Mercurial > repos > eschen42 > w4mclassfilter
changeset 1:371741d19743 draft
Deleted selected files
| author | eschen42 |
|---|---|
| date | Tue, 09 May 2017 18:37:51 -0400 |
| parents | bab3a658f74e |
| children | 23c6d271def9 |
| files | planemo_install_history.txt planemo_shed_init.sh run_test.sh test-data/output_dataMatrix.tsv test-data/output_sampleMetadata.tsv test-data/output_variableMetadata.tsv test_log.txt |
| diffstat | 7 files changed, 0 insertions(+), 499 deletions(-) [+] |
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--- a/planemo_install_history.txt Tue May 09 18:34:35 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -#!/bin/bash - -# abridged transcript of the steps that I used to test this wrapper - -ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install)" - -sudo apt-get install build-essential - -cat >> ~/.bashrc << . -# ACE -export PATH="/home/backdoor/.linuxbrew/bin:$PATH" -export MANPATH="/home/backdoor/.linuxbrew/share/man:$MANPATH" -export INFOPATH="/home/backdoor/.linuxbrew/share/info:$INFOPATH" -. - -brew update -brew install python -brew tap galaxyproject/tap -brew install planemo - -git clone https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper.git -cd w4mclassfilter_galaxy_wrapper/ - -./run_test.sh
--- a/planemo_shed_init.sh Tue May 09 18:34:35 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -#!/bin/bash -planemo shed_init --name=w4mclassfilter \ - --owner=eschen42 \ - --description="Filter W4M data files by class" \ - --homepage_url=https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper \ - --long_description="Filter Workflow4Metabolomics data matrix and metadata by sample-class" \ - --remote_repository_url="https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper" \ - --category="Metabolomics" - -# [--remote_repository_url=<URL to .shed.yml on github>] \
--- a/run_test.sh Tue May 09 18:34:35 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#!/bin/bash - -# purge old output files -if [ -f test_log.txt ]; then rm test_log.txt; fi -if [ -f tool_test_output.html ]; then rm tool_test_output.html; fi -if [ -f tool_test_output.json ]; then rm tool_test_output.json; fi - -# run test and write new output files, showing progress to command line output -planemo conda_install . -planemo test --conda_dependency_resolution w4mclassfilter.xml 2>&1 | grep -v -i observer | tee test_log.txt - -# summarize warnings and errors to command line output -grep -E "(ERROR)|(WARNING)" test_log.txt | grep -v samtools | grep -v "Dynamic Display Application links" | grep -v "twobit.loc"
--- a/test-data/output_dataMatrix.tsv Tue May 09 18:34:35 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ - HU_017 HU_034 HU_078 HU_091 HU_093 HU_099 HU_130 HU_134 HU_138 -HMDB03193 76043 44943 173175 242549 57066 559869 339188 471368 262271 -HMDB01101 30689 52217 229568 4763576 3878773 976436 608298 1605075 72021 -HMDB01101.1 6877586 3158 4763576 3878773 976436 831937 1605075 72021 442510 -HMDB10348 47259 60885 168264 176500 76457 610110 279156 524468 451573 -HMDB59717 357351 301983 1028110 1530493 270027 1378535 808334 1132813 871209 -HMDB13189 2644620 1661412 2755434 593863 837865 3526136 1608814 3446611 1941527 -HMDB00299 250551 456162 808657 614370 250403 768004 504108 1014041 1362408 -HMDB00191 560002 575790 785428 645785 591569 960658 639437 1092885 1409045 -HMDB00518 0 85944 129886 175800 13154 230242 440223 315368 10657 -HMDB00715 1252089 905408 5140022 2658555 814523 2558923 4184204 3865723 3236644 -HMDB01032 2569205 1604999 26222916 257139 675754 59906109 31151730 18648127 14989438 -HMDB00208 747080 595872 3143654 4059767 1433702 5593888 2477288 3346077 4230072 -HMDB04824 374028 539206 959381 605191 310260 1253319 477995 825691 1157093 -HMDB00512 0 280560 556003 590779 209285 342532 569970 525240 246282 -HMDB00251 368600 94936 293988 352855 767894 268331 310918 1248919 577184
--- a/test-data/output_sampleMetadata.tsv Tue May 09 18:34:35 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -sampleMetadata injectionOrder mode age bmi gender -HU_017 2 pos 41 23.03 M -HU_034 9 pos 52 23.37 M -HU_078 34 pos 46 25.18 M -HU_091 42 pos 61 26.12 M -HU_093 43 pos 53 21.71 M -HU_099 46 pos 23 21.3 M -HU_130 63 pos 33 26.06 M -HU_134 67 pos 48 22.89 M -HU_138 68 pos 42 21.88 M
