO 2017-11-18 18:11:58,806 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 18:11:58,806 VisualizationsRegistry, loaded plugin: csg galaxy.visualization.plugins.config_parser INFO 2017-11-18 18:11:58,811 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 18:11:58,812 VisualizationsRegistry, loaded plugin: graphviz galaxy.web.base.pluginframework INFO 2017-11-18 18:11:58,814 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2017-11-18 18:11:58,816 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2017-11-18 18:11:58,818 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2017-11-18 18:11:58,821 VisualizationsRegistry, loaded plugin: trackster galaxy.visualization.plugins.config_parser INFO 2017-11-18 18:11:58,823 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 18:11:58,823 VisualizationsRegistry, loaded plugin: unipept galaxy.tours INFO 2017-11-18 18:11:58,892 Loaded tour 'core.galaxy_ui' galaxy.tours INFO 2017-11-18 18:11:58,922 Loaded tour 'core.history' galaxy.tours INFO 2017-11-18 18:11:58,941 Loaded tour 'core.scratchbook' galaxy.webhooks WARNING 2017-11-18 18:11:58,941 directory not found: /galaxydir/galaxy/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config galaxy.jobs.manager DEBUG 2017-11-18 18:11:58,957 Starting job handler galaxy.jobs INFO 2017-11-18 18:11:58,957 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2017-11-18 18:11:58,964 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2017-11-18 18:11:58,964 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2017-11-18 18:11:58,966 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs DEBUG 2017-11-18 18:11:58,966 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2017-11-18 18:11:58,966 Loaded job runners plugins: local galaxy.jobs.handler INFO 2017-11-18 18:11:58,967 job handler stop queue started galaxy.jobs.handler INFO 2017-11-18 18:11:59,135 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 18:11:59,142 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 18:11:59,145 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.workflow.scheduling_manager DEBUG 2017-11-18 18:11:59,159 Starting workflow schedulers galaxy.app INFO 2017-11-18 18:11:59,161 Galaxy app startup finished (6992.119 ms) galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,179 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,618 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,619 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,621 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,623 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,626 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,630 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,632 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,636 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,638 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,642 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,646 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,648 Enabling 'interactive_environments' controller, class: InteractiveEnvironmentsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,662 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,664 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,664 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,668 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,671 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,673 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,676 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,676 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,679 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,682 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,685 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,687 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,689 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,692 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,698 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,705 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,705 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,705 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,707 Enabling 'authenticate' API controller, class: AuthenticationController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,709 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,711 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,714 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,716 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,718 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,718 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,723 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,726 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,728 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,730 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,733 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,735 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,737 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,741 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,744 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,746 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,747 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,747 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,751 Enabling 'job_files' API controller, class: JobFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,753 Enabling 'jobs' API controller, class: JobController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,755 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,757 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,764 Enabling 'library_datasets' API controller, class: LibraryDatasetsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,769 Enabling 'metrics' API controller, class: MetricsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,770 Enabling 'page_revisions' API controller, class: PageRevisionsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,773 Enabling 'pages' API controller, class: PagesController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,775 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,775 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,777 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,785 Enabling 'remote_files' API controller, class: RemoteFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,790 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,792 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,796 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,798 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,842 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,844 Enabling 'tool_data' API controller, class: ToolData galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,847 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,850 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,852 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,855 Enabling 'toolshed' API controller, class: ToolShedController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,857 Enabling 'tours' API controller, class: ToursController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,860 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,863 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,868 Enabling 'webhooks' API controller, class: WebhooksController galaxy.web.framework.base DEBUG 2017-11-18 18:11:59,870 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.webapps.util DEBUG 2017-11-18 18:12:00,233 Enabling 'paste.httpexceptions' middleware galaxy.webapps.util DEBUG 2017-11-18 18:12:00,236 Enabling 'RecursiveMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 18:12:00,258 Enabling 'ErrorMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 18:12:00,260 Enabling 'TransLogger' middleware galaxy.webapps.util DEBUG 2017-11-18 18:12:00,263 Enabling 'XForwardedHostMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 18:12:00,265 Enabling 'RequestIDMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 18:12:00,268 Enabling 'BatchMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 18:12:00,268 Enabling 'wrap_in_static' middleware galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,287 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,288 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,288 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,288 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,289 added url, path to static middleware: /plugins/visualizations/unipept/static, ./config/plugins/visualizations/unipept/static galaxy.queue_worker INFO 2017-11-18 18:12:00,289 Binding and starting galaxy control worker for main galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,289 Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 140735112855552)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,299 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145307660288)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,303 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-3, started daemon 123145328693248)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,303 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-1, started daemon 123145320280064)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,304 Prior to webapp return, Galaxy thread <Thread(JobHandlerQueue.monitor_thread, started daemon 123145341313024)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,304 Prior to webapp return, Galaxy thread <Thread(WorkflowRequestMonitor.monitor_thread, started daemon 123145345519616)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,304 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-4, started daemon 123145332899840)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,305 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145311866880)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,305 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-2, started daemon 123145324486656)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,305 Prior to webapp return, Galaxy thread <Thread(JobHandlerStopQueue.monitor_thread, started daemon 123145337106432)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,306 Prior to webapp return, Galaxy thread <GalaxyQueueWorker(Thread-1, started daemon 123145349726208)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:12:00,306 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-0, started daemon 123145316073472)> is alive. Starting server in PID 75712. serving on http://127.0.0.1:8080 /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. 'storage.' % (dialect.name, dialect.driver)) /galaxydir/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. 'strategies for improved performance.' % expr) 127.0.0.1 - - [18/Nov/2017:18:12:09 -0400] "GET / HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:10 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:10 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:10 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:10 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:10 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:10 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:10 -0400] "GET /welcome HTTP/1.1" 302 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:10 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:10 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:11 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:13 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:14 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=tmovt9ybcce&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:14 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:14 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:16 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 18:12:17,559 Validated and populated state for tool request (38.719 ms) galaxy.tools.actions INFO 2017-11-18 18:12:17,647 Handled output named html_file for tool seq_sero_reads_multiple (42.407 ms) galaxy.tools.actions INFO 2017-11-18 18:12:17,686 Handled output named text_file for tool seq_sero_reads_multiple (38.201 ms) galaxy.tools.actions INFO 2017-11-18 18:12:17,708 Added output datasets to history (22.046 ms) galaxy.tools.actions INFO 2017-11-18 18:12:17,774 Verified access to datasets for Job[unflushed,tool_id=seq_sero_reads_multiple] (24.081 ms) galaxy.tools.actions INFO 2017-11-18 18:12:17,775 Setup for job Job[unflushed,tool_id=seq_sero_reads_multiple] complete, ready to flush (67.151 ms) galaxy.tools.actions INFO 2017-11-18 18:12:17,836 Flushed transaction for job Job[id=14,tool_id=seq_sero_reads_multiple] (60.409 ms) galaxy.tools.execute DEBUG 2017-11-18 18:12:17,836 Tool [seq_sero_reads_multiple] created job [14] (255.486 ms) galaxy.tools.execute DEBUG 2017-11-18 18:12:17,859 Executed 1 job(s) for tool seq_sero_reads_multiple request: (298.996 ms) 127.0.0.1 - - [18/Nov/2017:18:12:17 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:17 -0400] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:17 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T23%3A12%3A10.576Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 18:12:18,843 (14) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/14 galaxy.jobs.handler DEBUG 2017-11-18 18:12:18,859 (14) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 18:12:18,911 (14) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 18:12:18,925 Job [14] queued (65.928 ms) galaxy.jobs.handler INFO 2017-11-18 18:12:18,940 (14) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 18:12:19,274 Built script [/galaxydir/galaxy/database/jobs_directory/000/14/tool_script.sh] for tool command [/galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/files/000/dataset_2.dat /galaxydir/galaxy/tools/GalaxySeqsero/] galaxy.tools.deps DEBUG 2017-11-18 18:12:19,810 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 18:12:19,810 Using dependency bcftools version 1.5 of type conda galaxy.jobs.runners DEBUG 2017-11-18 18:12:19,819 (14) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/14/tool_script.sh; return_code=$?; if [ -f /galaxydir/galaxy/database/jobs_directory/000/14/working/Seqsero_result.html ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/14/working/Seqsero_result.html /galaxydir/galaxy/database/files/000/dataset_25.dat ; fi; if [ -f /galaxydir/galaxy/database/jobs_directory/000/14/working/Seqsero_result.txt ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/14/working/Seqsero_result.txt /galaxydir/galaxy/database/files/000/dataset_26.dat ; fi; cd '/galaxydir/galaxy/database/jobs_directory/000/14'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; python "/galaxydir/galaxy/database/jobs_directory/000/14/set_metadata_gNrMMQ.py" "/galaxydir/galaxy/database/jobs_directory/000/14/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/14/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/14/metadata_in_HistoryDatasetAssociation_25_83pi7n,/galaxydir/galaxy/database/jobs_directory/000/14/metadata_kwds_HistoryDatasetAssociation_25_e4rhyP,/galaxydir/galaxy/database/jobs_directory/000/14/metadata_out_HistoryDatasetAssociation_25_kaA8Om,/galaxydir/galaxy/database/jobs_directory/000/14/metadata_results_HistoryDatasetAssociation_25_MW4yQ4,/galaxydir/galaxy/database/files/000/dataset_25.dat,/galaxydir/galaxy/database/jobs_directory/000/14/metadata_override_HistoryDatasetAssociation_25_9b4njJ" "/galaxydir/galaxy/database/jobs_directory/000/14/metadata_in_HistoryDatasetAssociation_26_9n5QNP,/galaxydir/galaxy/database/jobs_directory/000/14/metadata_kwds_HistoryDatasetAssociation_26_kcBTSV,/galaxydir/galaxy/database/jobs_directory/000/14/metadata_out_HistoryDatasetAssociation_26_FsBLnz,/galaxydir/galaxy/database/jobs_directory/000/14/metadata_results_HistoryDatasetAssociation_26_WeEHIH,/galaxydir/galaxy/database/files/000/dataset_26.dat,/galaxydir/galaxy/database/jobs_directory/000/14/metadata_override_HistoryDatasetAssociation_26_t15v1D" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 18:12:19,834 (14) executing job script: /galaxydir/galaxy/database/jobs_directory/000/14/galaxy_14.sh galaxy.jobs DEBUG 2017-11-18 18:12:19,843 (14) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:18:12:20 -0400] "GET /?