Mercurial > repos > oinizan > frogs
changeset 4:8d88c426e94c draft
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
| author | oinizan |
|---|---|
| date | Thu, 08 Apr 2021 12:43:51 +0000 |
| parents | 3d3268f0aa77 |
| children | 828d2003af85 |
| files | FROGS_data_manager/data_manager/FROGS_data_manager.py itsx.xml planemo_test/deseq2_preprocess.test.log |
| diffstat | 2 files changed, 826 insertions(+), 1 deletions(-) [+] |
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--- a/itsx.xml Thu Apr 08 09:02:33 2021 +0000 +++ b/itsx.xml Thu Apr 08 12:43:51 2021 +0000 @@ -73,9 +73,9 @@ </param> </inputs> <outputs> + <data format="fasta" name="out_excluded" label="${tool.name}: nonITS_sequence.fasta" from_work_dir="out_removed.fasta"/> <data format="fasta" name="out_fasta" label="${tool.name}: ITS_sequence.fasta" from_work_dir="itsx.fasta"/> <data format="biom1" name="out_abundance_biom" label="${tool.name}: itsx_abundance.biom" from_work_dir="itsx.biom"/> - <data format="fasta" name="out_excluded" label="${tool.name}: nonITS_sequence.fasta" from_work_dir="out_removed.fasta"/> <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/> </outputs> <tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_test/deseq2_preprocess.test.log Thu Apr 08 12:43:51 2021 +0000 @@ -0,0 +1,825 @@ +git --git-dir /home/maria/.planemo/gx_repo config remote.origin.fetch '+refs/*:refs/*' +git --git-dir /home/maria/.planemo/gx_repo config remote.origin.mirror true +git --git-dir /home/maria/.planemo/gx_repo remote update >/dev/null 2>&1 +galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input +git clone --branch master /home/maria/.planemo/gx_repo /tmp/tmpwlal_jyf/galaxy-dev +Clonage dans '/tmp/tmpwlal_jyf/galaxy-dev'... +error: object file ./objects/1d/3b5b4b0610a48d6950fbf2a3c49559fc28f85e is empty +fait. +Extraction des fichiers: 47% (2554/5411) Extraction des fichiers: 48% (2598/5411) Extraction des fichiers: 49% (2652/5411) Extraction des fichiers: 50% (2706/5411) Extraction des fichiers: 51% (2760/5411) Extraction des fichiers: 52% (2814/5411) Extraction des fichiers: 53% (2868/5411) Extraction des fichiers: 54% (2922/5411) Extraction des fichiers: 55% (2977/5411) Extraction des fichiers: 56% (3031/5411) Extraction des fichiers: 57% (3085/5411) Extraction des fichiers: 58% (3139/5411) Extraction des fichiers: 59% (3193/5411) Extraction des fichiers: 60% (3247/5411) Extraction des fichiers: 61% (3301/5411) Extraction des fichiers: 62% (3355/5411) Extraction des fichiers: 63% (3409/5411) Extraction des fichiers: 64% (3464/5411) Extraction des fichiers: 65% (3518/5411) Extraction des fichiers: 66% (3572/5411) Extraction des fichiers: 67% (3626/5411) Extraction des fichiers: 68% (3680/5411) Extraction des fichiers: 69% (3734/5411) Extraction des fichiers: 70% (3788/5411) Extraction des fichiers: 71% (3842/5411) Extraction des fichiers: 72% (3896/5411) Extraction des fichiers: 73% (3951/5411) Extraction des fichiers: 74% (4005/5411) Extraction des fichiers: 75% (4059/5411) Extraction des fichiers: 76% (4113/5411) Extraction des fichiers: 77% (4167/5411) Extraction des fichiers: 78% (4221/5411) Extraction des fichiers: 79% (4275/5411) Extraction des fichiers: 80% (4329/5411) Extraction des fichiers: 81% (4383/5411) Extraction des fichiers: 82% (4438/5411) Extraction des fichiers: 83% (4492/5411) Extraction des fichiers: 84% (4546/5411) Extraction des fichiers: 85% (4600/5411) Extraction des fichiers: 86% (4654/5411) Extraction des fichiers: 87% (4708/5411) Extraction des fichiers: 88% (4762/5411) Extraction des fichiers: 88% (4767/5411) Extraction des fichiers: 89% (4816/5411) Extraction des fichiers: 90% (4870/5411) Extraction des fichiers: 91% (4925/5411) Extraction des fichiers: 92% (4979/5411) Extraction des fichiers: 93% (5033/5411) Extraction des fichiers: 94% (5087/5411) Extraction des fichiers: 95% (5141/5411) Extraction des fichiers: 96% (5195/5411) Extraction des fichiers: 97% (5249/5411) Extraction des fichiers: 98% (5303/5411) Extraction des fichiers: 99% (5357/5411) Extraction des fichiers: 100% (5411/5411) Extraction des fichiers: 100% (5411/5411), fait. +if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/maria/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/maria/planemo/bin/virtualenv -p /home/maria/planemo/bin/python3 $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && 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} +galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input +Activated a virtualenv for Galaxy +/home/maria/.planemo/gx_venv_3 +Set COMMON_STARTUP_ARGS to --dev-wheels +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 static/welcome.html from welcome.html.sample +Activating virtualenv at /home/maria/.planemo/gx_venv_3 +Requirement already satisfied: pip>=8.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (21.0.1) +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple +Ignoring importlib-metadata: markers 'python_version < "3.8"' don't match your environment +Ignoring importlib-resources: markers 'python_version < "3.7"' don't match your environment +Ignoring pathlib2: markers 'python_version < "3.6"' don't match your environment +Ignoring ruamel.yaml.clib: markers 'platform_python_implementation == "CPython" and python_version < "3.8"' don't match your environment +Ignoring typing: markers 'python_version < "3.5"' don't match your environment +Ignoring zipp: markers 'python_version < "3.8"' don't match your environment +Ignoring importlib-metadata: markers 'python_version < "3.8"' don't match your environment +Ignoring pathlib2: markers 'python_version < "3.6"' don't match your environment +Ignoring zipp: markers 'python_version < "3.8"' don't match your environment +Requirement already satisfied: adal==1.2.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 3)) (1.2.4) +Requirement already satisfied: amqp==2.6.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 4)) (2.6.0) +Requirement already satisfied: appdirs==1.4.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 5)) (1.4.4) +Requirement already satisfied: attmap==0.12.11 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 6)) (0.12.11) +Requirement already satisfied: attrs==19.3.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 7)) (19.3.0) +Requirement already satisfied: azure-common==1.1.14 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 8)) (1.1.14) +Requirement already satisfied: azure-cosmosdb-nspkg==2.0.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 9)) (2.0.2) +Requirement already satisfied: azure-cosmosdb-table==1.0.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 10)) (1.0.4) +Requirement already satisfied: azure-mgmt-compute==4.0.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 11)) (4.0.1) +Requirement already satisfied: azure-mgmt-devtestlabs==2.2.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 12)) (2.2.0) +Requirement already satisfied: azure-mgmt-network==2.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 13)) (2.1.0) +Requirement already satisfied: azure-mgmt-nspkg==3.0.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 14)) (3.0.2) +Requirement already satisfied: azure-mgmt-resource==2.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 15)) (2.0.0) +Requirement already satisfied: azure-mgmt-storage==2.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 16)) (2.0.0) +Requirement already satisfied: azure-nspkg==3.0.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 17)) (3.0.2) +Requirement already satisfied: azure-storage-blob==1.3.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 18)) (1.3.1) +Requirement already satisfied: azure-storage-common==1.4.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 19)) (1.4.2) +Requirement already satisfied: azure-storage-nspkg==3.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 20)) (3.1.0) +Requirement already satisfied: babel==2.8.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 21)) (2.8.0) +Requirement already satisfied: bagit==1.7.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 22)) (1.7.0) +Requirement already satisfied: bcrypt==3.1.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 23)) (3.1.7) +Requirement already satisfied: bdbag==1.5.6 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 24)) (1.5.6) +Requirement already satisfied: beaker==1.11.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 25)) (1.11.0) +Requirement already satisfied: bioblend==0.13.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 26)) (0.13.0) +Requirement already satisfied: bleach==3.1.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 27)) (3.1.5) +Requirement already satisfied: boltons==20.2.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 28)) (20.2.0) +Requirement already satisfied: boto3==1.9.114 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 29)) (1.9.114) +Requirement already satisfied: boto==2.49.