| Previous changeset 0:bab3a658f74e (2017-05-09) Next changeset 2:23c6d271def9 (2017-05-10) |
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Commit message:
Deleted selected files |
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removed:
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 |
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| diff -r bab3a658f74e -r 371741d19743 planemo_install_history.txt --- a/planemo_install_history.txt Tue May 09 18:34:35 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r bab3a658f74e -r 371741d19743 planemo_shed_init.sh --- a/planemo_shed_init.sh Tue May 09 18:34:35 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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>] \ |
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| diff -r bab3a658f74e -r 371741d19743 run_test.sh --- a/run_test.sh Tue May 09 18:34:35 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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" |
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| diff -r bab3a658f74e -r 371741d19743 test-data/output_dataMatrix.tsv --- a/test-data/output_dataMatrix.tsv Tue May 09 18:34:35 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r bab3a658f74e -r 371741d19743 test-data/output_sampleMetadata.tsv --- a/test-data/output_sampleMetadata.tsv Tue May 09 18:34:35 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r bab3a658f74e -r 371741d19743 test-data/output_variableMetadata.tsv --- a/test-data/output_variableMetadata.tsv Tue May 09 18:34:35 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r bab3a658f74e -r 371741d19743 test_log.txt --- a/test_log.txt Tue May 09 18:34:35 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,410 +0,0 @@\n-git clone --bare \'https://github.com/galaxyproject/galaxy\' \'/home/backdoor/.planemo/gx_repo\'\n-Cloning into bare repository \'/home/backdoor/.planemo/gx_repo\'...\n-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}\n-Cloning into \'galaxy-dev\'...\n-done.\n-New python executable in /home/backdoor/.planemo/gx_venv/bin/python2.7\n-Also creating executable in /home/backdoor/.planemo/gx_venv/bin/python\n-Installing setuptools, pip, wheel...done.\n-Running virtualenv with interpreter /home/backdoor/.linuxbrew/bin/python2.7\n-Set COMMON_STARTUP_ARGS to --dev-wheels\n-Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample\n-Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample\n-Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample\n-Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample\n-Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample\n-Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/backdoor/.planemo/gx_venv\n-Collecting pip>=8.1\n- Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB)\n-Installing collected packages: pip\n- Found existing installation: pip 7.1.2\n- Uninstalling pip-7.1.2:\n- Successfully uninstalled pip-7.1.2\n-Successfully installed pip-9.0.1\n-Collecting bx-python==0.7.3 (from -r requirements.txt (line 2))\n- Downloading https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27m-manylinux1_x86_64.whl (2.1MB)\n-Collecting MarkupSafe==0.23 (from -r requirements.txt (line 3))\n- Downloading https://wheels.galaxyproject.org/packages/MarkupSafe-0.23-cp27-cp27m-manylinux1_x86_64.whl\n-Collecting PyYAML==3.11 (from -r requirements.txt (line 4))\n- Downloading https://wheels.galaxyproject.org/packages/PyYAML-3.11-cp27-cp27m-manylinux1_x86_64.whl (367kB)\n-Collecting SQLAlchemy==1.0.15 (from -r requirements.txt (line 5))\n- Downloading https://wheels.galaxyproject.org/packages/SQLAlchemy-1.0.15-cp27-cp27m-manylinux1_x86_64.whl (1.0MB)\n-Collecting mercurial==3.7.3 (from -r requirements.txt (line 6))\n- Downloading https://wheels.galaxyproject.org/packages/mercurial-3.7.3-cp27-cp27m-manylinux1_x86_64.whl (1.5MB)\n-Collecting numpy==1.9.2 (from -r requirements.txt (line 7))\n- Downloading https://wheels.galaxyproject.org/packages/numpy-1.9.2-cp27-cp27m-manylinux1_x86_64.whl (10.2MB)\n-Collecting pycrypto==2.6.1 (from -r requirements.txt (line 8))\n- Downloading https://wheels.galaxyproject.org/packages/pycrypto-2.6.1-cp27-cp27m-manylinux1_x86_64.whl (492kB)\n-Collecting Paste==2.0.2 (from -r requirements.txt (line 15))\n- Downloading https://wheels.galaxyproject.org/packages/Paste-2.0.2-py2-none-any.whl (610kB)\n-Collecting PasteDeploy==1.5.2 (from -r requirements.txt (line 16))\n- Downloading https://wheels.galaxyproject.org/packages/PasteDeploy-1.5.2-py2.py3-none-any.whl\n-Collecting docutils==0.12 (from -r requirements.txt (line 17))\n- D'..b'61 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda\n-2017-05-09 15:54:20,961 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda\n-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"]\n-2017-05-09 15:54:21,503 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda\n-2017-05-09 15:54:21,503 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda\n-ok\n-\n-----------------------------------------------------------------------\n-XML: /tmp/tmp4Jz5Zv/xunit.xml\n-----------------------------------------------------------------------\n-Ran 3 tests in 83.693s\n-\n-OK\n-2017-05-09 15:54:27,359 INFO [test_driver] Shutting down\n-2017-05-09 15:54:27,359 INFO [test_driver] Shutting down embedded galaxy web server\n-2017-05-09 15:54:27,361 INFO [test_driver] Embedded web server galaxy stopped\n-2017-05-09 15:54:27,361 INFO [test_driver] Stopping application galaxy\n-2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n-2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] job handler queue stopped\n-2017-05-09 15:54:27,361 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads\n-2017-05-09 15:54:27,361 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads\n-2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n-2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] job handler stop queue stopped\n-2017-05-09 15:54:27,362 INFO [test_driver] Application galaxy stopped.\n-2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n-2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] job handler queue stopped\n-2017-05-09 15:54:28,335 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads\n-2017-05-09 15:54:28,335 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads\n-2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n-2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] job handler stop queue stopped\n-Testing complete. HTML report is in "/home/backdoor/w4mclassfilter_galaxy_wrapper/tool_test_output.html".\n-All 3 test(s) executed passed.\n-W4MClassFilter[0]: passed\n-W4MClassFilter[1]: passed\n-W4MClassFilter[2]: passed\n' |