Mercurial > repos > eschen42 > w4mclassfilter
changeset 3:dbe02bb33ae1 draft
Deleted selected files
| author | eschen42 |
|---|---|
| date | Wed, 10 May 2017 15:24:06 -0400 |
| parents | 9a3462eff3bf |
| children | 2495d0019dbe |
| files | test_log.txt |
| diffstat | 1 files changed, 0 insertions(+), 334 deletions(-) [+] |
line wrap: on
line diff
--- a/test_log.txt Wed May 10 10:19:28 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,334 +0,0 @@ -git --git-dir /home/backdoor/.planemo/gx_repo fetch >/dev/null 2>&1 -cd /tmp/tmpBnX6kx; git clone --branch 'master' '/home/backdoor/.planemo/gx_repo' 'galaxy-dev'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/backdoor/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/backdoor/.linuxbrew/bin/virtualenv -p /home/backdoor/.linuxbrew/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS} -Cloning into 'galaxy-dev'... -done. -Set COMMON_STARTUP_ARGS to --dev-wheels -Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample -Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample -Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample -Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample -Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample -Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample -Initializing tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample -Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample -Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample -Initializing static/welcome.html from welcome.html.sample -Activating virtualenv at /home/backdoor/.planemo/gx_venv -Requirement already satisfied: pip>=8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages -Requirement already satisfied: bx-python==0.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) -Requirement already satisfied: MarkupSafe==0.23 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) -Requirement already satisfied: PyYAML==3.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) -Requirement already satisfied: SQLAlchemy==1.0.15 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) -Requirement already satisfied: mercurial==3.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) -Requirement already satisfied: numpy==1.9.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) -Requirement already satisfied: pycrypto==2.6.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) -Requirement already satisfied: Paste==2.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15)) -Requirement already satisfied: PasteDeploy==1.5.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) -Requirement already satisfied: docutils==0.12 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) -Requirement already satisfied: wchartype==0.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) -Requirement already satisfied: repoze.lru==0.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) -Requirement already satisfied: Routes==2.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) -Requirement already satisfied: WebOb==1.4.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) -Requirement already satisfied: WebHelpers==1.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) -Requirement already satisfied: Mako==1.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) -Requirement already satisfied: pytz==2015.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) -Requirement already satisfied: Babel==2.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) -Requirement already satisfied: Beaker==1.7.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) -Requirement already satisfied: dictobj==0.3.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) -Requirement already satisfied: nose==1.3.7 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) -Requirement already satisfied: Parsley==1.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) -Requirement already satisfied: six==1.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) -Requirement already satisfied: Whoosh==2.7.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) -Requirement already satisfied: testfixtures==4.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) -Requirement already satisfied: galaxy_sequence_utils==1.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) -Requirement already satisfied: Cheetah==2.4.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) -Requirement already satisfied: Markdown==2.6.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) -Requirement already satisfied: bioblend==0.7.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) -Requirement already satisfied: boto==2.38.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) -Requirement already satisfied: requests==2.8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) -Requirement already satisfied: requests-toolbelt==0.4.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 43)) -Requirement already satisfied: kombu==3.0.30 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) -Requirement already satisfied: amqp==1.4.8 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) -Requirement already satisfied: anyjson==0.3.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) -Requirement already satisfied: psutil==4.1.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) -Requirement already satisfied: pulsar-galaxy-lib==0.7.0.dev5 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) -Requirement already satisfied: sqlalchemy-migrate==0.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) -Requirement already satisfied: decorator==4.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) -Requirement already satisfied: Tempita==0.5.3dev in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) -Requirement already satisfied: sqlparse==0.1.16 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) -Requirement already satisfied: pbr==1.8.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) -Requirement already satisfied: svgwrite==1.1.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 62)) -Requirement already satisfied: pyparsing==2.1.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) -Requirement already satisfied: Fabric==1.10.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) -Requirement already satisfied: paramiko==1.15.