--- a/test-data/output_variableMetadata.tsv Tue May 09 18:34:35 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -variableMetadata name -HMDB03193 Testosterone_glucuronide -HMDB01101 p-Anisic_acid -HMDB01101.1 p-Anisic_acid_2 -HMDB10348 Dehydroepiandrosterone_3-glucuronide -HMDB59717 Glu-Val -HMDB13189 3-Indole_carboxylic_acid_glucuronide -HMDB00299 Xanthosine -HMDB00191 L-Aspartic_acid -HMDB00518 Chenodeoxycholic_acid -HMDB00715 Kynurenic_acid -HMDB01032 Dehydroepiandrosterone_sulfate -HMDB00208 Oxoglutaric_acid -HMDB04824 N2,N2-Dimethylguanosine -HMDB00512 N-Acetyl-L-phenylalanine -HMDB00251 Taurine
--- a/test_log.txt Tue May 09 18:34:35 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,410 +0,0 @@ -git clone --bare 'https://github.com/galaxyproject/galaxy' '/home/backdoor/.planemo/gx_repo' -Cloning into bare repository '/home/backdoor/.planemo/gx_repo'... -cd /tmp/tmp4Jz5Zv; 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. -New python executable in /home/backdoor/.planemo/gx_venv/bin/python2.7 -Also creating executable in /home/backdoor/.planemo/gx_venv/bin/python -Installing setuptools, pip, wheel...done. -Running virtualenv with interpreter /home/backdoor/.linuxbrew/bin/python2.7 -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 -Collecting pip>=8.1 - Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB) -Installing collected packages: pip - Found existing installation: pip 7.1.2 - Uninstalling pip-7.1.2: - Successfully uninstalled pip-7.1.2 -Successfully installed pip-9.0.1 -Collecting bx-python==0.7.3 (from -r requirements.txt (line 2)) - Downloading https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27m-manylinux1_x86_64.whl (2.1MB) -Collecting MarkupSafe==0.23 (from -r requirements.txt (line 3)) - Downloading https://wheels.galaxyproject.org/packages/MarkupSafe-0.23-cp27-cp27m-manylinux1_x86_64.whl -Collecting PyYAML==3.11 (from -r requirements.txt (line 4)) - Downloading https://wheels.galaxyproject.org/packages/PyYAML-3.11-cp27-cp27m-manylinux1_x86_64.whl (367kB) -Collecting SQLAlchemy==1.0.15 (from -r requirements.txt (line 5)) - Downloading https://wheels.galaxyproject.org/packages/SQLAlchemy-1.0.15-cp27-cp27m-manylinux1_x86_64.whl (1.0MB) -Collecting mercurial==3.7.3 (from -r requirements.txt (line 6)) - Downloading https://wheels.galaxyproject.org/packages/mercurial-3.7.3-cp27-cp27m-manylinux1_x86_64.whl (1.5MB) -Collecting numpy==1.9.2 (from -r requirements.txt (line 7)) - Downloading https://wheels.galaxyproject.org/packages/numpy-1.9.2-cp27-cp27m-manylinux1_x86_64.whl (10.2MB) -Collecting pycrypto==2.6.1 (from -r requirements.txt (line 8)) - Downloading https://wheels.galaxyproject.org/packages/pycrypto-2.6.1-cp27-cp27m-manylinux1_x86_64.whl (492kB) -Collecting Paste==2.0.2 (from -r requirements.txt (line 15)) - Downloading https://wheels.galaxyproject.org/packages/Paste-2.0.2-py2-none-any.whl (610kB) -Collecting PasteDeploy==1.5.2 (from -r requirements.txt (line 16)) - Downloading https://wheels.galaxyproject.org/packages/PasteDeploy-1.5.2-py2.py3-none-any.whl -Collecting docutils==0.12 (from -r requirements.txt (line 17)) - Downloading https://wheels.galaxyproject.org/packages/docutils-0.12-py2-none-any.whl (509kB) -Collecting wchartype==0.1 (from -r requirements.txt (line 18)) - Downloading https://wheels.galaxyproject.org/packages/wchartype-0.1-py2-none-any.whl -Collecting repoze.lru==0.6 (from -r requirements.txt (line 19)) - Downloading repoze.lru-0.6.tar.gz -Collecting Routes==2.2 (from -r requirements.txt (line 20)) - Downloading https://wheels.galaxyproject.org/packages/Routes-2.2-py2-none-any.whl (46kB) -Collecting WebOb==1.4.1 (from -r requirements.txt (line 21)) - Downloading https://wheels.galaxyproject.org/packages/WebOb-1.4.1-py2.py3-none-any.whl (73kB) -Collecting WebHelpers==1.3 (from -r requirements.txt (line 22)) - Downloading https://wheels.galaxyproject.org/packages/WebHelpers-1.3-py2-none-any.whl (149kB) -Collecting Mako==1.0.2 (from -r requirements.txt (line 23)) - Downloading https://wheels.galaxyproject.org/packages/Mako-1.0.2-py2-none-any.whl (76kB) -Collecting pytz==2015.4 (from -r requirements.txt (line 24)) - Downloading https://wheels.galaxyproject.org/packages/pytz-2015.4-py2-none-any.whl (475kB) -Collecting Babel==2.0 (from -r requirements.txt (line 25)) - Downloading https://wheels.galaxyproject.org/packages/Babel-2.0-py2-none-any.whl (3.6MB) -Collecting Beaker==1.7.0 (from -r requirements.txt (line 26)) - Downloading