| Previous changeset 2:9a3462eff3bf (2017-05-10) Next changeset 4:2495d0019dbe (2017-05-11) |
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Commit message:
Deleted selected files |
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removed:
test_log.txt |
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| diff -r 9a3462eff3bf -r dbe02bb33ae1 test_log.txt --- a/test_log.txt Wed May 10 10:19:28 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,334 +0,0 @@\n-git --git-dir /home/backdoor/.planemo/gx_repo fetch >/dev/null 2>&1\n-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}\n-Cloning into \'galaxy-dev\'...\n-done.\n-Set COMMON_STARTUP_ARGS to --dev-wheels\n-Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample\n-Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample\n-Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample\n-Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample\n-Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample\n-Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/backdoor/.planemo/gx_venv\n-Requirement already satisfied: pip>=8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages\n-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))\n-Requirement already satisfied: MarkupSafe==0.23 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3))\n-Requirement already satisfied: PyYAML==3.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))\n-Requirement already satisfied: SQLAlchemy==1.0.15 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))\n-Requirement already satisfied: mercurial==3.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6))\n-Requirement already satisfied: numpy==1.9.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7))\n-Requirement already satisfied: pycrypto==2.6.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))\n-Requirement already satisfied: Paste==2.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15))\n-Requirement already satisfied: PasteDeploy==1.5.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16))\n-Requirement already satisfied: docutils==0.12 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17))\n-Requirement already satisfied: wchartype==0.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18))\n-Requirement already satisfied: repoze.lru==0.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19))\n-Requirement already satisfied: Routes==2.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20))\n-Requirement already satisfied: WebOb==1.4.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21))\n-Requirement already satisfied: WebHelpers==1.3 in /home/backdoor/.planemo/'..b',903 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda\n-2017-05-09 17:42:26,903 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda\n-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"]\n-2017-05-09 17:42:27,374 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda\n-2017-05-09 17:42:27,375 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda\n-ok\n-\n-----------------------------------------------------------------------\n-XML: /tmp/tmpBnX6kx/xunit.xml\n-----------------------------------------------------------------------\n-Ran 3 tests in 69.356s\n-\n-OK\n-2017-05-09 17:42:33,110 INFO [test_driver] Shutting down\n-2017-05-09 17:42:33,110 INFO [test_driver] Shutting down embedded galaxy web server\n-2017-05-09 17:42:33,112 INFO [test_driver] Embedded web server galaxy stopped\n-2017-05-09 17:42:33,112 INFO [test_driver] Stopping application galaxy\n-2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n-2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] job handler queue stopped\n-2017-05-09 17:42:33,112 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads\n-2017-05-09 17:42:33,112 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads\n-2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n-2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] job handler stop queue stopped\n-2017-05-09 17:42:33,113 INFO [test_driver] Application galaxy stopped.\n-2017-05-09 17:42:34,087 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n-2017-05-09 17:42:34,088 INFO [galaxy.jobs.handler] job handler queue stopped\n-2017-05-09 17:42:34,088 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads\n-2017-05-09 17:42:34,089 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads\n-2017-05-09 17:42:34,089 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n-2017-05-09 17:42:34,089 INFO [galaxy.jobs.handler] job handler stop queue stopped\n-Testing complete. HTML report is in "/home/backdoor/toolshed_test/w4mclassfilter/tool_test_output.html".\n-All 3 test(s) executed passed.\n-W4MClassFilter[0]: passed\n-W4MClassFilter[1]: passed\n-W4MClassFilter[2]: passed\n' |