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) -Requirement already satisfied: ecdsa==0.13 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 68)) -Requirement already satisfied: pysam==0.8.4+gx5 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) -Requirement already satisfied: PasteScript in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 52)) -Requirement already satisfied: nose in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1)) -Requirement already satisfied: NoseHTML in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2)) -Requirement already satisfied: twill==0.9.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) -Requirement already satisfied: mock in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) -Requirement already satisfied: selenium in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) -Requirement already satisfied: pbr>=0.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) -Requirement already satisfied: funcsigs>=1; python_version < "3.3" in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) -Requirement already satisfied: six>=1.9 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) -Testing using galaxy_root /tmp/tmpBnX6kx/galaxy-dev -Testing tools with command [cd /tmp/tmpBnX6kx/galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/backdoor/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/backdoor/.linuxbrew/bin/virtualenv -p /home/backdoor/.linuxbrew/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /home/backdoor/toolshed_test/w4mclassfilter/tool_test_output.html --xunit_report_file /tmp/tmpBnX6kx/xunit.xml --structured_data_report_file /home/backdoor/toolshed_test/w4mclassfilter/tool_test_output.json functional.test_toolbox] -Activating virtualenv at /home/backdoor/.planemo/gx_venv -Requirement already satisfied: pip>=8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages -Requirement already satisfied: bx-python==0.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) -Requirement already satisfied: MarkupSafe==0.23 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) -Requirement already satisfied: PyYAML==3.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) -Requirement already satisfied: SQLAlchemy==1.0.15 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) -Requirement already satisfied: mercurial==3.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) -Requirement already satisfied: numpy==1.9.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) -Requirement already satisfied: pycrypto==2.6.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) -Requirement already satisfied: Paste==2.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15)) -Requirement already satisfied: PasteDeploy==1.5.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) -Requirement already satisfied: docutils==0.12 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) -Requirement already satisfied: wchartype==0.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) -Requirement already satisfied: repoze.lru==0.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) -Requirement already satisfied: Routes==2.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) -Requirement already satisfied: WebOb==1.4.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) -Requirement already satisfied: WebHelpers==1.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) -Requirement already satisfied: Mako==1.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) -Requirement already satisfied: pytz==2015.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) -Requirement already satisfied: Babel==2.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) -Requirement already satisfied: Beaker==1.7.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) -Requirement already satisfied: dictobj==0.3.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) -Requirement already satisfied: nose==1.3.7 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) -Requirement already satisfied: Parsley==1.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) -Requirement already satisfied: six==1.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) -Requirement already satisfied: Whoosh==2.7.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) -Requirement already satisfied: testfixtures==4.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) -Requirement already satisfied: galaxy_sequence_utils==1.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) -Requirement already satisfied: Cheetah==2.4.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) -Requirement already satisfied: Markdown==2.6.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) -Requirement already satisfied: bioblend==0.7.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) -Requirement already satisfied: boto==2.38.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) -Requirement already satisfied: requests==2.8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) -Requirement already satisfied: requests-toolbelt==0.4.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 43)) -Requirement already satisfied: kombu==3.0.30 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) -Requirement already satisfied: amqp==1.4.8 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) -Requirement already satisfied: anyjson==0.3.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) -Requirement already satisfied: psutil==4.1.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) -Requirement already satisfied: pulsar-galaxy-lib==0.7.0.dev5 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) -Requirement already satisfied: sqlalchemy-migrate==0.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) -Requirement already satisfied: decorator==4.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) -Requirement already satisfied: Tempita==0.5.3dev in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) -Requirement already satisfied: sqlparse==0.1.16 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) -Requirement already satisfied: pbr==1.8.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) -Requirement already satisfied: svgwrite==1.1.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 62)) -Requirement already satisfied: pyparsing==2.1.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) -Requirement already satisfied: Fabric==1.10.