Mercurial > repos > eschen42 > w4mclassfilter
changeset 0:bab3a658f74e draft
planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
| author | eschen42 |
|---|---|
| date | Tue, 09 May 2017 18:34:35 -0400 |
| parents | |
| children | 371741d19743 |
| files | LICENSE README README.md planemo_install_history.txt planemo_shed_init.sh run_test.sh test-data/expected_dataMatrix.tsv test-data/expected_sampleMetadata.tsv test-data/expected_variableMetadata.tsv test-data/input_dataMatrix.tsv test-data/input_sampleMetadata.tsv test-data/input_variableMetadata.tsv test-data/output_dataMatrix.tsv test-data/output_sampleMetadata.tsv test-data/output_variableMetadata.tsv test_log.txt w4mclassfilter.xml w4mclassfilter_wrapper.R |
| diffstat | 18 files changed, 1083 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2017 Hegeman Lab + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,7 @@ +# w4mclassfilter_galaxy_wrapper + +planemo <http://planemo.readthedocs.io/en/latest/> +oriented galaxy-tool-wrapper <https://docs.galaxyproject.org/en/latest/dev/schema.htm> +to wrap the w4mclassfilter R package <https://github.com/HegemanLab/w4mclassfilter> +for use with the Workflow4Metabolomics <http://workflow4metabolomics.org/> +flavor of Galaxy <https://galaxyproject.org/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,7 @@ +# w4mclassfilter_galaxy_wrapper + +[planemo](http://planemo.readthedocs.io/en/latest/)-oriented +[galaxy-tool-wrapper](https://docs.galaxyproject.org/en/latest/dev/schema.htm) to wrap the +[w4mclassfilter R package](https://github.com/HegemanLab/w4mclassfilter) for use with the +[Workflow4Metabolomics](http://workflow4metabolomics.org/) flavor of +[Galaxy](https://galaxyproject.org/)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_install_history.txt Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,24 @@ +#!/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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_shed_init.sh Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,10 @@ +#!/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>] \
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_test.sh Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,13 @@ +#!/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"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_dataMatrix.tsv Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,16 @@ + 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_sampleMetadata.tsv Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,10 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_variableMetadata.tsv Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,16 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_dataMatrix.tsv Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,17 @@ +dataMatrix HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_204 HU_208 +HMDB03193 76043 412165 44943 27242 436566 173175 242549 57066 559869 3732 339188 471368 262271 127285 451270 212500 79673 NA 891129 43907 +HMDB01101 30689 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 891129 32742 +HMDB01101 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 72900 891129 30689 +HMDB10348 47259 544877 60885 34582 529874 168264 176500 76457 610110 16262 279156 524468 451573 591487 433529 161069 214392 13781 891129 39315 +HMDB59717 357351 1030464 301983 67604 306862 1028110 1530493 270027 1378535 289677 808334 1132813 871209 895435 715190 1563158 784738 146195 891129 239030 +HMDB00822 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 +HMDB13189 2644620 727587 1661412 619181 136278 2755434 593863 837865 3526136 2003278 1608814 3446611 1941527 113937 3132404 2893445 2092753 1034666 891129 841661 +HMDB00299 250551 1046138 456162 159386 1013302 808657 614370 250403 768004 242085 504108 1014041 1362408 1057660 1110050 566050 411886 142233 891129 284775 +HMDB00191 560002 771533 575790 392284 888498 785428 645785 591569 960658 910201 639437 1092885 1409045 2292023 1246459 1945577 710519 773384 891129 622898 +HMDB00518 -34236 58249 85944 NA 342102 129886 175800 13154 230242 NA 440223 315368 10657 419508 48673 28361 514579 23108 891129 73831 +HMDB00715 1252089 2547452 905408 371059 4983588 5140022 2658555 814523 2558923 859466 4184204 3865723 3236644 2615560 3820724 3577833 2295288 625924 891129 1341900 +HMDB01032 2569205 26023086 1604999 430453 8103558 26222916 257139 675754 59906109 263055 31151730 18648127 14989438 1554658 20249262 5588731 871010 15920 891129 44276 +HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 891129 2540044 +HMDB04824 374028 1144386 539206 178517 1046190 959381 605191 310260 1253319 477259 477995 825691 1157093 1089284 1411802 1020206 782673 346761 891129 387811 +HMDB00512 NA 319783 280560 85009 1333877 556003 590779 209285 342532 198512 569970 525240 246282 1140422 542345 1171008 827723 222953 891129 85554 +HMDB00251 368600 616555 94936 622468 180988 293988 352855 767894 268331 167246 310918 1248919 577184 10985 335711 403815 80614 63393 891129 616061