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:21 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:21 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:21 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:21 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:21 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:21 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:21 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:21 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=tmovt9ybcce&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:21 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:21 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:21 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:24 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 18:12:25,461 execution finished: /galaxydir/galaxy/database/jobs_directory/000/14/galaxy_14.sh galaxy.jobs.output_checker INFO 2017-11-18 18:12:25,472 Job 14: Warning: Exit code 0 () galaxy.model.metadata DEBUG 2017-11-18 18:12:25,623 loading metadata from file for: HistoryDatasetAssociation 25 galaxy.model.metadata DEBUG 2017-11-18 18:12:25,750 loading metadata from file for: HistoryDatasetAssociation 26 galaxy.jobs INFO 2017-11-18 18:12:25,943 Collecting metrics for Job 14 galaxy.jobs DEBUG 2017-11-18 18:12:25,962 job 14 ended (finish() executed in (501.243 ms)) galaxy.model.metadata DEBUG 2017-11-18 18:12:25,971 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:18:12:26 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T23%3A12%3A21.656Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:26 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:26 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:26 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:12:26 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=tmovt9ybcce" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.queue_worker DEBUG 2017-11-18 18:18:08,661 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 18:18:08,694 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 18:18:08,702 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 18:18:08,704 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 18:18:08,708 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 18:18:08,713 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,713 Reading tools from config files finshed (19.681 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,714 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,716 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,716 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,717 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,717 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,717 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,719 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,720 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,720 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,720 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,722 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,722 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,722 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,722 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,722 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,724 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,724 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,724 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,724 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,725 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,726 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,726 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:18:08,726 Loading tool panel finished (12.823 ms) galaxy.tools.deps DEBUG 2017-11-18 18:18:08,729 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,755 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,755 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,755 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,756 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,756 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,756 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,756 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,756 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,757 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,757 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,757 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,757 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,757 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,757 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,758 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,758 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,758 Loaded converter: CONVERTER_fasta_to_fai galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,758 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,758 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,758 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,759 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,759 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,759 Loaded converter: CONVERTER_fastqgz_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,759 Loaded converter: CONVERTER_fastqsangergz_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,759 Loaded converter: CONVERTER_fastqsolexagz_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,759 Loaded converter: CONVERTER_fastqcssangergz_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,760 Loaded converter: CONVERTER_fastqilluminagz_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,760 Loaded converter: CONVERTER_fastqbz2_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,760 Loaded converter: CONVERTER_fastqsangerbz2_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,760 Loaded converter: CONVERTER_fastqsolexabz2_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,760 Loaded converter: CONVERTER_fastqcssangerbz2_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,760 Loaded converter: CONVERTER_fastqilluminabz2_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,761 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,761 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,761 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,761 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,761 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,762 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,762 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,762 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,763 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,763 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,763 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,763 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,763 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,764 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,764 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,764 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,764 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,764 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,764 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,764 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,765 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,765 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,765 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,765 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,765 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,765 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,765 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,766 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,766 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,766 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,766 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,766 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,766 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,766 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,766 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,767 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,767 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,767 Loaded converter: CONVERTER_biom1_to_biom2 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,767 Loaded converter: CONVERTER_biom2_to_biom1 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,767 Loaded converter: CONVERTER_SMILES_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,767 Loaded converter: CONVERTER_SMILES_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,767 Loaded converter: CONVERTER_SMILES_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,767 Loaded converter: CONVERTER_SMILES_to_MOL galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,768 Loaded converter: CONVERTER_SMILES_to_MOL2 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,768 Loaded converter: CONVERTER_smiles_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,768 Loaded converter: CONVERTER_sdf_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,768 Loaded converter: CONVERTER_sdf_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,768 Loaded converter: CONVERTER_sdf_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,768 Loaded converter: CONVERTER_sdf_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,768 Loaded converter: CONVERTER_inchi_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,768 Loaded converter: CONVERTER_inchi_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,769 Loaded converter: CONVERTER_inchi_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,769 Loaded converter: CONVERTER_inchi_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,769 Loaded converter: CONVERTER_inchi_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,769 Loaded converter: CONVERTER_mol_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,769 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,769 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,769 Loaded converter: CONVERTER_mol_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,769 Loaded converter: CONVERTER_mol2_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,770 Loaded converter: CONVERTER_mol2_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,770 Loaded converter: CONVERTER_mol2_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,770 Loaded converter: CONVERTER_mol2_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,770 Loaded converter: CONVERTER_mol2_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,770 Loaded converter: CONVERTER_cml_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,770 Loaded converter: CONVERTER_cml_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,770 Loaded converter: CONVERTER_cml_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,770 Loaded converter: CONVERTER_cml_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,771 Loaded converter: CONVERTER_ref_to_seq_taxomony galaxy.datatypes.registry DEBUG 2017-11-18 18:18:08,772 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 18:18:08,774 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 18:18:08,775 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 18:18:08,775 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 18:18:08,805 Toolbox reload (144.118 ms) galaxy.queue_worker INFO 2017-11-18 18:18:09,273 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 18:18:09,273 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 18:18:09,859 Toolbox index finished (586.041 ms) 127.0.0.1 - - [18/Nov/2017:18:18:15 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=2tcrov3uerh&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:16 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:16 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:18 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 18:18:18,867 Validated and populated state for tool request (39.654 ms) galaxy.tools.actions INFO 2017-11-18 18:18:18,943 Handled output named html_file for tool seq_sero_reads_multiple (29.845 ms) galaxy.tools.actions INFO 2017-11-18 18:18:18,982 Handled output named text_file for tool seq_sero_reads_multiple (39.299 ms) galaxy.tools.actions INFO 2017-11-18 18:18:19,002 Added output datasets to history (19.587 ms) galaxy.tools.actions INFO 2017-11-18 18:18:19,063 Verified access to datasets for Job[unflushed,tool_id=seq_sero_reads_multiple] (26.362 ms) galaxy.tools.actions INFO 2017-11-18 18:18:19,064 Setup for job Job[unflushed,tool_id=seq_sero_reads_multiple] complete, ready to flush (62.157 ms) galaxy.tools.actions INFO 2017-11-18 18:18:19,094 Flushed transaction for job Job[id=15,tool_id=seq_sero_reads_multiple] (29.531 ms) galaxy.tools.execute DEBUG 2017-11-18 18:18:19,094 Tool [seq_sero_reads_multiple] created job [15] (206.292 ms) galaxy.tools.execute DEBUG 2017-11-18 18:18:19,111 Executed 1 job(s) for tool seq_sero_reads_multiple request: (243.168 ms) 127.0.0.1 - - [18/Nov/2017:18:18:18 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:19 -0400] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:19 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T23%3A12%3A26.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 18:18:19,643 (15) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/15 galaxy.jobs.handler DEBUG 2017-11-18 18:18:19,655 (15) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 18:18:19,701 (15) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 18:18:19,716 Job [15] queued (60.511 ms) galaxy.jobs.handler INFO 2017-11-18 18:18:19,736 (15) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 18:18:20,021 Built script [/galaxydir/galaxy/database/jobs_directory/000/15/tool_script.sh] for tool command [/galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/files/000/dataset_2.dat /galaxydir/galaxy/tools/GalaxySeqsero/] galaxy.tools.deps DEBUG 2017-11-18 18:18:20,308 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 18:18:20,309 Using dependency bcftools version 1.5 of type conda galaxy.jobs.runners DEBUG 2017-11-18 18:18:20,317 (15) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/15/tool_script.sh; return_code=$?; if [ -f /galaxydir/galaxy/database/jobs_directory/000/15/working/Seqsero_result.html ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/15/working/Seqsero_result.html /galaxydir/galaxy/database/files/000/dataset_27.dat ; fi; if [ -f /galaxydir/galaxy/database/jobs_directory/000/15/working/Seqsero_result.txt ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/15/working/Seqsero_result.txt /galaxydir/galaxy/database/files/000/dataset_28.dat ; fi; cd '/galaxydir/galaxy/database/jobs_directory/000/15'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; python "/galaxydir/galaxy/database/jobs_directory/000/15/set_metadata_YeR3Zz.py" "/galaxydir/galaxy/database/jobs_directory/000/15/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/15/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/15/metadata_in_HistoryDatasetAssociation_27_lRrs2R,/galaxydir/galaxy/database/jobs_directory/000/15/metadata_kwds_HistoryDatasetAssociation_27_zthKji,/galaxydir/galaxy/database/jobs_directory/000/15/metadata_out_HistoryDatasetAssociation_27_TLFHeo,/galaxydir/galaxy/database/jobs_directory/000/15/metadata_results_HistoryDatasetAssociation_27_DuKOuc,/galaxydir/galaxy/database/files/000/dataset_27.dat,/galaxydir/galaxy/database/jobs_directory/000/15/metadata_override_HistoryDatasetAssociation_27_IVgdt9" "/galaxydir/galaxy/database/jobs_directory/000/15/metadata_in_HistoryDatasetAssociation_28_SSCYpV,/galaxydir/galaxy/database/jobs_directory/000/15/metadata_kwds_HistoryDatasetAssociation_28_Nym16t,/galaxydir/galaxy/database/jobs_directory/000/15/metadata_out_HistoryDatasetAssociation_28_4bwol9,/galaxydir/galaxy/database/jobs_directory/000/15/metadata_results_HistoryDatasetAssociation_28_cEPCxu,/galaxydir/galaxy/database/files/000/dataset_28.dat,/galaxydir/galaxy/database/jobs_directory/000/15/metadata_override_HistoryDatasetAssociation_28_z5Frz5" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 18:18:20,331 (15) executing job script: /galaxydir/galaxy/database/jobs_directory/000/15/galaxy_15.sh galaxy.jobs DEBUG 2017-11-18 18:18:20,339 (15) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:18:18:21 -0400] "GET /?