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) -Requirement already satisfied: paramiko==1.15.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) -Requirement already satisfied: ecdsa==0.13 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 68)) -Requirement already satisfied: pysam==0.8.4+gx5 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) -Requirement already satisfied: PasteScript in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 52)) -Requirement already satisfied: nose in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1)) -Requirement already satisfied: NoseHTML in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2)) -Requirement already satisfied: twill==0.9.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) -Requirement already satisfied: mock in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) -Requirement already satisfied: selenium in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) -Requirement already satisfied: pbr>=0.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) -Requirement already satisfied: funcsigs>=1; python_version < "3.3" in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) -Requirement already satisfied: six>=1.9 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) -Activating virtualenv at /home/backdoor/.planemo/gx_venv -2017-05-09 17:41:18,784 INFO [galaxy.queue_worker] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:// -2017-05-09 17:41:18,932 INFO [galaxy.model.migrate.check] Migrating 127 -> 128... -2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check] Migration script to add session update time (used for timeouts) -2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check] Migrating 128 -> 129... -2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check] Migration script to allow invalidation of job external output metadata temp files -2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check] Migrating 129 -> 130... -2017-05-09 17:41:20,242 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:20,243 INFO [galaxy.model.migrate.check] Migration script to change the value column of user_preference from varchar to text. -2017-05-09 17:41:20,243 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:20,243 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:20,243 INFO [galaxy.model.migrate.check] Migrating 130 -> 131... -2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check] Migration script to support subworkflows and workflow request input parameters -2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check] Migrating 131 -> 132... -2017-05-09 17:41:21,054 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:21,055 INFO [galaxy.model.migrate.check] Migrating 132 -> 133... -2017-05-09 17:41:21,452 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:21,452 INFO [galaxy.model.migrate.check] Add dependencies column to jobs table -2017-05-09 17:41:21,452 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:21,452 INFO [galaxy.model.migrate.check] -2017-05-09 17:41:21,467 INFO [galaxy.config] Install database targetting Galaxy's database configuration. -2017-05-09 17:41:22,106 ERROR [galaxy.visualization.genomes] Error reading twobit.loc: [Errno 2] No such file or directory: '/tmp/tmpBnX6kx/galaxy-dev/tool-data/twobit.loc' -Traceback (most recent call last): - File "/tmp/tmpBnX6kx/galaxy-dev/lib/galaxy/visualization/genomes.py", line 210, in reload_genomes - for line in open( os.path.join( self.app.config.tool_data_path, "twobit.loc" ) ): -IOError: [Errno 2] No such file or directory: '/tmp/tmpBnX6kx/galaxy-dev/tool-data/twobit.loc' -2017-05-09 17:41:22,117 INFO [galaxy.jobs] Setting <handlers> default to child with id 'main' -2017-05-09 17:41:22,135 INFO [galaxy.tools.toolbox.watcher] Watchdog library unavailable, cannot monitor tools. -2017-05-09 17:41:22,135 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmpBnX6kx/tool_conf.xml -2017-05-09 17:41:22,146 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmpBnX6kx/shed_tools_conf.xml -2017-05-09 17:41:22,146 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmpBnX6kx/empty_tool_conf.xml -No handlers could be found for logger "galaxy.datatypes.display_applications.application" -2017-05-09 17:41:22,482 WARNI [galaxy.webhooks] directory not found: /tmp/tmpBnX6kx/galaxy-dev/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config -2017-05-09 17:41:22,492 INFO [galaxy.jobs] Handler 'main' will load all configured runner plugins -2017-05-09 17:41:22,497 INFO [galaxy.jobs.handler] job handler stop queue started -2017-05-09 17:41:22,505 INFO [galaxy.jobs.handler] job handler queue started -2017-05-09 17:41:23,279 INFO [galaxy.queue_worker] Binding and starting galaxy control worker for main -/home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. - 'storage.' % (dialect.name, dialect.driver)) -/home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. - 'strategies for improved performance.' % expr) -W4MClassFilter ( W4MClassFilter ) > Test-1 ... 2017-05-09 17:41:24,463 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 1 -2017-05-09 17:41:24,891 INFO [galaxy.jobs.handler] (1) Job dispatched -2017-05-09 17:41:25,164 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:25,165 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:25,198 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/1/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpFEU_uZ 1:/tmp/tmpBnX6kx/job_working_directory/000/1/dataset_1_files:/tmp/tmpBnX6kx/files/000/dataset_1.dat] -2017-05-09 17:41:25,365 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:25,366 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:29,174 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 2 -2017-05-09 17:41:30,112 INFO [galaxy.jobs.handler] (2) Job dispatched -2017-05-09 17:41:30,372 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:30,377 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:30,415 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/2/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmp819dTL 2:/tmp/tmpBnX6kx/job_working_directory/000/2/dataset_2_files:/tmp/tmpBnX6kx/files/000/dataset_2.dat] -2017-05-09 17:41:30,642 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:30,642 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:34,617 