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 30)) (2.49.0) +Requirement already satisfied: botocore==1.12.253 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 31)) (1.12.253) +Requirement already satisfied: bx-python==0.8.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 32)) (0.8.9) +Requirement already satisfied: cachecontrol==0.11.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 33)) (0.11.7) +Requirement already satisfied: cachetools==4.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 34)) (4.1.0) +Requirement already satisfied: certifi==2020.6.20 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 35)) (2020.6.20) +Requirement already satisfied: cffi==1.14.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 36)) (1.14.0) +Requirement already satisfied: chardet==3.0.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 37)) (3.0.4) +Requirement already satisfied: cheetah3==3.2.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 38)) (3.2.5) +Requirement already satisfied: cliff==3.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 39)) (3.1.0) +Requirement already satisfied: cloudauthz==0.6.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 40)) (0.6.0) +Requirement already satisfied: cloudbridge==2.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 41)) (2.0.0) +Requirement already satisfied: cmd2==0.8.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 42)) (0.8.9) +Requirement already satisfied: coloredlogs==14.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 43)) (14.0) +Requirement already satisfied: cryptography==3.2.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 44)) (3.2.1) +Requirement already satisfied: cwltool==1.0.20191225192155 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 45)) (1.0.20191225192155) +Requirement already satisfied: debtcollector==1.22.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 46)) (1.22.0) +Requirement already satisfied: decorator==4.4.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 47)) (4.4.2) +Requirement already satisfied: defusedxml==0.6.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 48)) (0.6.0) +Requirement already satisfied: deprecated==1.2.10 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 49)) (1.2.10) +Requirement already satisfied: deprecation==2.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 50)) (2.1.0) +Requirement already satisfied: dictobj==0.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 51)) (0.4) +Requirement already satisfied: docopt==0.6.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 52)) (0.6.2) +Requirement already satisfied: docutils==0.15.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 53)) (0.15.2) +Requirement already satisfied: dogpile.cache==0.9.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 54)) (0.9.2) +Requirement already satisfied: ecdsa==0.15 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 55)) (0.15) +Requirement already satisfied: fabric3==1.14.post1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 56)) (1.14.post1) +Requirement already satisfied: future==0.18.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 57)) (0.18.2) +Requirement already satisfied: futures==3.1.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 58)) (3.1.1) +Requirement already satisfied: galaxy-sequence-utils==1.1.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 59)) (1.1.5) +Requirement already satisfied: google-api-python-client==1.7.8 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 60)) (1.7.8) +Requirement already satisfied: google-auth-httplib2==0.0.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 61)) (0.0.3) +Requirement already satisfied: google-auth==1.18.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 62)) (1.18.0) +Requirement already satisfied: gxformat2==0.11.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 63)) (0.11.3) +Requirement already satisfied: h5py==2.10.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 64)) (2.10.0) +Requirement already satisfied: httplib2==0.18.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 65)) (0.18.1) +Requirement already satisfied: humanfriendly==8.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 66)) (8.2) +Requirement already satisfied: idna==2.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 67)) (2.9) +Requirement already satisfied: isa-rwval==0.10.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 70)) (0.10.9) +Requirement already satisfied: iso8601==0.1.12 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 71)) (0.1.12) +Requirement already satisfied: isodate==0.6.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 72)) (0.6.0) +Requirement already satisfied: jmespath==0.10.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 73)) (0.10.0) +Requirement already satisfied: jsonpatch==1.26 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 74)) (1.26) +Requirement already satisfied: jsonpointer==2.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 75)) (2.0) +Requirement already satisfied: jsonschema==3.2.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 76)) (3.2.0) +Requirement already satisfied: keystoneauth1==4.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 77)) (4.1.0) +Requirement already satisfied: kombu==4.6.11 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 78)) (4.6.11) +Requirement already satisfied: lockfile==0.12.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 79)) (0.12.2) +Requirement already satisfied: lxml==4.6.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 80)) (4.6.2) +Requirement already satisfied: mako==1.1.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 81)) (1.1.3) +Requirement already satisfied: markdown==3.2.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 82)) (3.2.2) +Requirement already satisfied: markupsafe==1.1.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 83)) (1.1.1) +Requirement already satisfied: mercurial==5.4.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 84)) (5.4.1) +Requirement already satisfied: mistune==0.8.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 85)) (0.8.4) +Requirement already satisfied: msgpack==1.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 86)) (1.0.0) +Requirement already satisfied: msrest==0.5.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 87)) (0.5.5) +Requirement already satisfied: msrestazure==0.5.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 88)) (0.5.0) +Requirement already satisfied: munch==2.5.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 89)) (2.5.0) +Requirement already satisfied: mypy-extensions==0.4.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 90)) (0.4.3) +Requirement already satisfied: netaddr==0.7.20 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 91)) (0.7.20) +Requirement already satisfied: netifaces==0.10.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 92)) (0.10.9) +Requirement already satisfied: networkx==1.11 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 93)) (1.11) +Requirement already satisfied: nodeenv==1.4.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 94)) (1.4.0) +Requirement already satisfied: nose==1.3.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 95)) (1.3.7) +Requirement already satisfied: numpy==1.18.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 96)) (1.18.5) +Requirement already satisfied: oauth2client==4.1.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 97)) (4.1.3) +Requirement already satisfied: oauthlib==3.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 98)) (3.1.0) +Requirement already satisfied: openstacksdk==0.17.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 99)) (0.17.0) +Requirement already satisfied: os-client-config==2.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 100)) (2.1.0) +Requirement already satisfied: os-service-types==1.7.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 101)) (1.7.0) +Requirement already satisfied: osc-lib==2.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 102)) (2.0.0) +Requirement already satisfied: oslo.config==7.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 103)) (7.0.0) +Requirement already satisfied: oslo.context==2.23.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 104)) (2.23.1) +Requirement already satisfied: oslo.i18n==3.25.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 105)) (3.25.1) +Requirement already satisfied: oslo.log==3.45.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 106)) (3.45.2) +Requirement already satisfied: oslo.serialization==2.29.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 107)) (2.29.2) +Requirement already satisfied: oslo.utils==3.42.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 108)) (3.42.1) +Requirement already satisfied: oyaml==0.