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_sampleMetadata.tsv Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,21 @@ +sampleMetadata injectionOrder mode age bmi gender +HU_017 2 pos 41 23.03 M +HU_028 7 pos 41 23.92 F +HU_034 9 pos 52 23.37 M +HU_051 20 pos 24 23.23 F +HU_060 24 pos 55 28.72 F +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_110 53 pos 50 20.9 F +HU_130 63 pos 33 26.06 M +HU_134 67 pos 48 22.89 M +HU_138 68 pos 42 21.88 M +HU_149 72 pos 35 19.49 F +HU_152 75 pos 26 17.58 F +HU_175 87 pos 35 21.26 F +HU_178 88 pos 60 32.87 F +HU_185 95 pos 42 21.09 F +HU_204 104 pos 31 29.06 M +HU_208 106 pos 27 18.61 F
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_variableMetadata.tsv Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,17 @@ +variableMetadata name +HMDB03193 Testosterone_glucuronide +HMDB01101 p-Anisic_acid +HMDB01101 p-Anisic_acid_2 +HMDB10348 Dehydroepiandrosterone_3-glucuronide +HMDB59717 Glu-Val +HMDB00822 p-Hydroxymandelic_acid +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dataMatrix.tsv Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,16 @@ + 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_sampleMetadata.tsv Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,10 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_variableMetadata.tsv Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,16 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_log.txt Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,410 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/w4mclassfilter.xml Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,304 @@ +<tool id="W4MClassFilter" name="W4MClassFilter" version="0.98.1"> + <description>Filter W4M data by sample class</description> + + <requirements> + <requirement type="package" version="3.3.1">r-base</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="0.98.1">w4mclassfilter</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + + <command detect_errors="aggressive"><![CDATA[ + Rscript $__tool_directory__/w4mclassfilter_wrapper.R + dataMatrix_in "$dataMatrix_in" + sampleMetadata_in "$sampleMetadata_in" + variableMetadata_in "$variableMetadata_in" + sampleclassNames "$sampleclassNames" + inclusive "$inclusive" + classnameColumn "$classnameColumn" + samplenameColumn "$samplenameColumn" + dataMatrix_out "$dataMatrix_out" + sampleMetadata_out "$sampleMetadata_out" + variableMetadata_out "$variableMetadata_out" + information "$information" + ]]></command> + + <inputs> + <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" /> + <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> + <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> + <param name="sampleclassNames" label="Names of sample classes" type="text" value = "" help="comma-separated names of sample classes to filter in or out; defaults to no names" /> + <param name="inclusive" label="Include named classes" type="select" help="filter-in - include only the named sample classes; filter-out (the default) - exclude only the named sample classes"> + <option value="TRUE">filter-in</option> + <option value="FALSE" selected="true">filter-out</option> + </param> + <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" help="name of the column in sample metadata that has the values to be tested against the 'classes' input parameter - defaults to 'class'" /> + <param name="samplenameColumn" label="Column that names the sample" type="text" value = "sampleMetadata" help="name of the column in sample metadata that has the name of the sample - defaults to 'sampleMetadata'" /> + </inputs> + <outputs> + <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data> + <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data> + <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> + <data name="information" label="${tool.name}__information.txt" format="txt"/> + </outputs> + + <tests> + <test> + <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> + <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> + <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> + <param name="classnameColumn" value="gender"/> + <param name="sampleclassNames" value="M"/> + <param name="samplenameColumn" value="sampleMetadata"/> + <param name="inclusive" value="filter-in"/> + <param name="information" value="test-information.txt"/> + <output name="dataMatrix_out"> + <assert_contents> + <not_has_text text="HU_028" /> + <not_has_text text="HU_051" /> + <not_has_text text="HU_060" /> + <not_has_text text="HU_110" /> + <not_has_text text="HU_149" /> + <not_has_text text="HU_152" /> + <not_has_text text="HU_175" /> + <not_has_text text="HU_178" /> + <not_has_text text="HU_185" /> + <not_has_text text="HU_204" /> + <not_has_text text="HU_208" /> + <has_text text="HU_017" /> + <has_text text="HU_034" /> + <has_text text="HU_078" /> + <has_text text="HU_091" /> + <has_text text="HU_093" /> + <has_text text="HU_099" /> + <has_text text="HU_130" /> + <has_text text="HU_134" /> + <has_text text="HU_138" /> + <has_text text="HMDB03193" /> + <not_has_text text="HMDB00822" /> + <has_text text="HMDB01101" /> + <has_text text="HMDB01101.1" /> + <has_text text="HMDB10348" /> + <has_text