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 3 -2017-05-09 17:41:35,397 INFO [galaxy.jobs.handler] (3) Job dispatched -2017-05-09 17:41:35,661 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:35,661 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:35,707 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/3/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpOXdXDH 3:/tmp/tmpBnX6kx/job_working_directory/000/3/dataset_3_files:/tmp/tmpBnX6kx/files/000/dataset_3.dat] -2017-05-09 17:41:35,889 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:35,890 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:39,590 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (102.610 ms) -2017-05-09 17:41:39,630 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (39.109 ms) -2017-05-09 17:41:39,662 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (32.632 ms) -2017-05-09 17:41:39,694 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (31.837 ms) -2017-05-09 17:41:39,716 INFO [galaxy.tools.actions] Added output datasets to history (21.785 ms) -2017-05-09 17:41:39,760 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (23.849 ms) -2017-05-09 17:41:39,761 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (44.332 ms) -2017-05-09 17:41:39,795 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=4,tool_id=W4MClassFilter] (34.570 ms) -2017-05-09 17:41:40,615 INFO [galaxy.jobs.handler] (4) Job dispatched -2017-05-09 17:41:40,918 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda -2017-05-09 17:41:40,918 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda -2017-05-09 17:41:40,918 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda -2017-05-09 17:41:40,919 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda -2017-05-09 17:41:40,919 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda -2017-05-09 17:41:40,919 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda -2017-05-09 17:41:40,951 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/4/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; Rscript /home/backdoor/toolshed_test/w4mclassfilter/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmpBnX6kx/files/000/dataset_1.dat" sampleMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_2.dat" variableMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_3.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmpBnX6kx/files/000/dataset_4.dat" sampleMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_5.dat" variableMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_6.dat" information "/tmp/tmpBnX6kx/files/000/dataset_7.dat"] -2017-05-09 17:41:41,340 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:41,341 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -ok -W4MClassFilter ( W4MClassFilter ) > Test-2 ... 2017-05-09 17:41:47,453 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 5 -2017-05-09 17:41:47,929 INFO [galaxy.jobs.handler] (5) Job dispatched -2017-05-09 17:41:48,185 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:48,185 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:48,246 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/5/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpCJ6i2V 8:/tmp/tmpBnX6kx/job_working_directory/000/5/dataset_8_files:/tmp/tmpBnX6kx/files/000/dataset_8.dat] -2017-05-09 17:41:48,468 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:48,469 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:52,575 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 6 -2017-05-09 17:41:53,192 INFO [galaxy.jobs.handler] (6) Job dispatched -2017-05-09 17:41:53,442 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:53,444 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:53,484 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/6/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpTkRIU7 9:/tmp/tmpBnX6kx/job_working_directory/000/6/dataset_9_files:/tmp/tmpBnX6kx/files/000/dataset_9.dat] -2017-05-09 17:41:53,711 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:53,712 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:57,685 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 7 -2017-05-09 17:41:58,415 INFO [galaxy.jobs.handler] (7) Job dispatched -2017-05-09 17:41:58,668 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:58,669 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:58,718 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/7/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmppTa3ww 10:/tmp/tmpBnX6kx/job_working_directory/000/7/dataset_10_files:/tmp/tmpBnX6kx/files/000/dataset_10.dat] -2017-05-09 17:41:58,874 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:41:58,874 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:02,544 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (54.150 ms) -2017-05-09 17:42:02,576 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (32.411 ms) -2017-05-09 17:42:02,613 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (36.563 ms) -2017-05-09 17:42:02,660 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (46.442 ms) -2017-05-09 17:42:02,682 INFO [galaxy.tools.actions] Added output datasets to history (21.663 ms) -2017-05-09 17:42:02,732 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (25.405 ms) -2017-05-09 17:42:02,732 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (50.729 ms) -2017-05-09 17:42:02,766 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=8,tool_id=W4MClassFilter] (33.131 ms) -2017-05-09 17:42:03,604 INFO [galaxy.jobs.handler] (8) Job dispatched -2017-05-09 17:42:03,920 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda -2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda -2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda -2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda -2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda -2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda -2017-05-09 17:42:03,960 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/8/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; Rscript /home/backdoor/toolshed_test/w4mclassfilter/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmpBnX6kx/files/000/dataset_8.dat" sampleMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_9.dat" variableMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_10.