https://wheels.galaxyproject.org/packages/Beaker-1.7.0-py2-none-any.whl (44kB) -Collecting dictobj==0.3.1 (from -r requirements.txt (line 27)) - Downloading https://wheels.galaxyproject.org/packages/dictobj-0.3.1-py2-none-any.whl -Collecting nose==1.3.7 (from -r requirements.txt (line 28)) - Downloading https://wheels.galaxyproject.org/packages/nose-1.3.7-py2-none-any.whl (154kB) -Collecting Parsley==1.3 (from -r requirements.txt (line 29)) - Downloading https://wheels.galaxyproject.org/packages/Parsley-1.3-py2-none-any.whl (88kB) -Collecting six==1.10.0 (from -r requirements.txt (line 30)) - Downloading https://wheels.galaxyproject.org/packages/six-1.10.0-py2.py3-none-any.whl -Collecting Whoosh==2.7.4 (from -r requirements.txt (line 31)) - Downloading https://wheels.galaxyproject.org/packages/Whoosh-2.7.4-py2.py3-none-any.whl (468kB) -Collecting testfixtures==4.10.0 (from -r requirements.txt (line 32)) - Downloading testfixtures-4.10.0-py2.py3-none-any.whl (73kB) -Collecting galaxy_sequence_utils==1.0.2 (from -r requirements.txt (line 33)) - Downloading https://wheels.galaxyproject.org/packages/galaxy_sequence_utils-1.0.2-py2.py3-none-any.whl -Collecting Cheetah==2.4.4 (from -r requirements.txt (line 36)) - Downloading https://wheels.galaxyproject.org/packages/Cheetah-2.4.4-cp27-cp27m-manylinux1_x86_64.whl (193kB) -Collecting Markdown==2.6.3 (from -r requirements.txt (line 37)) - Downloading https://wheels.galaxyproject.org/packages/Markdown-2.6.3-py2-none-any.whl (158kB) -Collecting bioblend==0.7.0 (from -r requirements.txt (line 40)) - Downloading https://wheels.galaxyproject.org/packages/bioblend-0.7.0-py2.py3-none-any.whl (82kB) -Collecting boto==2.38.0 (from -r requirements.txt (line 41)) - Downloading https://wheels.galaxyproject.org/packages/boto-2.38.0-py2.py3-none-any.whl (1.3MB) -Collecting requests==2.8.1 (from -r requirements.txt (line 42)) - Downloading https://wheels.galaxyproject.org/packages/requests-2.8.1-py2.py3-none-any.whl (497kB) -Collecting requests-toolbelt==0.4.0 (from -r requirements.txt (line 43)) - Downloading https://wheels.galaxyproject.org/packages/requests_toolbelt-0.4.0-py2.py3-none-any.whl -Collecting kombu==3.0.30 (from -r requirements.txt (line 46)) - Downloading https://wheels.galaxyproject.org/packages/kombu-3.0.30-py2.py3-none-any.whl (241kB) -Collecting amqp==1.4.8 (from -r requirements.txt (line 47)) - Downloading https://wheels.galaxyproject.org/packages/amqp-1.4.8-py2.py3-none-any.whl (51kB) -Collecting anyjson==0.3.3 (from -r requirements.txt (line 48)) - Downloading https://wheels.galaxyproject.org/packages/anyjson-0.3.3-py2-none-any.whl -Collecting psutil==4.1.0 (from -r requirements.txt (line 51)) - Downloading https://wheels.galaxyproject.org/packages/psutil-4.1.0-cp27-cp27m-manylinux1_x86_64.whl (168kB) -Collecting pulsar-galaxy-lib==0.7.0.dev5 (from -r requirements.txt (line 52)) - Downloading https://wheels.galaxyproject.org/packages/pulsar_galaxy_lib-0.7.0.dev5-py2-none-any.whl (160kB) -Collecting sqlalchemy-migrate==0.10.0 (from -r requirements.txt (line 55)) - Downloading https://wheels.galaxyproject.org/packages/sqlalchemy_migrate-0.10.0-py2-none-any.whl (108kB) -Collecting decorator==4.0.2 (from -r requirements.txt (line 56)) - Downloading https://wheels.galaxyproject.org/packages/decorator-4.0.2-py2.py3-none-any.whl -Collecting Tempita==0.5.3dev (from -r requirements.txt (line 57)) - Downloading https://wheels.galaxyproject.org/packages/Tempita-0.5.3.dev0-py2-none-any.whl -Collecting sqlparse==0.1.16 (from -r requirements.txt (line 58)) - Downloading https://wheels.galaxyproject.org/packages/sqlparse-0.1.16-py2-none-any.whl -Collecting pbr==1.8.0 (from -r requirements.txt (line 59)) - Downloading https://wheels.galaxyproject.org/packages/pbr-1.8.0-py2.py3-none-any.whl (87kB) -Collecting svgwrite==1.1.6 (from -r requirements.txt (line 62)) - Downloading https://wheels.galaxyproject.org/packages/svgwrite-1.1.6-py2-none-any.whl (62kB) -Collecting pyparsing==2.1.1 (from -r requirements.txt (line 63)) - Downloading https://wheels.galaxyproject.org/packages/pyparsing-2.1.1-py2.py3-none-any.whl -Collecting Fabric==1.10.2 (from -r requirements.txt (line 66)) - Downloading https://wheels.galaxyproject.org/packages/Fabric-1.10.2-py2-none-any.whl (90kB) -Collecting paramiko==1.15.2 (from -r requirements.txt (line 67)) - Downloading https://wheels.galaxyproject.org/packages/paramiko-1.15.2-py2.py3-none-any.whl (165kB) -Collecting ecdsa==0.13 (from -r requirements.txt (line 68)) - Downloading https://wheels.galaxyproject.org/packages/ecdsa-0.13-py2.py3-none-any.whl (44kB) -Collecting pysam==0.8.4+gx5 (from -r requirements.txt (line 71)) - Downloading https://wheels.galaxyproject.org/packages/pysam-0.8.4+gx5-cp27-cp27m-manylinux1_x86_64.whl (11.8MB) -Collecting PasteScript (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 52)) - Downloading PasteScript-2.0.2-py2.py3-none-any.whl (74kB) -Building wheels for collected packages: repoze.lru - Running setup.py bdist_wheel for repoze.lru: started - Running setup.py bdist_wheel for repoze.lru: finished with status 'done' - Stored in directory: /home/backdoor/.cache/pip/wheels/b2/cd/b3/7e24400bff83325a01d492940eff6e9579f553f33348323d79 -Successfully built repoze.lru -Installing collected packages: bx-python, MarkupSafe, PyYAML, SQLAlchemy, mercurial, numpy, pycrypto, six, Paste, PasteDeploy, docutils, wchartype, repoze.lru, Routes, WebOb, WebHelpers, Mako, pytz, Babel, Beaker, dictobj, nose, Parsley, Whoosh, testfixtures, galaxy-sequence-utils, Markdown, Cheetah, boto, requests, requests-toolbelt, bioblend, anyjson, amqp, kombu, psutil, PasteScript, pulsar-galaxy-lib, pbr, Tempita, decorator, sqlparse, sqlalchemy-migrate, pyparsing, svgwrite, ecdsa, paramiko, Fabric, pysam -Successfully installed Babel-2.0 Beaker-1.7.0 Cheetah-2.4.4 Fabric-1.10.2 Mako-1.0.2 Markdown-2.6.3 MarkupSafe-0.23 Parsley-1.3 Paste-2.0.2 PasteDeploy-1.5.2 PasteScript-2.0.2 PyYAML-3.11 Routes-2.2 SQLAlchemy-1.0.15 Tempita-0.5.3.dev0 WebHelpers-1.3 WebOb-1.4.1 Whoosh-2.7.4 amqp-1.4.8 anyjson-0.3.3 bioblend-0.7.0 boto-2.38.0 bx-python-0.7.3 decorator-4.0.2 dictobj-0.3.1 docutils-0.12 ecdsa-0.13 galaxy-sequence-utils-1.0.2 kombu-3.0.30 mercurial-3.7.3 nose-1.3.7 numpy-1.9.2 paramiko-1.15.2 pbr-1.8.0 psutil-4.1.0 pulsar-galaxy-lib-0.7.0.dev5 pycrypto-2.6.1 pyparsing-2.1.1 pysam-0.8.4+gx5 pytz-2015.4 repoze.lru-0.6 requests-2.8.1 requests-toolbelt-0.4.0 six-1.10.0 sqlalchemy-migrate-0.10.0 sqlparse-0.1.16 svgwrite-1.1.6 testfixtures-4.10.0 wchartype-0.1 -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)) -Collecting NoseHTML (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2)) - Downloading NoseHTML-0.4.2-py2-none-any.whl -Collecting twill==0.9.1 (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) - Downloading https://wheels.galaxyproject.org/packages/twill-0.9.1-py2-none-any.whl (203kB) -Collecting mock (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) - Downloading mock-2.0.0-py2.py3-none-any.whl (56kB) -Collecting selenium (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) - Downloading https://wheels.galaxyproject.org/packages/selenium-3.0.1-py2.py3-none-any.whl (913kB) -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)) -Collecting funcsigs>=1; python_version < "3.3" (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) - Downloading funcsigs-1.0.2-py2.py3-none-any.whl -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)) -Installing collected packages: NoseHTML, twill, funcsigs, mock, selenium -Successfully installed NoseHTML-0.4.2 funcsigs-1.0.2 mock-2.0.0 selenium-3.0.1 twill-0.9.1 -Testing using galaxy_root /tmp/tmp4Jz5Zv/galaxy-dev -Testing tools with command [cd /tmp/tmp4Jz5Zv/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/w4mclassfilter_galaxy_wrapper/tool_test_output.html --xunit_report_file /tmp/tmp4Jz5Zv/xunit.xml --structured_data_report_file /home/backdoor/w4mclassfilter_galaxy_wrapper/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 15:52:58,568 INFO [galaxy.queue_worker] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:// -2017-05-09 15:52:58,717 INFO [galaxy.model.migrate.check] Migrating 127 -> 128... -2017-05-09 15:52:59,159 INFO [galaxy.model.migrate.check] -2017-05-09 15:52:59,159 INFO [galaxy.model.migrate.check] Migration script to add session update time (used for timeouts) -2017-05-09 15:52:59,159 INFO [galaxy.model.migrate.check] -2017-05-09 15:52:59,159 INFO [galaxy.model.migrate.check] -2017-05-09 15:52:59,160 INFO [galaxy.model.migrate.check] Migrating 128 -> 129... -2017-05-09 15:52:59,576 INFO [galaxy.model.migrate.check] -2017-05-09 15:52:59,576 INFO [galaxy.model.migrate.check] Migration script to allow invalidation of job external output metadata temp files -2017-05-09 15:52:59,576 