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 109)) (0.9) +Requirement already satisfied: packaging==20.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 110)) (20.4) +Requirement already satisfied: paramiko==2.7.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 111)) (2.7.1) +Requirement already satisfied: parsley==1.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 112)) (1.3) +Requirement already satisfied: paste==3.4.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 113)) (3.4.1) +Requirement already satisfied: pastedeploy==2.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 114)) (2.1.0) +Requirement already satisfied: pastescript==3.2.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 115)) (3.2.0) +Requirement already satisfied: pbr==5.4.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 117)) (5.4.5) +Requirement already satisfied: prettytable==0.7.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 118)) (0.7.2) +Requirement already satisfied: prov==1.5.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 119)) (1.5.1) +Requirement already satisfied: psutil==5.7.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 120)) (5.7.0) +Requirement already satisfied: pulsar-galaxy-lib==0.14.0.dev4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 121)) (0.14.0.dev4) +Requirement already satisfied: pyasn1-modules==0.2.8 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 122)) (0.2.8) +Requirement already satisfied: pyasn1==0.4.8 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 123)) (0.4.8) +Requirement already satisfied: pycparser==2.20 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 124)) (2.20) +Requirement already satisfied: pycryptodome==3.9.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 125)) (3.9.7) +Requirement already satisfied: pyeventsystem==0.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 126)) (0.1.0) +Requirement already satisfied: pyinotify==0.9.6 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 127)) (0.9.6) +Requirement already satisfied: pyjwt==1.7.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 128)) (1.7.1) +Requirement already satisfied: pykwalify==1.7.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 129)) (1.7.0) +Requirement already satisfied: pynacl==1.4.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 130)) (1.4.0) +Requirement already satisfied: pyopenssl==19.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 131)) (19.1.0) +Requirement already satisfied: pyparsing==2.4.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 132)) (2.4.7) +Requirement already satisfied: pyperclip==1.8.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 133)) (1.8.0) +Requirement already satisfied: pyrsistent==0.16.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 134)) (0.16.0) +Requirement already satisfied: pysam==0.16.0.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 135)) (0.16.0.1) +Requirement already satisfied: pysftp==0.2.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 136)) (0.2.9) +Requirement already satisfied: python-cinderclient==4.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 137)) (4.0.0) +Requirement already satisfied: python-dateutil==2.8.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 138)) (2.8.1) +Requirement already satisfied: python-glanceclient==2.12.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 139)) (2.12.0) +Requirement already satisfied: python-jose==3.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 140)) (3.1.0) +Requirement already satisfied: python-keystoneclient==3.17.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 141)) (3.17.0) +Requirement already satisfied: python-neutronclient==6.9.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 142)) (6.9.0) +Requirement already satisfied: python-novaclient==11.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 143)) (11.0.0) +Requirement already satisfied: python-swiftclient==3.6.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 144)) (3.6.0) +Requirement already satisfied: python3-openid==3.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 145)) (3.1.0) +Requirement already satisfied: pytz==2020.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 146)) (2020.1) +Requirement already satisfied: pyuwsgi==2.0.19.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 147)) (2.0.19.1) +Requirement already satisfied: pyyaml==5.3.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 148)) (5.3.1) +Requirement already satisfied: rdflib-jsonld==0.4.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 149)) (0.4.0) +Requirement already satisfied: rdflib==4.2.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 150)) (4.2.2) +Requirement already satisfied: refgenconf==0.7.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 151)) (0.7.0) +Requirement already satisfied: repoze.lru==0.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 152)) (0.7) +Requirement already satisfied: requests-oauthlib==1.3.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 153)) (1.3.0) +Requirement already satisfied: requests-toolbelt==0.9.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 154)) (0.9.1) +Requirement already satisfied: requests==2.24.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 155)) (2.24.0) +Requirement already satisfied: requestsexceptions==1.4.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 156)) (1.4.0) +Requirement already satisfied: rfc3986==1.4.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 157)) (1.4.0) +Requirement already satisfied: routes==2.4.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 158)) (2.4.1) +Requirement already satisfied: rsa==4.6 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 159)) (4.6) +Requirement already satisfied: ruamel.yaml==0.16.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 161)) (0.16.0) +Requirement already satisfied: s3transfer==0.2.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 162)) (0.2.1) +Requirement already satisfied: scandir==1.10.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 163)) (1.10.0) +Requirement already satisfied: schema-salad==4.5.20191229160203 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 164)) (4.5.20191229160203) +Requirement already satisfied: setuptools-scm==4.1.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 165)) (4.1.2) +Requirement already satisfied: shellescape==3.4.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 166)) (3.4.1) +Requirement already satisfied: simplejson==3.17.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 167)) (3.17.0) +Requirement already satisfied: six==1.15.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 168)) (1.15.0) +Requirement already satisfied: social-auth-core[openidconnect]==3.3.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 169)) (3.3.0) +Requirement already satisfied: sortedcontainers==2.2.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 170)) (2.2.2) +Requirement already satisfied: sqlalchemy-migrate==0.13.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 171)) (0.13.0) +Requirement already satisfied: sqlalchemy-utils==0.36.6 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 172)) (0.36.6) +Requirement already satisfied: sqlalchemy==1.3.17 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 173)) (1.3.17) +Requirement already satisfied: sqlitedict==1.7.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 174)) (1.7.0) +Requirement already satisfied: sqlparse==0.3.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 175)) (0.3.1) +Requirement already satisfied: stevedore==1.32.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 176)) (1.32.0) +Requirement already satisfied: svgwrite==1.3.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 177)) (1.3.1) +Requirement already satisfied: tempita==0.5.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 178)) (0.5.2) +Requirement already satisfied: tenacity==4.12.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 179)) (4.12.0) +Requirement already satisfied: tqdm==4.46.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 180)) (4.46.1) +Requirement already satisfied: typing-extensions==3.7.4.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 181)) (3.7.4.2) +Requirement already satisfied: tzlocal==2.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 183)) (2.1) +Requirement already satisfied: ubiquerg==0.5.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 184)) (0.5.2) +Requirement already satisfied: unidecode==1.1.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 185)) (1.1.1) +Requirement already satisfied: uritemplate==3.0.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 186)) (3.0.1) +Requirement already satisfied: urllib3==1.25.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 187)) (1.25.9) +Requirement already satisfied: vine==1.3.