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmpBnX6kx/files/000/dataset_11.dat" sampleMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_12.dat" variableMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_13.dat" information "/tmp/tmpBnX6kx/files/000/dataset_14.dat"] -2017-05-09 17:42:04,366 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:04,366 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -ok -W4MClassFilter ( W4MClassFilter ) > Test-3 ... 2017-05-09 17:42:10,658 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 9 -2017-05-09 17:42:10,906 INFO [galaxy.jobs.handler] (9) Job dispatched -2017-05-09 17:42:11,150 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:11,151 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:11,233 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/9/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmp0F7oAs 15:/tmp/tmpBnX6kx/job_working_directory/000/9/dataset_15_files:/tmp/tmpBnX6kx/files/000/dataset_15.dat] -2017-05-09 17:42:11,471 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:11,472 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:15,491 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 10 -2017-05-09 17:42:16,194 INFO [galaxy.jobs.handler] (10) Job dispatched -2017-05-09 17:42:16,447 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:16,448 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:16,485 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/10/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpmkABaW 16:/tmp/tmpBnX6kx/job_working_directory/000/10/dataset_16_files:/tmp/tmpBnX6kx/files/000/dataset_16.dat] -2017-05-09 17:42:16,649 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:16,650 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:20,509 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 11 -2017-05-09 17:42:21,426 INFO [galaxy.jobs.handler] (11) Job dispatched -2017-05-09 17:42:21,680 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:21,681 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:21,764 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/11/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpfEj6tV 17:/tmp/tmpBnX6kx/job_working_directory/000/11/dataset_17_files:/tmp/tmpBnX6kx/files/000/dataset_17.dat] -2017-05-09 17:42:21,991 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:21,991 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:25,709 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (34.677 ms) -2017-05-09 17:42:25,751 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (41.778 ms) -2017-05-09 17:42:25,784 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (32.888 ms) -2017-05-09 17:42:25,815 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (30.527 ms) -2017-05-09 17:42:25,838 INFO [galaxy.tools.actions] Added output datasets to history (22.886 ms) -2017-05-09 17:42:25,886 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (26.826 ms) -2017-05-09 17:42:25,887 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (48.981 ms) -2017-05-09 17:42:25,936 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=12,tool_id=W4MClassFilter] (48.570 ms) -2017-05-09 17:42:26,617 INFO [galaxy.jobs.handler] (12) Job dispatched -2017-05-09 17:42:26,893 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda -2017-05-09 17:42:26,900 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda -2017-05-09 17:42:26,902 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda -2017-05-09 17:42:26,903 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda -2017-05-09 17:42:26,903 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda -2017-05-09 17:42:26,903 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda -2017-05-09 17:42:26,955 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/12/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; Rscript /home/backdoor/toolshed_test/w4mclassfilter/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmpBnX6kx/files/000/dataset_15.dat" sampleMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_16.dat" variableMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_17.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmpBnX6kx/files/000/dataset_18.dat" sampleMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_19.dat" variableMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_20.dat" information "/tmp/tmpBnX6kx/files/000/dataset_21.dat"] -2017-05-09 17:42:27,374 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 17:42:27,375 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -ok - ----------------------------------------------------------------------- -XML: /tmp/tmpBnX6kx/xunit.xml ----------------------------------------------------------------------- -Ran 3 tests in 69.356s - -OK -2017-05-09 17:42:33,110 INFO [test_driver] Shutting down -2017-05-09 17:42:33,110 INFO [test_driver] Shutting down embedded galaxy web server -2017-05-09 17:42:33,112 INFO [test_driver] Embedded web server galaxy stopped -2017-05-09 17:42:33,112 INFO [test_driver] Stopping application galaxy -2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] sending stop signal to worker thread -2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] job handler queue stopped -2017-05-09 17:42:33,112 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads -2017-05-09 17:42:33,112 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads -2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] sending stop signal to worker thread -2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] job handler stop queue stopped -2017-05-09 17:42:33,113 INFO [test_driver] Application galaxy stopped. -2017-05-09 17:42:34,087 INFO [galaxy.jobs.handler] sending stop signal to worker thread -2017-05-09 17:42:34,088 INFO [galaxy.jobs.handler] job handler queue stopped -2017-05-09 17:42:34,088 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads -2017-05-09 17:42:34,089 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads -2017-05-09 17:42:34,089 INFO [galaxy.jobs.handler] sending stop signal to worker thread -2017-05-09 17:42:34,089 INFO [galaxy.jobs.handler] job handler stop queue stopped -Testing complete. HTML report is in "/home/backdoor/toolshed_test/w4mclassfilter/tool_test_output.html". -All 3 test(s) executed passed. -W4MClassFilter[0]: passed -W4MClassFilter[1]: passed -W4MClassFilter[2]: passed