INFO [galaxy.model.migrate.check] -2017-05-09 15:52:59,576 INFO [galaxy.model.migrate.check] -2017-05-09 15:52:59,576 INFO [galaxy.model.migrate.check] Migrating 129 -> 130... -2017-05-09 15:53:00,112 INFO [galaxy.model.migrate.check] -2017-05-09 15:53:00,112 INFO [galaxy.model.migrate.check] Migration script to change the value column of user_preference from varchar to text. -2017-05-09 15:53:00,112 INFO [galaxy.model.migrate.check] -2017-05-09 15:53:00,112 INFO [galaxy.model.migrate.check] -2017-05-09 15:53:00,112 INFO [galaxy.model.migrate.check] Migrating 130 -> 131... -2017-05-09 15:53:00,885 INFO [galaxy.model.migrate.check] -2017-05-09 15:53:00,885 INFO [galaxy.model.migrate.check] Migration script to support subworkflows and workflow request input parameters -2017-05-09 15:53:00,885 INFO [galaxy.model.migrate.check] -2017-05-09 15:53:00,885 INFO [galaxy.model.migrate.check] -2017-05-09 15:53:00,885 INFO [galaxy.model.migrate.check] Migrating 131 -> 132... -2017-05-09 15:53:00,932 INFO [galaxy.model.migrate.check] -2017-05-09 15:53:00,932 INFO [galaxy.model.migrate.check] Migrating 132 -> 133... -2017-05-09 15:53:01,340 INFO [galaxy.model.migrate.check] -2017-05-09 15:53:01,340 INFO [galaxy.model.migrate.check] Add dependencies column to jobs table -2017-05-09 15:53:01,340 INFO [galaxy.model.migrate.check] -2017-05-09 15:53:01,340 INFO [galaxy.model.migrate.check] -2017-05-09 15:53:01,357 INFO [galaxy.config] Install database targetting Galaxy's database configuration. -2017-05-09 15:53:02,016 ERROR [galaxy.visualization.genomes] Error reading twobit.loc: [Errno 2] No such file or directory: '/tmp/tmp4Jz5Zv/galaxy-dev/tool-data/twobit.loc' -Traceback (most recent call last): - File "/tmp/tmp4Jz5Zv/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/tmp4Jz5Zv/galaxy-dev/tool-data/twobit.loc' -2017-05-09 15:53:02,027 INFO [galaxy.jobs] Setting <handlers> default to child with id 'main' -2017-05-09 15:53:02,045 INFO [galaxy.tools.toolbox.watcher] Watchdog library unavailable, cannot monitor tools. -2017-05-09 15:53:02,045 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp4Jz5Zv/tool_conf.xml -2017-05-09 15:53:02,056 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp4Jz5Zv/shed_tools_conf.xml -2017-05-09 15:53:02,057 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp4Jz5Zv/empty_tool_conf.xml -No handlers could be found for logger "galaxy.datatypes.display_applications.application" -2017-05-09 15:53:02,392 WARNI [galaxy.webhooks] directory not found: /tmp/tmp4Jz5Zv/galaxy-dev/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config -2017-05-09 15:53:02,402 INFO [galaxy.jobs] Handler 'main' will load all configured runner plugins -2017-05-09 15:53:02,408 INFO [galaxy.jobs.handler] job handler stop queue started -2017-05-09 15:53:02,419 INFO [galaxy.jobs.handler] job handler queue started -2017-05-09 15:53:03,184 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 15:53:04,374 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 1 -2017-05-09 15:53:04,877 INFO [galaxy.jobs.handler] (1) Job dispatched -2017-05-09 15:53:05,148 DEBUG [galaxy.tools.deps.conda_util] Executing command: /home/backdoor/miniconda2/bin/conda create -y --name __samtools@1.3.1 samtools=1.3.1 -2017-05-09 15:53:11,359 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:11,361 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:11,415 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/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/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpJkw_yw 1:/tmp/tmp4Jz5Zv/job_working_directory/000/1/dataset_1_files:/tmp/tmp4Jz5Zv/files/000/dataset_1.dat] -2017-05-09 15:53:11,591 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:11,591 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:15,598 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 2 -2017-05-09 15:53:16,226 INFO [galaxy.jobs.handler] (2) Job dispatched -2017-05-09 15:53:16,481 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:16,483 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:16,521 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/2/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpytFdxz 2:/tmp/tmp4Jz5Zv/job_working_directory/000/2/dataset_2_files:/tmp/tmp4Jz5Zv/files/000/dataset_2.dat] -2017-05-09 15:53:16,678 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:16,678 