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 188)) (1.3.0) +Requirement already satisfied: warlock==1.3.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 189)) (1.3.3) +Requirement already satisfied: wcwidth==0.2.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 190)) (0.2.5) +Requirement already satisfied: webencodings==0.5.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 191)) (0.5.1) +Requirement already satisfied: webob==1.8.6 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 192)) (1.8.6) +Requirement already satisfied: whoosh==2.7.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 193)) (2.7.4) +Requirement already satisfied: wrapt==1.12.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 194)) (1.12.1) +Requirement already satisfied: yacman==0.6.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 195)) (0.6.7) +Requirement already satisfied: alabaster==0.7.12 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (0.7.12) +Requirement already satisfied: commonmark==0.9.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 8)) (0.9.1) +Requirement already satisfied: coverage==5.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 9)) (5.1) +Requirement already satisfied: gunicorn==20.0.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 12)) (20.0.4) +Requirement already satisfied: imagesize==1.2.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 14)) (1.2.0) +Requirement already satisfied: jinja2==2.11.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 16)) (2.11.2) +Requirement already satisfied: mirakuru==2.0.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (2.0.2) +Requirement already satisfied: mock==3.0.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 21)) (3.0.5) +Requirement already satisfied: more-itertools==8.4.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 22)) (8.4.0) +Requirement already satisfied: nosehtml==0.4.6 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 24)) (0.4.6) +Requirement already satisfied: pathtools==0.1.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (0.1.2) +Requirement already satisfied: pluggy==0.13.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 28)) (0.13.1) +Requirement already satisfied: port-for==0.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 29)) (0.4) +Requirement already satisfied: py==1.8.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 32)) (1.8.2) +Requirement already satisfied: pygithub==1.51 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 33)) (1.51) +Requirement already satisfied: pygments==2.6.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 34)) (2.6.1) +Requirement already satisfied: pytest-cov==2.10.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 37)) (2.10.0) +Requirement already satisfied: pytest-html==1.22.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 38)) (1.22.1) +Requirement already satisfied: pytest-metadata==1.8.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 39)) (1.8.0) +Requirement already satisfied: pytest-mock==3.1.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 40)) (3.1.1) +Requirement already satisfied: pytest-postgresql==2.3.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 41)) (2.3.0) +Requirement already satisfied: pytest-pythonpath==0.7.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 42)) (0.7.3) +Requirement already satisfied: pytest==5.4.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 43)) (5.4.3) +Requirement already satisfied: python-irodsclient==0.8.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (0.8.3) +Requirement already satisfied: recommonmark==0.6.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 46)) (0.6.0) +Requirement already satisfied: responses==0.10.15 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 48)) (0.10.15) +Requirement already satisfied: selenium==3.141.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 49)) (3.141.0) +Requirement already satisfied: snowballstemmer==2.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (2.0.0) +Requirement already satisfied: sphinx-markdown-tables==0.0.15 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 52)) (0.0.15) +Requirement already satisfied: sphinx-rtd-theme==0.5.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 53)) (0.5.0) +Requirement already satisfied: sphinx==3.1.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 54)) (3.1.1) +Requirement already satisfied: sphinxcontrib-applehelp==1.0.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55)) (1.0.2) +Requirement already satisfied: sphinxcontrib-devhelp==1.0.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 56)) (1.0.2) +Requirement already satisfied: sphinxcontrib-htmlhelp==1.0.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 57)) (1.0.3) +Requirement already satisfied: sphinxcontrib-jsmath==1.0.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 58)) (1.0.1) +Requirement already satisfied: sphinxcontrib-qthelp==1.0.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 59)) (1.0.3) +Requirement already satisfied: sphinxcontrib-serializinghtml==1.1.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 60)) (1.1.4) +Requirement already satisfied: testfixtures==6.14.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 61)) (6.14.1) +Requirement already satisfied: twill==2.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 62)) (2.0) +Requirement already satisfied: watchdog==0.10.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 64)) (0.10.2) +Requirement already satisfied: xmlrunner==1.7.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 67)) (1.7.7) +Requirement already satisfied: pathlib2!=2.3.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 45)) (2.3.5) +Requirement already satisfied: setuptools in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 45)) (52.0.0) +The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable. +Testing using galaxy_root /tmp/tmpwlal_jyf/galaxy-dev +Testing tools with command [cd /tmp/tmpwlal_jyf/galaxy-dev && if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/maria/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/maria/planemo/bin/virtualenv -p /home/maria/planemo/bin/python3 $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./run_tests.sh $COMMON_STARTUP_ARGS --report_file /home/maria/workspace/FROGS-wrappers_dev/tool_test_output.html --xunit_report_file /tmp/tmpwlal_jyf/xunit.xml --structured_data_report_file /home/maria/workspace/FROGS-wrappers_dev/tool_test_output.json functional.test_toolbox] +galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input +Activated a virtualenv for Galaxy +/home/maria/.planemo/gx_venv_3 +Activating virtualenv at /home/maria/.planemo/gx_venv_3 +Requirement already satisfied: pip>=8.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (21.0.1) +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple +Ignoring importlib-metadata: markers 'python_version < "3.8"' don't match your environment +Ignoring importlib-resources: markers 'python_version < "3.7"' don't match your environment +Ignoring pathlib2: markers 'python_version < "3.6"' don't match your environment +Ignoring ruamel.yaml.clib: markers 'platform_python_implementation == "CPython" and python_version < "3.8"' don't match your environment +Ignoring typing: markers 'python_version < "3.5"' don't match your environment +Ignoring zipp: markers 'python_version < "3.8"' don't match your environment +Ignoring importlib-metadata: markers 'python_version < "3.8"' don't match your environment +Ignoring pathlib2: markers 'python_version < "3.6"' don't match your environment +Ignoring zipp: markers 'python_version < "3.8"' don't match your environment +Requirement already satisfied: adal==1.2.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 3)) (1.2.4) +Requirement already satisfied: amqp==2.6.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 4)) (2.6.0) +Requirement already satisfied: appdirs==1.4.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 5)) (1.4.4) +Requirement already satisfied: attmap==0.12.11 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 6)) (0.12.11) +Requirement already satisfied: attrs==19.3.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 7)) (19.3.0) +Requirement already satisfied: azure-common==1.1.14 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 8)) (1.1.14) +Requirement already satisfied: azure-cosmosdb-nspkg==2.0.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 9)) (2.0.2) +Requirement already satisfied: azure-cosmosdb-table==1.0.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 10)) (1.0.4) +Requirement already satisfied: azure-mgmt-compute==4.0.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 11)) (4.0.1) +Requirement already satisfied: azure-mgmt-devtestlabs==2.2.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 12)) (2.2.0) +Requirement already satisfied: azure-mgmt-network==2.