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:22 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:22 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:22 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:22 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:22 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:22 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:22 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:22 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=2tcrov3uerh&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:22 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:22 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:22 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:25 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 18:18:25,750 execution finished: /galaxydir/galaxy/database/jobs_directory/000/15/galaxy_15.sh galaxy.jobs.output_checker INFO 2017-11-18 18:18:25,761 Job 15: Warning: Exit code 0 () galaxy.model.metadata DEBUG 2017-11-18 18:18:25,914 loading metadata from file for: HistoryDatasetAssociation 27 galaxy.model.metadata DEBUG 2017-11-18 18:18:26,040 loading metadata from file for: HistoryDatasetAssociation 28 galaxy.jobs INFO 2017-11-18 18:18:26,222 Collecting metrics for Job 15 galaxy.jobs DEBUG 2017-11-18 18:18:26,240 job 15 ended (finish() executed in (489.921 ms)) galaxy.model.metadata DEBUG 2017-11-18 18:18:26,249 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:18:18:27 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T23%3A18%3A22.505Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:27 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:27 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:27 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:27 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:28 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/a7db2fac67043c7e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:31 -0400] "GET /datasets/a7db2fac67043c7e/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=2tcrov3uerh" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:31 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/a7db2fac67043c7e/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:18:32 -0400] "GET /datasets/a7db2fac67043c7e/stderr HTTP/1.1" 200 - "http://localhost:8080/datasets/a7db2fac67043c7e/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.queue_worker DEBUG 2017-11-18 18:19:46,708 Executing toolbox reload on 'main' galaxy.tools.toolbox.base INFO 2017-11-18 18:19:46,723 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 18:19:46,731 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 18:19:46,734 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 18:19:46,737 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 18:19:46,741 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,741 Reading tools from config files finshed (17.769 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,741 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,745 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,745 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,745 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,747 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,747 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,749 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,749 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,750 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,750 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,751 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,751 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,751 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,752 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,752 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,754 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,754 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,754 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,754 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,754 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,755 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,755 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:19:46,756 Loading tool panel finished (14.466 ms) galaxy.tools.deps DEBUG 2017-11-18 18:19:46,757 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-11-18 18:19:46,787 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 18:19:46,788 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 18:19:46,789 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-11-18 18:19:46,790 Queuing async task rebuild_toolbox_search_index for main. galaxy.queue_worker DEBUG 2017-11-18 18:19:46,796 Toolbox reload (88.868 ms) galaxy.queue_worker INFO 2017-11-18 18:19:47,722 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. galaxy.tools.search DEBUG 2017-11-18 18:19:47,722 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 18:19:47,759 Toolbox index finished (36.167 ms) 127.0.0.1 - - [18/Nov/2017:18:19:56 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=4tmfq3lpsz2&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:19:56 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:19:56 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:19:59 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.tools DEBUG 2017-11-18 18:20:00,159 Validated and populated state for tool request (45.765 ms) galaxy.tools.actions INFO 2017-11-18 18:20:00,229 Handled output named html_file for tool seq_sero_reads_multiple (27.777 ms) galaxy.tools.actions INFO 2017-11-18 18:20:00,268 Handled output named text_file for tool seq_sero_reads_multiple (39.092 ms) galaxy.tools.actions INFO 2017-11-18 18:20:00,289 Added output datasets to history (20.447 ms) galaxy.tools.actions INFO 2017-11-18 18:20:00,343 Verified access to datasets for Job[unflushed,tool_id=seq_sero_reads_multiple] (23.914 ms) galaxy.tools.actions INFO 2017-11-18 18:20:00,343 Setup for job Job[unflushed,tool_id=seq_sero_reads_multiple] complete, ready to flush (54.588 ms) galaxy.tools.actions INFO 2017-11-18 18:20:00,379 Flushed transaction for job Job[id=16,tool_id=seq_sero_reads_multiple] (35.812 ms) galaxy.tools.execute DEBUG 2017-11-18 18:20:00,380 Tool [seq_sero_reads_multiple] created job [16] (198.882 ms) galaxy.tools.execute DEBUG 2017-11-18 18:20:00,400 Executed 1 job(s) for tool seq_sero_reads_multiple request: (240.656 ms) 127.0.0.1 - - [18/Nov/2017:18:20:00 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:00 -0400] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:00 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7%2Ca7db2fac67043c7e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T23%3A18%3A27.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs DEBUG 2017-11-18 18:20:00,618 (16) Working directory for job is: /galaxydir/galaxy/database/jobs_directory/000/16 galaxy.jobs.handler DEBUG 2017-11-18 18:20:00,634 (16) Dispatching to local runner galaxy.jobs DEBUG 2017-11-18 18:20:00,680 (16) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2017-11-18 18:20:00,692 Job [16] queued (58.456 ms) galaxy.jobs.handler INFO 2017-11-18 18:20:00,711 (16) Job dispatched galaxy.jobs.command_factory INFO 2017-11-18 18:20:01,006 Built script [/galaxydir/galaxy/database/jobs_directory/000/16/tool_script.sh] for tool command [/galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_1.dat,/galaxydir/galaxy/database/files/000/dataset_2.dat /galaxydir/galaxy/tools/GalaxySeqsero/] galaxy.tools.deps DEBUG 2017-11-18 18:20:01,304 Using dependency samtools version None of type conda galaxy.tools.deps DEBUG 2017-11-18 18:20:01,304 Using dependency bcftools version 1.5 of type conda galaxy.jobs.runners DEBUG 2017-11-18 18:20:01,313 (16) command is: rm -rf working; mkdir -p working; cd working; /galaxydir/galaxy/database/jobs_directory/000/16/tool_script.sh; return_code=$?; if [ -f /galaxydir/galaxy/database/jobs_directory/000/16/working/Seqsero_result.html ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/16/working/Seqsero_result.html /galaxydir/galaxy/database/files/000/dataset_29.dat ; fi; if [ -f /galaxydir/galaxy/database/jobs_directory/000/16/working/Seqsero_result.txt ] ; then cp /galaxydir/galaxy/database/jobs_directory/000/16/working/Seqsero_result.txt /galaxydir/galaxy/database/files/000/dataset_30.dat ; fi; cd '/galaxydir/galaxy/database/jobs_directory/000/16'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; export PATH=$PATH:'/galaxydir/galaxy/database/dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; python "/galaxydir/galaxy/database/jobs_directory/000/16/set_metadata_PPs53p.py" "/galaxydir/galaxy/database/jobs_directory/000/16/registry.xml" "/galaxydir/galaxy/database/jobs_directory/000/16/working/galaxy.json" "/galaxydir/galaxy/database/jobs_directory/000/16/metadata_in_HistoryDatasetAssociation_29_0jBhLn,/galaxydir/galaxy/database/jobs_directory/000/16/metadata_kwds_HistoryDatasetAssociation_29_McH1BV,/galaxydir/galaxy/database/jobs_directory/000/16/metadata_out_HistoryDatasetAssociation_29_whZ5kV,/galaxydir/galaxy/database/jobs_directory/000/16/metadata_results_HistoryDatasetAssociation_29_2Q0TU8,/galaxydir/galaxy/database/files/000/dataset_29.dat,/galaxydir/galaxy/database/jobs_directory/000/16/metadata_override_HistoryDatasetAssociation_29_JgxUy3" "/galaxydir/galaxy/database/jobs_directory/000/16/metadata_in_HistoryDatasetAssociation_30_XFcjVB,/galaxydir/galaxy/database/jobs_directory/000/16/metadata_kwds_HistoryDatasetAssociation_30_BhBi1R,/galaxydir/galaxy/database/jobs_directory/000/16/metadata_out_HistoryDatasetAssociation_30_AK4j65,/galaxydir/galaxy/database/jobs_directory/000/16/metadata_results_HistoryDatasetAssociation_30_4HF9IO,/galaxydir/galaxy/database/files/000/dataset_30.dat,/galaxydir/galaxy/database/jobs_directory/000/16/metadata_override_HistoryDatasetAssociation_30_Tz5psq" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2017-11-18 18:20:01,329 (16) executing job script: /galaxydir/galaxy/database/jobs_directory/000/16/galaxy_16.sh galaxy.jobs DEBUG 2017-11-18 18:20:01,340 (16) Persisting job destination (destination id: local:///) 127.0.0.1 - - [18/Nov/2017:18:20:02 -0400] "GET /?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2 HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:03 -0400] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:03 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:03 -0400] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:03 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:03 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:03 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:03 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:03 -0400] "GET /api/tools/seq_sero_reads_multiple/build?version=0.1.0&__identifer=4tmfq3lpsz2&tool_version=0.1.0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:03 -0400] "GET /api/webhooks/tool-menu/all HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:04 -0400] "GET /api/tools/seq_sero_reads_multiple/citations HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:03 -0400] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7%2Ca7db2fac67043c7e&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:06 -0400] "GET /api/histories/f597429621d6eb2b/contents?keys=type_id%2Celement_count&details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7%2Ca7db2fac67043c7e&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" galaxy.jobs.runners.local DEBUG 2017-11-18 18:20:07,001 execution finished: /galaxydir/galaxy/database/jobs_directory/000/16/galaxy_16.sh galaxy.jobs.output_checker INFO 2017-11-18 18:20:07,019 Job 16: Warning: Exit code 0 () galaxy.model.metadata DEBUG 2017-11-18 18:20:07,210 loading metadata from file for: HistoryDatasetAssociation 29 galaxy.model.metadata DEBUG 2017-11-18 18:20:07,392 loading metadata from file for: HistoryDatasetAssociation 30 galaxy.jobs INFO 2017-11-18 18:20:07,591 Collecting metrics for Job 16 galaxy.jobs DEBUG 2017-11-18 18:20:07,608 job 16 ended (finish() executed in (607.192 ms)) galaxy.model.metadata DEBUG 2017-11-18 18:20:07,615 Cleaning up external metadata files 127.0.0.1 - - [18/Nov/2017:18:20:09 -0400] "GET /api/histories/f597429621d6eb2b/contents?details=e144222fed44799a%2C13cea0e6d733b865%2C9ce617df390851fc%2Cfa6833a4eadf9064%2C6505e875ddb66fd2%2Cbf60fd5f5f7f44bf%2C86cf1d3beeec9f1c%2C8c959c9304a2bc4b%2Ceca0af6fb47bf90c%2C6fb17d0cc6e8fae5%2Ca0c15f4d91084599%2C81991b32733a4fc4%2Cbe0a27b9edd0db03%2Cc851ab275e52f8af%2Cf1b9846ab84237e7%2C84ffe6fca6c4fbda%2C319886f37b7797fe%2Cf3a63b25ef201245%2C0998682e795f41c2%2Ca03c847bfa9a8077%2C7e2da049d9f5c1fa%2C6ee95371d25d237b%2C60559d1a5f859493%2C7ca8f1b7f24e5a2d%2Cf30a35c999095ed7%2C7d08ada97da61dfd%2Cebfb8f50c6abde6d%2Ca799d38679e985db%2Cdf7a1f0c02a5b08e%2C0a248a1f62a0cc04%2Ce85a3be143d5905b%2C1e8ab44153008be8%2C417e33144b294c21%2Cf09437b8822035f7%2Ca7db2fac67043c7e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-11-18T23%3A20%3A03.741Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:09 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:09 -0400] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:09 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:09 -0400] "POST /api/tools/seq_sero_reads_multiple/build HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:21 -0400] "GET /api/histories/f597429621d6eb2b/contents/datasets/e89067bb68bee7a0 HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:23 -0400] "GET /datasets/e89067bb68bee7a0/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:24 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/e89067bb68bee7a0/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:25 -0400] "GET /datasets/e89067bb68bee7a0/show_params HTTP/1.1" 200 - "http://localhost:8080/?tool_id=seq_sero_reads_multiple&version=0.1.0&__identifer=4tmfq3lpsz2" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:25 -0400] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://localhost:8080/datasets/e89067bb68bee7a0/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" 127.0.0.1 - - [18/Nov/2017:18:20:27 -0400] "GET /datasets/e89067bb68bee7a0/stderr HTTP/1.1" 200 - "http://localhost:8080/datasets/e89067bb68bee7a0/show_params" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.94 Safari/537.36" ^Cgalaxy.jobs.handler INFO 2017-11-18 18:20:41,468 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 18:20:41,468 job handler queue stopped galaxy.jobs.runners INFO 2017-11-18 18:20:41,469 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2017-11-18 18:20:41,469 sending stop signal to worker thread galaxy.jobs.handler INFO 2017-11-18 18:20:41,470 job handler stop queue stopped CFM5081985:galaxy charles.strittmatter$ clear CFM5081985:galaxy charles.strittmatter$ sh run.sh Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) Requirement already satisfied: botocore<1.8.0,>=1.7.0 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) Activating virtualenv at .venv galaxy.tools.deps DEBUG 2017-11-18 18:20:53,348 Unable to find config file './dependency_resolvers_conf.xml' DEBUG:galaxy.app:python path is: /galaxydir/galaxy/scripts, /galaxydir/galaxy/lib, /galaxydir/galaxy/.venv/lib/python27.zip, /galaxydir/galaxy/.venv/lib/python2.7, /galaxydir/galaxy/.venv/lib/python2.7/plat-darwin, /galaxydir/galaxy/.venv/lib/python2.7/plat-mac, /galaxydir/galaxy/.venv/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/Extras/lib/python, /galaxydir/galaxy/.venv/lib/python2.7/lib-tk, /galaxydir/galaxy/.venv/lib/python2.7/lib-old, /galaxydir/galaxy/.venv/lib/python2.7/lib-dynload, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages, /galaxydir/galaxy/.venv/lib/python2.7/site-packages DEBUG:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config INFO:galaxy.config:Logging at '10' level to 'stdout' galaxy.queue_worker INFO 2017-11-18 18:20:55,737 Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE tool_shed.tool_shed_registry DEBUG 2017-11-18 18:20:55,820 Loading references to tool sheds from ./config/tool_sheds_conf.xml.sample tool_shed.tool_shed_registry DEBUG 2017-11-18 18:20:55,820 Loaded reference to tool shed: Galaxy Main Tool Shed galaxy.app DEBUG 2017-11-18 18:20:55,825 Using "galaxy.ini" config file: /galaxydir/galaxy/config/galaxy.ini migrate.versioning.repository DEBUG 2017-11-18 18:20:55,999 Loading repository lib/galaxy/model/migrate... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,001 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,002 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,002 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,002 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,002 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,002 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,003 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,003 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,003 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,003 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,003 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,004 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,004 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,004 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,004 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,004 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,004 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,004 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,004 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,005 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,005 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,005 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,005 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,005 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,005 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,005 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,005 Loading script lib/galaxy/model/migrate/versions/0014_pages.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,006 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,006 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,006 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,006 Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,006 Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,006 Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,006 Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,006 Loading script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,007 Script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,007 Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,007 Script lib/galaxy/model/migrate/versions/0019_request_library_folder.