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:20,584 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 3 -2017-05-09 15:53:21,476 INFO [galaxy.jobs.handler] (3) Job dispatched -2017-05-09 15:53:21,731 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:21,732 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:21,815 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/3/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpnOpUXZ 3:/tmp/tmp4Jz5Zv/job_working_directory/000/3/dataset_3_files:/tmp/tmp4Jz5Zv/files/000/dataset_3.dat] -2017-05-09 15:53:22,056 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:22,057 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:25,797 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (34.243 ms) -2017-05-09 15:53:25,853 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (55.183 ms) -2017-05-09 15:53:25,891 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (38.127 ms) -2017-05-09 15:53:25,924 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (32.700 ms) -2017-05-09 15:53:25,944 INFO [galaxy.tools.actions] Added output datasets to history (20.286 ms) -2017-05-09 15:53:25,996 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (32.287 ms) -2017-05-09 15:53:25,996 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (52.038 ms) -2017-05-09 15:53:26,036 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=4,tool_id=W4MClassFilter] (39.310 ms) -2017-05-09 15:53:26,653 INFO [galaxy.jobs.handler] (4) Job dispatched -2017-05-09 15:53:26,888 DEBUG [galaxy.tools.deps.conda_util] Executing command: /home/backdoor/miniconda2/bin/conda create -y --name mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4 r-base=3.3.1 r-batch=1.1_4 w4mclassfilter=0.98.1 -2017-05-09 15:53:32,394 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda -2017-05-09 15:53:32,394 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda -2017-05-09 15:53:32,394 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda -2017-05-09 15:53:32,394 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda -2017-05-09 15:53:32,394 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda -2017-05-09 15:53:32,394 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda -2017-05-09 15:53:32,483 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/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 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; Rscript /home/backdoor/w4mclassfilter_galaxy_wrapper/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmp4Jz5Zv/files/000/dataset_1.dat" sampleMetadata_in "/tmp/tmp4Jz5Zv/files/000/dataset_2.dat" variableMetadata_in "/tmp/tmp4Jz5Zv/files/000/dataset_3.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmp4Jz5Zv/files/000/dataset_4.dat" sampleMetadata_out "/tmp/tmp4Jz5Zv/files/000/dataset_5.dat" variableMetadata_out "/tmp/tmp4Jz5Zv/files/000/dataset_6.dat" information "/tmp/tmp4Jz5Zv/files/000/dataset_7.dat"] -2017-05-09 15:53:33,012 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:33,013 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -ok -W4MClassFilter ( W4MClassFilter ) > Test-2 ... 2017-05-09 15:53:40,192 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 5 -2017-05-09 15:53:41,186 INFO [galaxy.jobs.handler] (5) Job dispatched -2017-05-09 15:53:41,438 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:41,439 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:41,474 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/5/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpzHo4ws 8:/tmp/tmp4Jz5Zv/job_working_directory/000/5/dataset_8_files:/tmp/tmp4Jz5Zv/files/000/dataset_8.dat] -2017-05-09 15:53:41,652 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:41,652 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:45,610 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 6 -2017-05-09 15:53:46,393 INFO [galaxy.jobs.handler] (6) Job dispatched -2017-05-09 15:53:46,638 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:46,645 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:46,690 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/6/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpWL9Sp3 9:/tmp/tmp4Jz5Zv/job_working_directory/000/6/dataset_9_files:/tmp/tmp4Jz5Zv/files/000/dataset_9.dat] -2017-05-09 15:53:46,917 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:46,918 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:50,908 