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 13)) (2.1.0) +Requirement already satisfied: azure-mgmt-nspkg==3.0.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 14)) (3.0.2) +Requirement already satisfied: azure-mgmt-resource==2.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 15)) (2.0.0) +Requirement already satisfied: azure-mgmt-storage==2.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 16)) (2.0.0) +Requirement already satisfied: azure-nspkg==3.0.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 17)) (3.0.2) +Requirement already satisfied: azure-storage-blob==1.3.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 18)) (1.3.1) +Requirement already satisfied: azure-storage-common==1.4.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 19)) (1.4.2) +Requirement already satisfied: azure-storage-nspkg==3.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 20)) (3.1.0) +Requirement already satisfied: babel==2.8.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 21)) (2.8.0) +Requirement already satisfied: bagit==1.7.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 22)) (1.7.0) +Requirement already satisfied: bcrypt==3.1.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 23)) (3.1.7) +Requirement already satisfied: bdbag==1.5.6 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 24)) (1.5.6) +Requirement already satisfied: beaker==1.11.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 25)) (1.11.0) +Requirement already satisfied: bioblend==0.13.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 26)) (0.13.0) +Requirement already satisfied: bleach==3.1.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 27)) (3.1.5) +Requirement already satisfied: boltons==20.2.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 28)) (20.2.0) +Requirement already satisfied: boto3==1.9.114 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 29)) (1.9.114) +Requirement already satisfied: boto==2.49.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 30)) (2.49.0) +Requirement already satisfied: botocore==1.12.253 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 31)) (1.12.253) +Requirement already satisfied: bx-python==0.8.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 32)) (0.8.9) +Requirement already satisfied: cachecontrol==0.11.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 33)) (0.11.7) +Requirement already satisfied: cachetools==4.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 34)) (4.1.0) +Requirement already satisfied: certifi==2020.6.20 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 35)) (2020.6.20) +Requirement already satisfied: cffi==1.14.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 36)) (1.14.0) +Requirement already satisfied: chardet==3.0.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 37)) (3.0.4) +Requirement already satisfied: cheetah3==3.2.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 38)) (3.2.5) +Requirement already satisfied: cliff==3.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 39)) (3.1.0) +Requirement already satisfied: cloudauthz==0.6.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 40)) (0.6.0) +Requirement already satisfied: cloudbridge==2.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 41)) (2.0.0) +Requirement already satisfied: cmd2==0.8.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 42)) (0.8.9) +Requirement already satisfied: coloredlogs==14.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 43)) (14.0) +Requirement already satisfied: cryptography==3.2.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 44)) (3.2.1) +Requirement already satisfied: cwltool==1.0.20191225192155 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 45)) (1.0.20191225192155) +Requirement already satisfied: debtcollector==1.22.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 46)) (1.22.0) +Requirement already satisfied: decorator==4.4.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 47)) (4.4.2) +Requirement already satisfied: defusedxml==0.6.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 48)) (0.6.0) +Requirement already satisfied: deprecated==1.2.10 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 49)) (1.2.10) +Requirement already satisfied: deprecation==2.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 50)) (2.1.0) +Requirement already satisfied: dictobj==0.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 51)) (0.4) +Requirement already satisfied: docopt==0.6.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 52)) (0.6.2) +Requirement already satisfied: docutils==0.15.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 53)) (0.15.2) +Requirement already satisfied: dogpile.cache==0.9.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 54)) (0.9.2) +Requirement already satisfied: ecdsa==0.15 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 55)) (0.15) +Requirement already satisfied: fabric3==1.14.post1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 56)) (1.14.post1) +Requirement already satisfied: future==0.18.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 57)) (0.18.2) +Requirement already satisfied: futures==3.1.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 58)) (3.1.1) +Requirement already satisfied: galaxy-sequence-utils==1.1.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 59)) (1.1.5) +Requirement already satisfied: google-api-python-client==1.7.8 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 60)) (1.7.8) +Requirement already satisfied: google-auth-httplib2==0.0.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 61)) (0.0.3) +Requirement already satisfied: google-auth==1.18.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 62)) (1.18.0) +Requirement already satisfied: gxformat2==0.11.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 63)) (0.11.3) +Requirement already satisfied: h5py==2.10.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 64)) (2.10.0) +Requirement already satisfied: httplib2==0.18.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 65)) (0.18.1) +Requirement already satisfied: humanfriendly==8.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 66)) (8.2) +Requirement already satisfied: idna==2.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 67)) (2.9) +Requirement already satisfied: isa-rwval==0.10.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 70)) (0.10.9) +Requirement already satisfied: iso8601==0.1.12 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 71)) (0.1.12) +Requirement already satisfied: isodate==0.6.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 72)) (0.6.0) +Requirement already satisfied: jmespath==0.10.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 73)) (0.10.0) +Requirement already satisfied: jsonpatch==1.26 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 74)) (1.26) +Requirement already satisfied: jsonpointer==2.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 75)) (2.0) +Requirement already satisfied: jsonschema==3.2.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 76)) (3.2.0) +Requirement already satisfied: keystoneauth1==4.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 77)) (4.1.0) +Requirement already satisfied: kombu==4.6.11 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 78)) (4.6.11) +Requirement already satisfied: lockfile==0.12.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 79)) (0.12.2) +Requirement already satisfied: lxml==4.6.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 80)) (4.6.2) +Requirement already satisfied: mako==1.1.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 81)) (1.1.3) +Requirement already satisfied: markdown==3.2.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 82)) (3.2.2) +Requirement already satisfied: markupsafe==1.1.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 83)) (1.1.1) +Requirement already satisfied: mercurial==5.4.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 84)) (5.4.1) +Requirement already satisfied: mistune==0.8.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 85)) (0.8.4) +Requirement already satisfied: msgpack==1.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 86)) (1.0.0) +Requirement already satisfied: msrest==0.5.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 87)) (0.5.5) +Requirement already satisfied: msrestazure==0.5.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 88)) (0.5.0) +Requirement already satisfied: munch==2.5.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 89)) (2.5.0) +Requirement already satisfied: mypy-extensions==0.4.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 90)) (0.4.3) +Requirement already satisfied: netaddr==0.7.20 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 91)) (0.7.20) +Requirement already satisfied: netifaces==0.10.