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,007 Loading script lib/galaxy/model/migrate/versions/0020_library_upload_job.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,007 Script lib/galaxy/model/migrate/versions/0020_library_upload_job.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,007 Loading script lib/galaxy/model/migrate/versions/0021_user_prefs.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,007 Script lib/galaxy/model/migrate/versions/0021_user_prefs.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,008 Loading script lib/galaxy/model/migrate/versions/0022_visualization_tables.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,008 Script lib/galaxy/model/migrate/versions/0022_visualization_tables.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,008 Loading script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,008 Script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,008 Loading script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,008 Script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,008 Loading script lib/galaxy/model/migrate/versions/0025_user_info.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,008 Script lib/galaxy/model/migrate/versions/0025_user_info.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,009 Loading script lib/galaxy/model/migrate/versions/0026_cloud_tables.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,009 Script lib/galaxy/model/migrate/versions/0026_cloud_tables.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,009 Loading script lib/galaxy/model/migrate/versions/0027_request_events.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,009 Script lib/galaxy/model/migrate/versions/0027_request_events.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,009 Loading script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,009 Script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,009 Loading script lib/galaxy/model/migrate/versions/0029_user_actions.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,009 Script lib/galaxy/model/migrate/versions/0029_user_actions.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,010 Loading script lib/galaxy/model/migrate/versions/0030_history_slug_column.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,010 Script lib/galaxy/model/migrate/versions/0030_history_slug_column.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,010 Loading script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,010 Script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,010 Loading script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,010 Script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,010 Loading script lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,011 Script lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,011 Loading script lib/galaxy/model/migrate/versions/0034_page_user_share_association.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,011 Script lib/galaxy/model/migrate/versions/0034_page_user_share_association.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,011 Loading script lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py... migrate.versioning.script.base DEBUG 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lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,032 Loading script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,032 Script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,032 Loading script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,032 Script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,032 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,032 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,033 Loading script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,033 Script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,033 Loading script lib/galaxy/model/migrate/versions/0119_job_metrics.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,033 Script lib/galaxy/model/migrate/versions/0119_job_metrics.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,033 Loading script lib/galaxy/model/migrate/versions/0120_dataset_collections.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,033 Script lib/galaxy/model/migrate/versions/0120_dataset_collections.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,033 Loading script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,034 Script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,034 Loading script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,034 Script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,034 Loading script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,034 Script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,034 Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,034 Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,035 Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,035 Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,035 Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,035 Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,035 Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,035 Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,035 Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,035 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,036 Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,036 Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,036 Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,036 Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,036 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,036 Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,036 Loading script lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,037 Script lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,037 Loading script lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,037 Script lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,037 Loading script lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,037 Script lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,037 Loading script lib/galaxy/model/migrate/versions/0135_add_library_tags.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,037 Script lib/galaxy/model/migrate/versions/0135_add_library_tags.py loaded successfully migrate.versioning.repository DEBUG 2017-11-18 18:20:56,038 Repository lib/galaxy/model/migrate loaded successfully migrate.versioning.repository DEBUG 2017-11-18 18:20:56,038 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) galaxy.model.migrate.check INFO 2017-11-18 18:20:56,135 At database version 135 migrate.versioning.repository DEBUG 2017-11-18 18:20:56,138 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,140 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,140 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,140 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,140 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,141 Loading script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,141 Script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,141 Loading script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,141 Script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,141 Loading script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,142 Script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,142 Loading script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,142 Script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,142 Loading script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,142 Script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,142 Loading script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,142 Script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,143 Loading script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,143 Script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,143 Loading script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,143 Script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,143 Loading script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,143 Script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py loaded successfully migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,144 Loading script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py... migrate.versioning.script.base DEBUG 2017-11-18 18:20:56,144 Script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py loaded successfully migrate.versioning.repository DEBUG 2017-11-18 18:20:56,144 Repository lib/tool_shed/galaxy_install/migrate loaded successfully migrate.versioning.repository DEBUG 2017-11-18 18:20:56,144 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))]) tool_shed.galaxy_install.migrate.check INFO 2017-11-18 18:20:56,166 At migrate_tools version 12 galaxy.config INFO 2017-11-18 18:20:56,190 Install database targetting Galaxy's database configuration. /galaxydir/galaxy/lib/galaxy/datatypes/registry.py:98: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if root_dir and config: galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,283 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,283 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,284 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/binary: No module named binary galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,284 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,285 Exception importing proprietary code file /galaxydir/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,285 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,286 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,296 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,297 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,297 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,297 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,297 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,298 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,298 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,298 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,298 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,319 Loading datatypes from ./config/datatypes_conf.xml.sample galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,320 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,321 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,321 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,322 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,322 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,322 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,322 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,322 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,322 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,322 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,322 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,322 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,323 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,323 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,326 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,326 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,326 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,327 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,327 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,327 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,327 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,328 Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,328 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,329 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,329 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,329 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,329 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,329 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,330 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,330 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,330 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,330 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,331 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,331 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,331 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,331 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,332 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,332 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,332 Retrieved datatype module galaxy.datatypes.sequence:FastqGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,333 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,333 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,334 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,334 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,334 Retrieved datatype module galaxy.datatypes.sequence:FastqBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,335 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,336 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,336 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,337 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,337 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,337 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,338 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,338 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,338 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,338 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,339 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,339 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,339 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,339 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,339 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,340 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,340 Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,340 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,340 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,341 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,341 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,341 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,342 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,342 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,343 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,343 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,343 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,343 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,343 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,344 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,344 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,344 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,344 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,345 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,345 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,345 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,345 Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,346 Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,346 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,346 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,346 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,346 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,346 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,347 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,347 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,347 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,347 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,347 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,348 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,348 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,348 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,348 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,348 Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,349 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,351 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,351 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,352 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,352 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,352 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,352 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,353 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,353 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,353 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,353 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,353 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,353 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,354 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,354 