text="HMDB59717" /> + <has_text text="HMDB13189" /> + <has_text text="HMDB00299" /> + <has_text text="HMDB00191" /> + <has_text text="HMDB00518" /> + <has_text text="HMDB00715" /> + <has_text text="HMDB01032" /> + <has_text text="HMDB00208" /> + <has_text text="HMDB04824" /> + <has_text text="HMDB00512" /> + <has_text text="HMDB00251" /> + </assert_contents> + </output> + </test> + <test> + <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> + <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> + <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> + <param name="classnameColumn" value="gender"/> + <param name="sampleclassNames" value="M"/> + <param name="samplenameColumn" value="sampleMetadata"/> + <param name="inclusive" value="filter-in"/> + <param name="information" value="test-information.txt"/> + <output name="sampleMetadata_out"> + <assert_contents> + <not_has_text text="HU_028" /> + <not_has_text text="HU_051" /> + <not_has_text text="HU_060" /> + <not_has_text text="HU_110" /> + <not_has_text text="HU_149" /> + <not_has_text text="HU_152" /> + <not_has_text text="HU_175" /> + <not_has_text text="HU_178" /> + <not_has_text text="HU_185" /> + <not_has_text text="HU_204" /> + <not_has_text text="HU_208" /> + <has_text text="HU_017" /> + <has_text text="HU_034" /> + <has_text text="HU_078" /> + <has_text text="HU_091" /> + <has_text text="HU_093" /> + <has_text text="HU_099" /> + <has_text text="HU_130" /> + <has_text text="HU_134" /> + <has_text text="HU_138" /> + </assert_contents> + </output> + </test> + <test> + <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> + <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> + <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> + <param name="classnameColumn" value="gender"/> + <param name="sampleclassNames" value="M"/> + <param name="samplenameColumn" value="sampleMetadata"/> + <param name="inclusive" value="filter-in"/> + <param name="information" value="test-information.txt"/> + <output name="variableMetadata_out"> + <assert_contents> + <has_text text="HMDB03193" /> + <not_has_text text="HMDB00822" /> + <has_text text="HMDB01101" /> + <has_text text="HMDB01101.1" /> + <has_text text="HMDB10348" /> + <has_text text="HMDB59717" /> + <has_text text="HMDB13189" /> + <has_text text="HMDB00299" /> + <has_text text="HMDB00191" /> + <has_text text="HMDB00518" /> + <has_text text="HMDB00715" /> + <has_text text="HMDB01032" /> + <has_text text="HMDB00208" /> + <has_text text="HMDB04824" /> + <has_text text="HMDB00512" /> + <has_text text="HMDB00251" /> + </assert_contents> + </output> + </test> + </tests> + + + + <help> + +.. class:: infomark + +**Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu) + +-------------------------------------------------------------------------- + +.. class:: infomark + +**R package** + +The *w4mclassfilter* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases). + +----------------------------------------------------------------------------------------------------------------------------------------- + +.. class:: infomark + +**Tool updates** + +See the **NEWS** section at the bottom of this page + +--------------------------------------------------- + +============================================== +Filter Workflow4Metabolomics data matrix files +============================================== + +----------- +Description +----------- + +Filter set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample class + +-------- +Comments +-------- + +The *inclusive* parameter indicates: + - when 'filter-in', that only the sample-classes named should be included + - when 'filter-out', that all sample-classes should be included excepting the sample-classes named + +----------- +Input files +----------- + ++---------------------------+------------+ +| File | Format | ++===========================+============+ +| 1) Data matrix | tabular | ++---------------------------+------------+ +| 2) Sample metadata | tabular | ++---------------------------+------------+ +| 3) Variable metadata | tabular | ++---------------------------+------------+ + + +---------- +Parameters +---------- + +Data matrix file + | variable x sample **dataMatrix** tabular separated file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below) + | + +Sample metadata file + | sample x metadata **sampleMetadata** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values + | + +Variable metadata file + | variable x metadata **variableMetadata** tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values + | + +Names of sample classes (default = no names) + | comma-separated names of sample classes to include or exclude + | + +Include named classes (default = filter-out) + | *filter-in* - include only the named sample classes + | *filter-out* - exclude only the named sample classes + | + +Column that names the sample-class (default = 'class') + | name of the column in sample metadata that has the values to be tested against the 'classes' input parameter + | + +Column that names the sample (default = 'sampleMetadata') + | name of the column in