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 92)) (0.10.9) +Requirement already satisfied: networkx==1.11 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 93)) (1.11) +Requirement already satisfied: nodeenv==1.4.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 94)) (1.4.0) +Requirement already satisfied: nose==1.3.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 95)) (1.3.7) +Requirement already satisfied: numpy==1.18.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 96)) (1.18.5) +Requirement already satisfied: oauth2client==4.1.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 97)) (4.1.3) +Requirement already satisfied: oauthlib==3.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 98)) (3.1.0) +Requirement already satisfied: openstacksdk==0.17.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 99)) (0.17.0) +Requirement already satisfied: os-client-config==2.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 100)) (2.1.0) +Requirement already satisfied: os-service-types==1.7.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 101)) (1.7.0) +Requirement already satisfied: osc-lib==2.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 102)) (2.0.0) +Requirement already satisfied: oslo.config==7.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 103)) (7.0.0) +Requirement already satisfied: oslo.context==2.23.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 104)) (2.23.1) +Requirement already satisfied: oslo.i18n==3.25.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 105)) (3.25.1) +Requirement already satisfied: oslo.log==3.45.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 106)) (3.45.2) +Requirement already satisfied: oslo.serialization==2.29.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 107)) (2.29.2) +Requirement already satisfied: oslo.utils==3.42.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 108)) (3.42.1) +Requirement already satisfied: oyaml==0.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 109)) (0.9) +Requirement already satisfied: packaging==20.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 110)) (20.4) +Requirement already satisfied: paramiko==2.7.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 111)) (2.7.1) +Requirement already satisfied: parsley==1.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 112)) (1.3) +Requirement already satisfied: paste==3.4.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 113)) (3.4.1) +Requirement already satisfied: pastedeploy==2.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 114)) (2.1.0) +Requirement already satisfied: pastescript==3.2.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 115)) (3.2.0) +Requirement already satisfied: pbr==5.4.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 117)) (5.4.5) +Requirement already satisfied: prettytable==0.7.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 118)) (0.7.2) +Requirement already satisfied: prov==1.5.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 119)) (1.5.1) +Requirement already satisfied: psutil==5.7.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 120)) (5.7.0) +Requirement already satisfied: pulsar-galaxy-lib==0.14.0.dev4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 121)) (0.14.0.dev4) +Requirement already satisfied: pyasn1-modules==0.2.8 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 122)) (0.2.8) +Requirement already satisfied: pyasn1==0.4.8 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 123)) (0.4.8) +Requirement already satisfied: pycparser==2.20 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 124)) (2.20) +Requirement already satisfied: pycryptodome==3.9.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 125)) (3.9.7) +Requirement already satisfied: pyeventsystem==0.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 126)) (0.1.0) +Requirement already satisfied: pyinotify==0.9.6 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 127)) (0.9.6) +Requirement already satisfied: pyjwt==1.7.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 128)) (1.7.1) +Requirement already satisfied: pykwalify==1.7.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 129)) (1.7.0) +Requirement already satisfied: pynacl==1.4.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 130)) (1.4.0) +Requirement already satisfied: pyopenssl==19.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 131)) (19.1.0) +Requirement already satisfied: pyparsing==2.4.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 132)) (2.4.7) +Requirement already satisfied: pyperclip==1.8.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 133)) (1.8.0) +Requirement already satisfied: pyrsistent==0.16.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 134)) (0.16.0) +Requirement already satisfied: pysam==0.16.0.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 135)) (0.16.0.1) +Requirement already satisfied: pysftp==0.2.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 136)) (0.2.9) +Requirement already satisfied: python-cinderclient==4.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 137)) (4.0.0) +Requirement already satisfied: python-dateutil==2.8.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 138)) (2.8.1) +Requirement already satisfied: python-glanceclient==2.12.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 139)) (2.12.0) +Requirement already satisfied: python-jose==3.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 140)) (3.1.0) +Requirement already satisfied: python-keystoneclient==3.17.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 141)) (3.17.0) +Requirement already satisfied: python-neutronclient==6.9.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 142)) (6.9.0) +Requirement already satisfied: python-novaclient==11.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 143)) (11.0.0) +Requirement already satisfied: python-swiftclient==3.6.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 144)) (3.6.0) +Requirement already satisfied: python3-openid==3.1.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 145)) (3.1.0) +Requirement already satisfied: pytz==2020.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 146)) (2020.1) +Requirement already satisfied: pyuwsgi==2.0.19.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 147)) (2.0.19.1) +Requirement already satisfied: pyyaml==5.3.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 148)) (5.3.1) +Requirement already satisfied: rdflib-jsonld==0.4.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 149)) (0.4.0) +Requirement already satisfied: rdflib==4.2.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 150)) (4.2.2) +Requirement already satisfied: refgenconf==0.7.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 151)) (0.7.0) +Requirement already satisfied: repoze.lru==0.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 152)) (0.7) +Requirement already satisfied: requests-oauthlib==1.3.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 153)) (1.3.0) +Requirement already satisfied: requests-toolbelt==0.9.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 154)) (0.9.1) +Requirement already satisfied: requests==2.24.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 155)) (2.24.0) +Requirement already satisfied: requestsexceptions==1.4.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 156)) (1.4.0) +Requirement already satisfied: rfc3986==1.4.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 157)) (1.4.0) +Requirement already satisfied: routes==2.4.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 158)) (2.4.1) +Requirement already satisfied: rsa==4.6 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 159)) (4.6) +Requirement already satisfied: ruamel.yaml==0.16.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 161)) (0.16.0) +Requirement already satisfied: s3transfer==0.2.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 162)) (0.2.1) +Requirement already satisfied: scandir==1.10.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 163)) (1.10.0) +Requirement already satisfied: schema-salad==4.5.20191229160203 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 164)) (4.5.20191229160203) +Requirement already satisfied: setuptools-scm==4.1.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 165)) (4.1.2) +Requirement already satisfied: shellescape==3.4.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 166)) (3.4.1) +Requirement already satisfied: simplejson==3.17.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 167)) (3.17.0) +Requirement already satisfied: six==1.15.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 168)) (1.15.0) +Requirement already satisfied: social-auth-core[openidconnect]==3.3.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 169)) (3.3.0) +Requirement already satisfied: sortedcontainers==2.2.