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,354 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,354 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,354 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,355 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,355 Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,355 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,355 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,356 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,356 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,356 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,356 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,356 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,356 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,357 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,357 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,357 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,357 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,357 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,358 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,358 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,358 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,358 Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,358 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,359 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,359 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,359 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,360 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,360 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,360 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,361 Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,361 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,361 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,362 Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,362 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,362 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,362 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,362 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,362 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,363 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,363 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,363 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,363 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,363 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,363 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,364 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,364 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,364 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,364 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,364 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,364 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,365 Roadmaps is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,365 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,365 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,365 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,365 Sequences is not lower case, that could cause troubles in the future. Please change it to lower case galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,365 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,365 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,366 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,366 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,366 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,366 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,367 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,367 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,367 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,368 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,368 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,368 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,369 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,369 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,369 Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,369 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,369 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,370 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,370 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,370 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,370 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,371 Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,371 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,371 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,371 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,371 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,372 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,372 Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,372 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,372 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,373 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,375 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,376 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,376 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,376 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,376 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,376 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,377 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,377 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,377 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,377 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,377 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,378 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,378 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,378 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,378 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,378 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,379 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,379 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,379 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,379 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,381 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,382 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,384 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,384 Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,385 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,385 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,386 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,387 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,388 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,388 Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,388 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,388 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,389 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,389 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,389 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,389 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,475 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,475 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,475 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,476 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,476 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,476 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,476 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,476 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,477 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,477 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,477 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,477 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,478 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,478 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,478 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,478 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,479 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,479 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,479 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,479 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,480 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,480 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,480 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,480 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,480 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,481 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,481 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,481 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,481 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,482 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,482 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,482 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,482 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,483 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,483 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,483 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,483 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,484 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,484 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,484 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,484 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,485 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,485 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,485 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,485 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,485 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,486 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,486 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,486 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,487 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,487 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,487 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,487 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,487 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,488 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,488 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,488 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,489 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,489 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,489 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,489 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,489 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,490 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,490 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,490 Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,490 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,491 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,491 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,491 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,491 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,492 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,492 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,492 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,492 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,492 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,493 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,493 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,493 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,493 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,494 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,494 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,494 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,494 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,495 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,495 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,495 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,495 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,495 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,496 Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,496 Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,498 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,498 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,498 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,498 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,498 Retrieved datatype module galaxy.datatypes.binary:Cel from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,499 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,500 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,500 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,500 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,501 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,501 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,501 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,502 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,502 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,503 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,503 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,503 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,503 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,504 Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,504 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,506 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,506 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,507 Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,507 Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,507 Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,507 Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,507 Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,508 Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,508 Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,508 Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,508 Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,508 Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,509 Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,509 Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,514 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,514 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,514 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,514 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,515 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,515 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,515 Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,515 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,516 Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,516 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,516 Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,516 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,517 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,517 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,517 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,518 Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,518 Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,518 Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,518 Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,518 Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,519 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,519 Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,520 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,520 Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,520 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,520 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,522 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,522 Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,522 Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,523 Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,523 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,523 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,523 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,524 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,524 Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,524 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,524 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,525 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,525 Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,527 Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,527 Overriding conflicting datatype with extension 'blastxml', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,527 Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,527 Overriding conflicting datatype with extension 'blastdbn', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,528 Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,528 Overriding conflicting datatype with extension 'blastdbp', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,528 Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,528 Overriding conflicting datatype with extension 'blastdbd', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,528 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,528 Overriding conflicting datatype with extension 'maskinfo-asn1', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,529 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,529 Overriding conflicting datatype with extension 'maskinfo-asn1-binary', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,529 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,529 Overriding conflicting datatype with extension 'pssm-asn1', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,531 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,531 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,531 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,531 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,532 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,532 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,532 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,532 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrtho from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,532 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,533 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylip from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,533 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,534 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,534 Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,535 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,535 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,536 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,536 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,537 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,538 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,538 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,539 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,539 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,539 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,539 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,539 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,539 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,539 Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,540 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,540 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,540 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,540 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,540 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,540 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,540 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,541 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,541 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,541 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,541 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,541 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,541 Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,541 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,541 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,542 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,542 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,542 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,542 Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,542 Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,542 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,543 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,543 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,543 Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,543 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,543 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,544 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,544 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,544 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,544 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,544 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,544 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,544 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,544 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,545 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,545 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,545 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,545 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,545 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,545 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,546 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,546 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,546 Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,546 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,546 Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,546 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,546 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,547 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,547 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,547 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,547 Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,547 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,547 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,548 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,548 Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,548 Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,548 Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,548 Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,549 Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,549 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,549 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,549 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerGz' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,549 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerBz2' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,549 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,550 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqGz' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,550 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqBz2' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,550 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,550 Loaded sniffer for datatype 'galaxy.datatypes.text:Html' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,550 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,550 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,551 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,551 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,551 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,551 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,551 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,551 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,552 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,552 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,552 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,552 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,553 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,553 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,553 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,553 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,553 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,553 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,554 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,554 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,554 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,554 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,554 Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,554 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,555 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,555 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,555 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,555 Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,555 Loaded sniffer for datatype 'galaxy.datatypes.binary:Cel' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,555 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,556 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,556 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,556 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,556 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,556 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,556 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,556 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,557 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,557 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,557 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,557 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,557 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,557 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,558 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,558 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,558 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,558 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,558 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,558 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,558 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,558 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,558 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,558 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,567 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,568 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,569 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,569 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,570 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,570 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,570 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,571 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2017-11-18 18:20:56,571 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample galaxy.tools.data INFO 2017-11-18 18:20:57,400 Could not find tool data tool-data/all_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:20:57,402 Loaded 0 lines from 'tool-data/all_fasta.loc.sample' for 'all_fasta' galaxy.tools.data DEBUG 2017-11-18 18:20:57,402 Loaded tool data table 'all_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:20:57,402 Could not find tool data tool-data/bfast_indexes.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:20:57,404 Loaded 0 lines from 'tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' galaxy.tools.data DEBUG 2017-11-18 18:20:57,404 Loaded tool data table 'bfast_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 18:20:57,406 Loaded 0 lines from 'tool-data/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 18:20:57,406 Loaded tool data table 'blastdb' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 18:20:57,408 Loaded 0 lines from 'tool-data/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 18:20:57,408 Loaded tool data table 'blastdb_p' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 18:20:57,410 Loaded 0 lines from 'tool-data/blastdb_d.loc' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 18:20:57,410 Loaded tool data table 'blastdb_d' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 18:20:57,412 Loaded 0 lines from 'tool-data/bwa_index.loc' for 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 18:20:57,412 Loaded tool data table 'bwa_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 18:20:57,414 Loaded 0 lines from 'tool-data/bwa_index_color.loc' for 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 18:20:57,414 Loaded tool data table 'bwa_indexes_color' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:20:57,415 Could not find tool data tool-data/maf_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:20:57,416 Loaded 0 lines from 'tool-data/maf_index.loc.sample' for 'indexed_maf_files' galaxy.tools.data DEBUG 2017-11-18 18:20:57,416 Loaded tool data table 'indexed_maf_files' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:20:57,417 Could not find tool data tool-data/ngs_sim_fasta.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:20:57,418 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' galaxy.tools.data DEBUG 2017-11-18 18:20:57,419 Loaded tool data table 'ngs_sim_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:20:57,419 Could not find tool data tool-data/perm_base_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:20:57,421 Loaded 0 lines from 'tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' galaxy.tools.data DEBUG 2017-11-18 18:20:57,421 Loaded tool data table 'perm_base_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:20:57,421 Could not find tool data tool-data/perm_color_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:20:57,423 Loaded 0 lines from 'tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' galaxy.tools.data DEBUG 2017-11-18 18:20:57,423 Loaded tool data table 'perm_color_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:20:57,423 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:20:57,424 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'picard_indexes' galaxy.tools.data DEBUG 2017-11-18 18:20:57,424 Loaded tool data table 'picard_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:20:57,424 Could not find tool data tool-data/picard_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:20:57,425 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'srma_indexes' galaxy.tools.data DEBUG 2017-11-18 18:20:57,425 Loaded tool data table 'srma_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:20:57,425 Could not find tool data tool-data/mosaik_index.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:20:57,426 Loaded 0 lines from 'tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' galaxy.tools.data DEBUG 2017-11-18 18:20:57,427 Loaded tool data table 'mosaik_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:20:57,427 Could not find tool data tool-data/twobit.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:20:57,428 Loaded 0 lines from 'tool-data/twobit.loc.sample' for 'twobit' galaxy.tools.data DEBUG 2017-11-18 18:20:57,429 Loaded tool data table 'twobit' from file './config/tool_data_table_conf.xml.sample' requests.packages.urllib3.connectionpool INFO 2017-11-18 18:20:57,443 Starting new HTTP connection (1): igv.broadinstitute.org requests.packages.urllib3.connectionpool DEBUG 2017-11-18 18:20:57,496 "GET /genomes/genomes.txt HTTP/1.1" 200 15681 galaxy.tools.data DEBUG 2017-11-18 18:20:57,504 Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-zzTBYE". galaxy.tools.data WARNING 2017-11-18 18:20:57,506 Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields): <Server-Side Genome List> galaxy.tools.data DEBUG 2017-11-18 18:20:57,508 Loaded 156 lines from '/galaxydir/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-zzTBYE' for 'igv_broad_genomes' galaxy.tools.data DEBUG 2017-11-18 18:20:57,509 Loaded tool data table 'igv_broad_genomes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:20:57,510 Could not find tool data tool-data/liftOver.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:20:57,511 Loaded 0 lines from 'tool-data/liftOver.loc.sample' for 'liftOver' galaxy.tools.data DEBUG 2017-11-18 18:20:57,511 Loaded tool data table 'liftOver' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:20:57,512 Could not find tool data tool-data/bam_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:20:57,513 Loaded 1 lines from 'tool-data/bam_iobio.loc.sample' for 'bam_iobio' galaxy.tools.data DEBUG 2017-11-18 18:20:57,513 Loaded tool data table 'bam_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:20:57,514 Could not find tool data tool-data/vcf_iobio.