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 7 -2017-05-09 15:53:51,594 INFO [galaxy.jobs.handler] (7) Job dispatched -2017-05-09 15:53:51,849 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:51,849 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:51,902 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/7/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpmj2ueZ 10:/tmp/tmp4Jz5Zv/job_working_directory/000/7/dataset_10_files:/tmp/tmp4Jz5Zv/files/000/dataset_10.dat] -2017-05-09 15:53:52,065 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:52,066 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:55,798 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (36.686 ms) -2017-05-09 15:53:55,828 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (30.091 ms) -2017-05-09 15:53:55,860 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (31.485 ms) -2017-05-09 15:53:55,895 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (35.815 ms) -2017-05-09 15:53:55,918 INFO [galaxy.tools.actions] Added output datasets to history (22.862 ms) -2017-05-09 15:53:55,962 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (24.036 ms) -2017-05-09 15:53:55,963 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (44.286 ms) -2017-05-09 15:53:56,001 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=8,tool_id=W4MClassFilter] (37.669 ms) -2017-05-09 15:53:56,817 INFO [galaxy.jobs.handler] (8) Job dispatched -2017-05-09 15:53:57,142 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda -2017-05-09 15:53:57,142 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda -2017-05-09 15:53:57,142 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda -2017-05-09 15:53:57,142 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda -2017-05-09 15:53:57,142 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda -2017-05-09 15:53:57,142 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda -2017-05-09 15:53:57,179 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/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 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; Rscript /home/backdoor/w4mclassfilter_galaxy_wrapper/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmp4Jz5Zv/files/000/dataset_8.dat" sampleMetadata_in "/tmp/tmp4Jz5Zv/files/000/dataset_9.dat" variableMetadata_in "/tmp/tmp4Jz5Zv/files/000/dataset_10.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmp4Jz5Zv/files/000/dataset_11.dat" sampleMetadata_out "/tmp/tmp4Jz5Zv/files/000/dataset_12.dat" variableMetadata_out "/tmp/tmp4Jz5Zv/files/000/dataset_13.dat" information "/tmp/tmp4Jz5Zv/files/000/dataset_14.dat"] -2017-05-09 15:53:57,599 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:53:57,599 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -ok -W4MClassFilter ( W4MClassFilter ) > Test-3 ... 2017-05-09 15:54:03,918 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 9 -2017-05-09 15:54:05,128 INFO [galaxy.jobs.handler] (9) Job dispatched -2017-05-09 15:54:05,380 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:54:05,381 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:54:05,422 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/9/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmp4WoSDp 15:/tmp/tmp4Jz5Zv/job_working_directory/000/9/dataset_15_files:/tmp/tmp4Jz5Zv/files/000/dataset_15.dat] -2017-05-09 15:54:05,591 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:54:05,592 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:54:09,490 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 10 -2017-05-09 15:54:10,366 INFO [galaxy.jobs.handler] (10) Job dispatched -2017-05-09 15:54:10,613 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:54:10,615 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:54:10,658 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/10/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpGDoAhy 16:/tmp/tmp4Jz5Zv/job_working_directory/000/10/dataset_16_files:/tmp/tmp4Jz5Zv/files/000/dataset_16.dat] -2017-05-09 15:54:10,844 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:54:10,844 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:54:14,773 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 11 -2017-05-09 15:54:15,569 INFO [galaxy.jobs.handler] (11) Job dispatched -2017-05-09 15:54:15,834 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:54:15,834 