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 170)) (2.2.2) +Requirement already satisfied: sqlalchemy-migrate==0.13.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 171)) (0.13.0) +Requirement already satisfied: sqlalchemy-utils==0.36.6 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 172)) (0.36.6) +Requirement already satisfied: sqlalchemy==1.3.17 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 173)) (1.3.17) +Requirement already satisfied: sqlitedict==1.7.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 174)) (1.7.0) +Requirement already satisfied: sqlparse==0.3.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 175)) (0.3.1) +Requirement already satisfied: stevedore==1.32.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 176)) (1.32.0) +Requirement already satisfied: svgwrite==1.3.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 177)) (1.3.1) +Requirement already satisfied: tempita==0.5.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 178)) (0.5.2) +Requirement already satisfied: tenacity==4.12.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 179)) (4.12.0) +Requirement already satisfied: tqdm==4.46.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 180)) (4.46.1) +Requirement already satisfied: typing-extensions==3.7.4.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 181)) (3.7.4.2) +Requirement already satisfied: tzlocal==2.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 183)) (2.1) +Requirement already satisfied: ubiquerg==0.5.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 184)) (0.5.2) +Requirement already satisfied: unidecode==1.1.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 185)) (1.1.1) +Requirement already satisfied: uritemplate==3.0.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 186)) (3.0.1) +Requirement already satisfied: urllib3==1.25.9 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 187)) (1.25.9) +Requirement already satisfied: vine==1.3.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 188)) (1.3.0) +Requirement already satisfied: warlock==1.3.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 189)) (1.3.3) +Requirement already satisfied: wcwidth==0.2.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 190)) (0.2.5) +Requirement already satisfied: webencodings==0.5.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 191)) (0.5.1) +Requirement already satisfied: webob==1.8.6 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 192)) (1.8.6) +Requirement already satisfied: whoosh==2.7.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 193)) (2.7.4) +Requirement already satisfied: wrapt==1.12.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 194)) (1.12.1) +Requirement already satisfied: yacman==0.6.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 195)) (0.6.7) +Requirement already satisfied: alabaster==0.7.12 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (0.7.12) +Requirement already satisfied: commonmark==0.9.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 8)) (0.9.1) +Requirement already satisfied: coverage==5.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 9)) (5.1) +Requirement already satisfied: gunicorn==20.0.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 12)) (20.0.4) +Requirement already satisfied: imagesize==1.2.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 14)) (1.2.0) +Requirement already satisfied: jinja2==2.11.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 16)) (2.11.2) +Requirement already satisfied: mirakuru==2.0.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (2.0.2) +Requirement already satisfied: mock==3.0.5 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 21)) (3.0.5) +Requirement already satisfied: more-itertools==8.4.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 22)) (8.4.0) +Requirement already satisfied: nosehtml==0.4.6 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 24)) (0.4.6) +Requirement already satisfied: pathtools==0.1.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (0.1.2) +Requirement already satisfied: pluggy==0.13.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 28)) (0.13.1) +Requirement already satisfied: port-for==0.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 29)) (0.4) +Requirement already satisfied: py==1.8.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 32)) (1.8.2) +Requirement already satisfied: pygithub==1.51 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 33)) (1.51) +Requirement already satisfied: pygments==2.6.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 34)) (2.6.1) +Requirement already satisfied: pytest-cov==2.10.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 37)) (2.10.0) +Requirement already satisfied: pytest-html==1.22.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 38)) (1.22.1) +Requirement already satisfied: pytest-metadata==1.8.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 39)) (1.8.0) +Requirement already satisfied: pytest-mock==3.1.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 40)) (3.1.1) +Requirement already satisfied: pytest-postgresql==2.3.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 41)) (2.3.0) +Requirement already satisfied: pytest-pythonpath==0.7.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 42)) (0.7.3) +Requirement already satisfied: pytest==5.4.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 43)) (5.4.3) +Requirement already satisfied: python-irodsclient==0.8.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (0.8.3) +Requirement already satisfied: recommonmark==0.6.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 46)) (0.6.0) +Requirement already satisfied: responses==0.10.15 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 48)) (0.10.15) +Requirement already satisfied: selenium==3.141.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 49)) (3.141.0) +Requirement already satisfied: snowballstemmer==2.0.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (2.0.0) +Requirement already satisfied: sphinx-markdown-tables==0.0.15 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 52)) (0.0.15) +Requirement already satisfied: sphinx-rtd-theme==0.5.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 53)) (0.5.0) +Requirement already satisfied: sphinx==3.1.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 54)) (3.1.1) +Requirement already satisfied: sphinxcontrib-applehelp==1.0.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55)) (1.0.2) +Requirement already satisfied: sphinxcontrib-devhelp==1.0.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 56)) (1.0.2) +Requirement already satisfied: sphinxcontrib-htmlhelp==1.0.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 57)) (1.0.3) +Requirement already satisfied: sphinxcontrib-jsmath==1.0.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 58)) (1.0.1) +Requirement already satisfied: sphinxcontrib-qthelp==1.0.3 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 59)) (1.0.3) +Requirement already satisfied: sphinxcontrib-serializinghtml==1.1.4 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 60)) (1.1.4) +Requirement already satisfied: testfixtures==6.14.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 61)) (6.14.1) +Requirement already satisfied: twill==2.0 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 62)) (2.0) +Requirement already satisfied: watchdog==0.10.2 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 64)) (0.10.2) +Requirement already satisfied: xmlrunner==1.7.7 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 67)) (1.7.7) +Requirement already satisfied: pathlib2!=2.3.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 45)) (2.3.5) +Requirement already satisfied: setuptools in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 45)) (52.0.0) +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple +Requirement already satisfied: watchdog in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r /dev/stdin (line 1)) (0.10.2) +Requirement already satisfied: pathtools>=0.1.