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:20:57,515 Loaded 1 lines from 'tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' galaxy.tools.data DEBUG 2017-11-18 18:20:57,515 Loaded tool data table 'vcf_iobio' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2017-11-18 18:20:57,516 Could not find tool data tool-data/biom_simple_display.loc, reading sample galaxy.tools.data DEBUG 2017-11-18 18:20:57,517 Loaded 1 lines from 'tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' galaxy.tools.data DEBUG 2017-11-18 18:20:57,517 Loaded tool data table 'biom_simple_display' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2017-11-18 18:20:57,521 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2017-11-18 18:20:57,522 Loading another instance of data table 'blastdb' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 18:20:57,523 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2017-11-18 18:20:57,524 Loading another instance of data table 'blastdb_p' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 18:20:57,526 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/6f386c5dc4fb/blastdb_d.loc' for 'blastdb_d' galaxy.tools.data DEBUG 2017-11-18 18:20:57,526 Loading another instance of data table 'blastdb_d' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 18:20:57,528 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/bwa_index.loc' for 'bwa_indexes' galaxy.tools.data DEBUG 2017-11-18 18:20:57,528 Loading another instance of data table 'bwa_indexes' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2017-11-18 18:20:57,530 Loaded 0 lines from '/galaxydir/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/3a001705dc94/bwa_index_color.loc' for 'bwa_indexes_color' galaxy.tools.data DEBUG 2017-11-18 18:20:57,530 Loading another instance of data table 'bwa_indexes_color' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.jobs WARNING 2017-11-18 18:20:57,630 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/galaxydir/galaxy/config/galaxy.ini" instead galaxy.jobs DEBUG 2017-11-18 18:20:57,630 Loading job configuration from /galaxydir/galaxy/config/galaxy.ini galaxy.jobs DEBUG 2017-11-18 18:20:57,630 Done loading job configuration beaker.container DEBUG 2017-11-18 18:20:57,858 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache galaxy.tools.toolbox.base INFO 2017-11-18 18:20:57,871 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.toolbox.base ERROR 2017-11-18 18:20:58,320 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base ERROR 2017-11-18 18:20:58,420 Error reading tool configuration file from path: test/testdep.xml galaxy.tools.toolbox.base INFO 2017-11-18 18:20:58,480 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-11-18 18:20:59,149 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,150 Reading tools from config files finshed (1279.476 ms) galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,150 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,151 Loaded tool id: toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/bwa_color_wrapper/1.0.2, version: 1.0.2 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,151 Loaded tool id: toolshed.g2.bx.psu.edu/repos/evan/bwa_wrappers/bwa_wrapper/1.2.3, version: 1.2.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,151 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.8.1.2, version: 2.8.1.2 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,151 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,151 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,152 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.3, version: 2.8.1.3 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,152 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,152 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,152 Loaded tool id: biomart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,153 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,153 Loaded tool id: gramenemart, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,153 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,153 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,153 Loaded tool id: flymine_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,154 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,154 Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,154 Loaded tool id: flymine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,154 Loaded tool id: modmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,154 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,154 Loaded tool id: mousemine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,155 Loaded tool id: ratmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,155 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,155 Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,155 Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,155 Loaded tool id: hbvar, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,156 Loaded tool id: wormbase, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,156 Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,156 Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,156 Loaded tool id: genomespace_importer, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,156 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,156 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,157 Loaded tool id: genomespace_exporter, version: 0.0.5 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,157 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,157 Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,157 Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,157 Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,157 Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,158 Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,158 Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,158 Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,158 Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,158 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,158 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,159 Loaded tool id: addValue, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,159 Loaded tool id: cat1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,159 Loaded tool id: Cut1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,159 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,159 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,159 Loaded tool id: createInterval, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,160 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,160 Loaded tool id: Paste1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,160 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,160 Loaded tool id: random_lines1, version: 2.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,161 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,161 Loaded tool id: Show tail1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,161 Loaded tool id: trimmer, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,161 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,161 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,161 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,162 Loaded tool id: Filter1, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,162 Loaded tool id: sort1, version: 1.0.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,162 Loaded tool id: Grep1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,162 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,163 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,163 Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,163 Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,163 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,163 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,164 Loaded tool id: join1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,164 Loaded tool id: comp1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,164 Loaded tool id: Grouping1, version: 2.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,164 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,164 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,165 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,165 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,165 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,165 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,165 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,166 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,166 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,166 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,166 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,166 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,166 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,167 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,167 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,167 Loading section: Fetch Alignments/Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,167 Loading section: Operate on Genomic Intervals galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,167 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,168 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,168 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,168 Loaded tool id: Extract genomic DNA 1, version: 2.2.3 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,168 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,168 Loaded tool id: seq_sero_reads_multiple, version: 0.1.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,168 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,169 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,169 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_convert2blastmask_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,169 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,169 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,170 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,170 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,170 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_segmasker_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,170 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,171 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,171 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,171 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,171 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,172 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.2.01, version: 0.2.01 into tool panel.... galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,172 Loading section: Phenotype Association galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,172 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,172 Loading section: NGS: Mapping galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,172 Loading section: NGS: GATK Tools (beta) galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,172 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,172 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,173 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,173 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,173 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,174 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,174 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,174 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,175 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,175 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,175 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,175 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,175 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,176 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,176 Loaded tool id: Summary_Statistics1, version: 1.1.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,176 Loaded tool id: Count1, version: 1.0.2 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,176 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,177 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,177 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,177 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2017-11-18 18:20:59,177 Loading tool panel finished (27.004 ms) galaxy.tools.deps DEBUG 2017-11-18 18:20:59,181 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.search DEBUG 2017-11-18 18:20:59,203 Starting to build toolbox index. galaxy.tools.search DEBUG 2017-11-18 18:21:01,205 Toolbox index finished (2002.135 ms) galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,211 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,215 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,263 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,267 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,269 Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,271 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,273 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,277 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,280 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,283 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,285 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,289 Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,330 Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,339 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,384 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,387 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,394 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,407 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,410 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,454 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,458 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,461 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,509 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,512 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,516 Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,519 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,571 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,573 Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,575 Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,578 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,578 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,578 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,579 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,579 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,579 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,579 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,579 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,587 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,587 Adding inherited display application 'igv_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,596 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,597 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,597 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,597 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,599 Adding inherited display application 'igv_fasta' to datatype 'sequences' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,599 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,599 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,600 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,600 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,602 Adding inherited display application 'igv_fasta' to datatype 'mothur.align' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,604 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,604 Adding inherited display application 'igv_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,613 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,613 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,613 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,613 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,614 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,614 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,614 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,614 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,618 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,618 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,618 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,618 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,621 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,622 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,623 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,624 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,626 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,627 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,628 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,629 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,633 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,636 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,637 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,638 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,640 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,641 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,642 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,643 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,645 Loaded converter: CONVERTER_fasta_to_fai galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,646 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,647 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,649 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,650 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,652 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,654 Loaded converter: CONVERTER_fastqgz_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,656 Loaded