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:54:15,923 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/11/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpmnqkmg 17:/tmp/tmp4Jz5Zv/job_working_directory/000/11/dataset_17_files:/tmp/tmp4Jz5Zv/files/000/dataset_17.dat] -2017-05-09 15:54:16,158 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:54:16,158 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:54:19,917 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (55.485 ms) -2017-05-09 15:54:19,960 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (43.180 ms) -2017-05-09 15:54:19,995 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (34.516 ms) -2017-05-09 15:54:20,036 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (40.337 ms) -2017-05-09 15:54:20,062 INFO [galaxy.tools.actions] Added output datasets to history (26.650 ms) -2017-05-09 15:54:20,115 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (28.845 ms) -2017-05-09 15:54:20,116 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (52.996 ms) -2017-05-09 15:54:20,153 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=12,tool_id=W4MClassFilter] (37.779 ms) -2017-05-09 15:54:20,742 INFO [galaxy.jobs.handler] (12) Job dispatched -2017-05-09 15:54:20,961 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda -2017-05-09 15:54:20,961 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda -2017-05-09 15:54:20,961 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda -2017-05-09 15:54:20,961 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda -2017-05-09 15:54:20,961 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda -2017-05-09 15:54:20,961 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda -2017-05-09 15:54:21,013 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/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/w4mclassfilter_galaxy_wrapper/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmp4Jz5Zv/files/000/dataset_15.dat" sampleMetadata_in "/tmp/tmp4Jz5Zv/files/000/dataset_16.dat" variableMetadata_in "/tmp/tmp4Jz5Zv/files/000/dataset_17.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmp4Jz5Zv/files/000/dataset_18.dat" sampleMetadata_out "/tmp/tmp4Jz5Zv/files/000/dataset_19.dat" variableMetadata_out "/tmp/tmp4Jz5Zv/files/000/dataset_20.dat" information "/tmp/tmp4Jz5Zv/files/000/dataset_21.dat"] -2017-05-09 15:54:21,503 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -2017-05-09 15:54:21,503 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda -ok - ----------------------------------------------------------------------- -XML: /tmp/tmp4Jz5Zv/xunit.xml ----------------------------------------------------------------------- -Ran 3 tests in 83.693s - -OK -2017-05-09 15:54:27,359 INFO [test_driver] Shutting down -2017-05-09 15:54:27,359 INFO [test_driver] Shutting down embedded galaxy web server -2017-05-09 15:54:27,361 INFO [test_driver] Embedded web server galaxy stopped -2017-05-09 15:54:27,361 INFO [test_driver] Stopping application galaxy -2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] sending stop signal to worker thread -2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] job handler queue stopped -2017-05-09 15:54:27,361 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads -2017-05-09 15:54:27,361 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads -2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] sending stop signal to worker thread -2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] job handler stop queue stopped -2017-05-09 15:54:27,362 INFO [test_driver] Application galaxy stopped. -2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] sending stop signal to worker thread -2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] job handler queue stopped -2017-05-09 15:54:28,335 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads -2017-05-09 15:54:28,335 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads -2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] sending stop signal to worker thread -2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] job handler stop queue stopped -Testing complete. HTML report is in "/home/backdoor/w4mclassfilter_galaxy_wrapper/tool_test_output.html". -All 3 test(s) executed passed. -W4MClassFilter[0]: passed -W4MClassFilter[1]: passed -W4MClassFilter[2]: passed