sample metadata that has the name of the sample + | + + +------------ +Output files +------------ + + +sampleMetadata_out.tabular + | **sampleMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for samples that have been filtered out + | + +variableMetadata_out.tabular + | **variableMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance) + | + +dataMatrix_out.tabular + | **dataMatrix** tabular separated file identical to the file given as argument, excepting lacking columns for samples that have been filtered out (because of the sample-classes specified in the input parameters) and rows for variables (xC-MS features) that have been filtered out (because of zero variance) + | + +information.txt + | Text file with all messages and warnings generated during the computation + | + +----------------------------------------------------------------------------- + +---- +NEWS +---- + +CHANGES IN VERSION 0.98.1 +========================= + +NEW FEATURES + +First release - R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample. + +*dataMatrix* *is* modified by the tool, so it *does* appear as an output file + +INTERNAL MODIFICATIONS + +none + + </help> + <citations> + </citations> +</tool> +<!-- vim: et sw=2 ts=2 : +-->
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/w4mclassfilter_wrapper.R Tue May 09 18:34:35 2017 -0400 @@ -0,0 +1,148 @@ +#!/usr/bin/env Rscript + +library(batch) ## parseCommandArgs + +######## +# MAIN # +######## + +argVc <- unlist(parseCommandArgs(evaluate=FALSE)) + +##------------------------------ +## Initializing +##------------------------------ + +## options +##-------- + +strAsFacL <- options()$stringsAsFactors +options(stringsAsFactors = FALSE) + +## libraries +##---------- + +suppressMessages(library(w4mclassfilter)) + +if(packageVersion("w4mclassfilter") < "0.98.0") + stop("Please use 'w4mclassfilter' versions of 0.98.0 and above") + +## constants +##---------- + +modNamC <- "w4mclassfilter" ## module name + +topEnvC <- environment() +flgC <- "\n" + +## functions +##---------- + +flgF <- function(tesC, + envC = topEnvC, + txtC = NA) { ## management of warning and error messages + + tesL <- eval(parse(text = tesC), envir = envC) + + if(!tesL) { + + #sink(NULL) + stpTxtC <- ifelse(is.na(txtC), + paste0(tesC, " is FALSE"), + txtC) + + stop(stpTxtC, + call. = FALSE) + + } + +} ## flgF + + +## log file +##--------- + +information <- as.character(argVc["information"]) + +#sink(information) + +my_print <- function(x, ...) { cat(c(x, ...))} + +my_print("\nStart of the '", modNamC, "' Galaxy module call: ", + format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") + +## arguments +##---------- + +# files + +dataMatrix_in <- as.character(argVc["dataMatrix_in"]) +dataMatrix_out <- as.character(argVc["dataMatrix_out"]) + +sampleMetadata_in <- as.character(argVc["sampleMetadata_in"]) +sampleMetadata_out <- as.character(argVc["sampleMetadata_out"]) + +variableMetadata_in <- as.character(argVc["variableMetadata_in"]) +variableMetadata_out <- as.character(argVc["variableMetadata_out"]) + +# other parameters + +sampleclassNames <- as.character(argVc["sampleclassNames"]) +# if (sampleclassNames == "NONE_SPECIFIED") { +# sampleclassNames <- as.character(c()) +# +# } else { +# sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] +# } +sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] +inclusive <- as.logical(argVc["inclusive"]) +# print(sprintf("inclusive = '%s'", as.character(inclusive))) +classnameColumn <- as.character(argVc["classnameColumn"]) +samplenameColumn <- as.character(argVc["samplenameColumn"]) + +##------------------------------ +## Computation +##------------------------------ + +result <- w4m_filter_by_sample_class( + dataMatrix_in = dataMatrix_in +, sampleMetadata_in = sampleMetadata_in +, variableMetadata_in = variableMetadata_in +, dataMatrix_out = dataMatrix_out +, sampleMetadata_out = sampleMetadata_out +, variableMetadata_out = variableMetadata_out +, classes = sampleclassNames +, include = inclusive +, class_column = classnameColumn +, samplename_column = samplenameColumn +, failure_action = my_print +) + +my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ", + as.character(result), "\n", sep = "") + +##-------- +## Closing +##-------- + +my_print("\nEnd of '", modNamC, "' Galaxy module call: ", + as.character(Sys.time()), "\n", sep = "") + +#sink() + +if (!file.exists(dataMatrix_out)) { + print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, dataMatrix_out)) +}# else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, dataMatrix_out)) } + +if (!file.exists(variableMetadata_out)) { + print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, variableMetadata_out)) +} # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, variableMetadata_out)) } + +if (!file.exists(sampleMetadata_out)) { + print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, sampleMetadata_out)) +} # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, sampleMetadata_out)) } + +if( !result ) { + stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC)) +} + +rm(list = ls())