converter: CONVERTER_fastqsangergz_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,658 Loaded converter: CONVERTER_fastqsolexagz_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,660 Loaded converter: CONVERTER_fastqcssangergz_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,662 Loaded converter: CONVERTER_fastqilluminagz_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,663 Loaded converter: CONVERTER_fastqbz2_to_fastq galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,668 Loaded converter: CONVERTER_fastqsangerbz2_to_fastqsanger galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,670 Loaded converter: CONVERTER_fastqsolexabz2_to_fastqsolexa galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,671 Loaded converter: CONVERTER_fastqcssangerbz2_to_fastqcssanger galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,672 Loaded converter: CONVERTER_fastqilluminabz2_to_fastqillumina galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,673 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,674 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,676 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,677 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,678 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,680 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,681 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,682 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,684 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,686 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,687 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,688 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,690 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,691 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,692 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,693 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,695 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,699 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,700 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,701 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,703 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,704 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,705 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,707 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,709 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,711 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,712 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,714 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,719 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,721 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,722 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,723 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,725 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,726 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,727 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,728 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,730 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,732 Loaded converter: CONVERTER_biom1_to_biom2 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,735 Loaded converter: CONVERTER_biom2_to_biom1 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,737 Loaded converter: CONVERTER_SMILES_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,739 Loaded converter: CONVERTER_SMILES_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,742 Loaded converter: CONVERTER_SMILES_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,744 Loaded converter: CONVERTER_SMILES_to_MOL galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,746 Loaded converter: CONVERTER_SMILES_to_MOL2 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,750 Loaded converter: CONVERTER_smiles_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,754 Loaded converter: CONVERTER_sdf_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,756 Loaded converter: CONVERTER_sdf_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,757 Loaded converter: CONVERTER_sdf_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,758 Loaded converter: CONVERTER_sdf_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,760 Loaded converter: CONVERTER_inchi_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,761 Loaded converter: CONVERTER_inchi_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,763 Loaded converter: CONVERTER_inchi_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,766 Loaded converter: CONVERTER_inchi_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,767 Loaded converter: CONVERTER_inchi_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,768 Loaded converter: CONVERTER_mol_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,772 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,773 Loaded converter: CONVERTER_mol_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,781 Loaded converter: CONVERTER_mol_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,782 Loaded converter: CONVERTER_mol2_to_smi galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,783 Loaded converter: CONVERTER_mol2_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,785 Loaded converter: CONVERTER_mol2_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,786 Loaded converter: CONVERTER_mol2_to_mol galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,788 Loaded converter: CONVERTER_mol2_to_cml galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,790 Loaded converter: CONVERTER_cml_to_smiles galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,791 Loaded converter: CONVERTER_cml_to_inchi galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,792 Loaded converter: CONVERTER_cml_to_sdf galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,794 Loaded converter: CONVERTER_cml_to_mol2 galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,795 Loaded converter: CONVERTER_ref_to_seq_taxomony galaxy.datatypes.registry DEBUG 2017-11-18 18:21:01,799 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-11-18 18:21:01,809 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-11-18 18:21:01,811 Loaded history export tool: __EXPORT_HISTORY__ galaxy.web.base.pluginframework INFO 2017-11-18 18:21:01,815 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2017-11-18 18:21:01,818 Visualizations plugin disabled: Circster. Skipping... galaxy.visualization.plugins.config_parser INFO 2017-11-18 18:21:01,821 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 18:21:01,822 VisualizationsRegistry, loaded plugin: csg galaxy.visualization.plugins.config_parser INFO 2017-11-18 18:21:01,825 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 18:21:01,825 VisualizationsRegistry, loaded plugin: graphviz galaxy.web.base.pluginframework INFO 2017-11-18 18:21:01,827 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2017-11-18 18:21:01,830 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2017-11-18 18:21:01,833 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2017-11-18 18:21:01,837 VisualizationsRegistry, loaded plugin: trackster galaxy.visualization.plugins.config_parser INFO 2017-11-18 18:21:01,839 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-11-18 18:21:01,840 VisualizationsRegistry, loaded plugin: unipept galaxy.tours INFO 2017-11-18 18:21:01,889 Loaded tour 'core.galaxy_ui' galaxy.tours INFO 2017-11-18 18:21:01,918 Loaded tour 'core.history' galaxy.tours INFO 2017-11-18 18:21:01,936 Loaded tour 'core.scratchbook' galaxy.webhooks WARNING 2017-11-18 18:21:01,936 directory not found: /galaxydir/galaxy/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config galaxy.jobs.manager DEBUG 2017-11-18 18:21:01,955 Starting job handler galaxy.jobs INFO 2017-11-18 18:21:01,955 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2017-11-18 18:21:01,961 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2017-11-18 18:21:01,961 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2017-11-18 18:21:01,963 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs DEBUG 2017-11-18 18:21:01,963 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2017-11-18 18:21:01,963 Loaded job runners plugins: local galaxy.jobs.handler INFO 2017-11-18 18:21:01,964 job handler stop queue started galaxy.jobs.handler INFO 2017-11-18 18:21:01,978 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 18:21:01,993 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2017-11-18 18:21:01,997 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.workflow.scheduling_manager DEBUG 2017-11-18 18:21:02,178 Starting workflow schedulers galaxy.app INFO 2017-11-18 18:21:02,180 Galaxy app startup finished (6551.278 ms) galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,196 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,588 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,588 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,590 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,592 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,594 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,598 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,600 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,605 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,606 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,609 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,613 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,615 Enabling 'interactive_environments' controller, class: InteractiveEnvironmentsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,628 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,631 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,631 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,636 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,638 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,641 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,645 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,646 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,649 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,653 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,656 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,658 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,660 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,664 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,670 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,676 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,676 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,676 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,678 Enabling 'authenticate' API controller, class: AuthenticationController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,680 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,682 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,685 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,687 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,689 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,689 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,693 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,695 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,697 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,699 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,702 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,705 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,707 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,712 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,714 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,716 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,716 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,716 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,719 Enabling 'job_files' API controller, class: JobFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,721 Enabling 'jobs' API controller, class: JobController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,725 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,727 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,732 Enabling 'library_datasets' API controller, class: LibraryDatasetsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,735 Enabling 'metrics' API controller, class: MetricsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,738 Enabling 'page_revisions' API controller, class: PageRevisionsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,740 Enabling 'pages' API controller, class: PagesController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,742 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,742 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,745 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,752 Enabling 'remote_files' API controller, class: RemoteFilesAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,757 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,759 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,761 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,763 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,807 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,809 Enabling 'tool_data' API controller, class: ToolData galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,814 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,818 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,821 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,824 Enabling 'toolshed' API controller, class: ToolShedController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,826 Enabling 'tours' API controller, class: ToursController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,829 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,831 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,833 Enabling 'webhooks' API controller, class: WebhooksController galaxy.web.framework.base DEBUG 2017-11-18 18:21:02,836 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.webapps.util DEBUG 2017-11-18 18:21:03,300 Enabling 'paste.httpexceptions' middleware galaxy.webapps.util DEBUG 2017-11-18 18:21:03,303 Enabling 'RecursiveMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 18:21:03,321 Enabling 'ErrorMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 18:21:03,324 Enabling 'TransLogger' middleware galaxy.webapps.util DEBUG 2017-11-18 18:21:03,326 Enabling 'XForwardedHostMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 18:21:03,328 Enabling 'RequestIDMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 18:21:03,330 Enabling 'BatchMiddleware' middleware galaxy.webapps.util DEBUG 2017-11-18 18:21:03,332 Enabling 'wrap_in_static' middleware galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,346 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,347 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,347 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,347 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,348 added url, path to static middleware: /plugins/visualizations/unipept/static, ./config/plugins/visualizations/unipept/static galaxy.queue_worker INFO 2017-11-18 18:21:03,348 Binding and starting galaxy control worker for main galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,348 Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 140735112855552)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,349 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145308196864)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,349 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-2, started daemon 123145325023232)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,360 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-0, started daemon 123145316610048)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,360 Prior to webapp return, Galaxy thread <Thread(JobHandlerStopQueue.monitor_thread, started daemon 123145337643008)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,362 Prior to webapp return, Galaxy thread <Thread(WorkflowRequestMonitor.monitor_thread, started daemon 123145346056192)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,362 Prior to webapp return, Galaxy thread <GalaxyQueueWorker(Thread-1, started daemon 123145350262784)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,362 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-3, started daemon 123145329229824)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,364 Prior to webapp return, Galaxy thread <Thread(JobHandlerQueue.monitor_thread, started daemon 123145341849600)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,364 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-1, started daemon 123145320816640)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,364 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-4, started daemon 123145333436416)> is alive. galaxy.webapps.galaxy.buildapp DEBUG 2017-11-18 18:21:03,364 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145312403456)> is alive. Starting server in PID 76049. serving on http://127.0.0.1:8080