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (from watchdog->-r /dev/stdin (line 1)) (0.1.2) +The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable. +Activating virtualenv at /home/maria/.planemo/gx_venv_3 +2021-04-08 14:17:42,276 INFO [galaxy.queue_worker] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////tmp/tmpadfmv368/tmptimuq3h3/tmpxuw5b8fu/database/control.sqlite?isolation_level=IMMEDIATE +2021-04-08 14:17:42,374 INFO [galaxy.model.migrate.check] Creating database for URI [sqlite:////tmp/tmpwlal_jyf/galaxy.sqlite?isolation_level=IMMEDIATE] +2021-04-08 14:17:42,439 INFO [galaxy.model.migrate.check] Creating new database from scratch, skipping migrations +2021-04-08 14:17:53,853 INFO [galaxy.config] Install database targetting Galaxy's database configuration. +2021-04-08 14:17:53,873 ERROR [galaxy.visualization.genomes] Error reading twobit.loc +Traceback (most recent call last): + File "/tmp/tmpwlal_jyf/galaxy-dev/lib/galaxy/visualization/genomes.py", line 211, in reload_genomes + for line in open(os.path.join(self.app.config.tool_data_path, "twobit.loc")): +FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpwlal_jyf/galaxy-dev/tool-data/twobit.loc' +2021-04-08 14:17:53,995 INFO [galaxy.web_stack.handlers] JobConfiguration: No job handler assignment method is set, defaulting to 'db-preassign', set the `assign_with` attribute on <handlers> to override the default +2021-04-08 14:17:53,995 INFO [galaxy.jobs] Job handler assignment methods set to: db-preassign +2021-04-08 14:17:53,995 INFO [galaxy.jobs] Tag [_default_] handlers: main +2021-04-08 14:17:54,955 WARNI [galaxy.tools] The default shed tool config file (/tmp/tmpwlal_jyf/galaxy-dev/lib/galaxy/config/sample/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +2021-04-08 14:17:54,955 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmpwlal_jyf/tool_conf.xml +2021-04-08 14:17:55,001 WARNI [galaxy.tools] The default shed tool config file (/tmp/tmpwlal_jyf/galaxy-dev/lib/galaxy/config/sample/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +2021-04-08 14:17:55,001 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmpwlal_jyf/shed_tools_conf.xml +2021-04-08 14:17:55,001 WARNI [galaxy.tools] The default shed tool config file (/tmp/tmpwlal_jyf/galaxy-dev/lib/galaxy/config/sample/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +2021-04-08 14:17:55,001 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmpwlal_jyf/empty_tool_conf.xml +Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +Error loading a set of Dynamic Display Application links: Unable to find data table named "bam_iobio". +Error loading a set of Dynamic Display Application links: Unable to find data table named "intermine_simple_display". +Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +Error loading a set of Dynamic Display Application links: Unable to find data table named "vcf_iobio". +Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +Error loading a set of Dynamic Display Application links: Unable to find data table named "biom_simple_display". +Error loading a set of Dynamic Display Application links: Unable to find data table named "icn3d_simple_display". +Error loading a set of Dynamic Display Application links: Unable to find data table named "icn3d_simple_display". +Error loading a set of Dynamic Display Application links: Unable to find data table named "icn3d_simple_display". +2021-04-08 14:17:55,648 INFO [galaxy.jobs] Handler 'main' will load all configured runner plugins +2021-04-08 14:17:55,700 INFO [galaxy.jobs.handler] job handler stop queue started +2021-04-08 14:17:55,844 INFO [galaxy.jobs.handler] job handler queue started +2021-04-08 14:17:55,848 INFO [galaxy.jobs.handler] job handler stop queue started +2021-04-08 14:17:55,869 INFO [galaxy.workflow.scheduling_manager] No workflow schedulers plugin config file defined, using default scheduler. +2021-04-08 14:17:55,889 INFO [galaxy.queue_worker] Binding and starting galaxy control worker for main +2021-04-08 14:17:55,912 INFO [galaxy.queue_worker] Queuing async task rebuild_toolbox_search_index for main. +2021-04-08 14:17:56,089 INFO [galaxy.app] Galaxy app startup finished (14136.524 ms) +2021-04-08 14:17:56,130 INFO [galaxy.queue_worker] Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. +2021-04-08 14:17:58,068 INFO [galaxy.web_stack] Galaxy server instance 'main' is running +/home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/sqltypes.py:660: 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. + util.warn( +2021-04-08 14:17:58,713 INFO [galaxy.webapps.base.webapp] Session authenticated using Galaxy master api key +2021-04-08 14:17:58,729 INFO [galaxy.webapps.base.webapp] Session authenticated using Galaxy master api key +2021-04-08 14:17:59,033 INFO [galaxy.webapps.base.webapp] Session authenticated using Galaxy master api key +( FROGSSTAT_DESeq2_Preprocess ) > Test-1 ... 2021-04-08 14:17:59,547 INFO [galaxy.tools] Validated and populated state for tool request (29.197 ms) +2021-04-08 14:18:00,054 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 1 +2021-04-08 14:18:00,166 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=1,tool_id=upload1] (61.375 ms) +2021-04-08 14:18:00,167 INFO [galaxy.web_stack.handlers] (Job[id=1,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method +2021-04-08 14:18:00,210 INFO [galaxy.web_stack.handlers] (Job[id=1,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method +2021-04-08 14:18:00,557 INFO [galaxy.jobs.handler] (1) Job dispatched +2021-04-08 14:18:00,831 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpwlal_jyf/job_working_directory/000/1/tool_script.sh] for tool command [python '/tmp/tmpwlal_jyf/galaxy-dev/tools/data_source/upload.py' '/tmp/tmpwlal_jyf/galaxy-dev' '/tmp/tmpwlal_jyf/job_working_directory/000/1/registry.xml' '/tmp/tmpwlal_jyf/job_working_directory/000/1/upload_params.json' '1:/tmp/tmpwlal_jyf/job_working_directory/000/1/working/dataset_56914c31-1da1-4ba6-9d8d-bee435b6ff27_files:/tmp/tmpwlal_jyf/files/5/6/9/dataset_56914c31-1da1-4ba6-9d8d-bee435b6ff27.dat'] +2021-04-08 14:18:07,515 INFO [galaxy.tools] Validated and populated state for tool request (29.591 ms) +2021-04-08 14:18:07,576 INFO [galaxy.tools.actions] Handled output named dds for tool FROGSSTAT_DESeq2_Preprocess (3.358 ms) +2021-04-08 14:18:07,576 INFO [galaxy.tools.actions] Added output datasets to history (0.048 ms) +2021-04-08 14:18:07,578 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=FROGSSTAT_DESeq2_Preprocess] complete, ready to be enqueued (1.689 ms) +2021-04-08 14:18:07,645 INFO [galaxy.web_stack.handlers] (Job[id=2,tool_id=FROGSSTAT_DESeq2_Preprocess]) Handler 'main' assigned using 'db-preassign' assignment method +2021-04-08 14:18:08,266 INFO [galaxy.jobs.handler] (2) Job dispatched +2021-04-08 14:18:08,501 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpwlal_jyf/job_working_directory/000/2/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/maria/miniconda3/bin/activate' '/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/maria/miniconda3/bin/activate' '/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/maria/miniconda3/bin/activate' '/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/maria/miniconda3/bin/activate' '/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/maria/miniconda3/bin/activate' '/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/maria/miniconda3/bin/activate' '/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; deseq2_preprocess.py --data /tmp/tmpwlal_jyf/files/5/6/9/dataset_56914c31-1da1-4ba6-9d8d-bee435b6ff27.dat --var EnvType --out-Rdata /tmp/tmpwlal_jyf/files/5/7/c/dataset_57c160d0-66fb-4cec-9b5d-b1bf8b8b959d.dat] +2021-04-08 14:18:12,643 INFO [galaxy.tool_util.output_checker] Job error detected, failing job. Reasons are [{'type': 'exit_code', 'desc': 'Fatal error: Exit code 127 ()', 'exit_code': 127, 'code_desc': '', 'error_level': 3}] +FAIL + +====================================================================== +FAIL: ( FROGSSTAT_DESeq2_Preprocess ) > Test-1 +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/tmp/tmpwlal_jyf/galaxy-dev/test/functional/test_toolbox.py", line 99, in test_tool + self.do_it(tool_version=tool_version, test_index=test_index) + File "/tmp/tmpwlal_jyf/galaxy-dev/test/functional/test_toolbox.py", line 36, in do_it + verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data) + File "/tmp/tmpwlal_jyf/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 958, in verify_tool + raise e + File "/tmp/tmpwlal_jyf/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 954, in verify_tool + job_stdio = _verify_outputs(testdef, test_history, jobs, tool_id, data_list, data_collection_list, galaxy_interactor, quiet=quiet) + File "/tmp/tmpwlal_jyf/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 1126, in _verify_outputs + raise JobOutputsError(found_exceptions, job_stdio) +galaxy.tool_util.verify.interactor.JobOutputsError: Job in error state. +Job in error state. +-------------------- >> begin captured stdout << --------------------- +Problem in history with id 2891970512fa2d5a - summary of history's datasets and jobs below. +-------------------------------------- +| 1 - 16-phylo_import.Rdata (HID - NAME) +| Dataset State: +| ok +| Dataset Blurb: +| 390.5 KB +| Dataset Info: +| The uploaded binary file format cannot be determined automatically, please set the file 'Type' manually +| Peek: +| <table cellspacing="0" cellpadding="3"><tr><td>binary data</td></tr></table> +| Dataset Job Standard Output: +| *Standard output was empty.* +| Dataset Job Standard Error: +| *Standard error was empty.* +| +-------------------------------------- +| 2 - FROGSSTAT DESeq2 Preprocess: dds.Rdata (HID - NAME) +| Dataset State: +| error +| Dataset Blurb: +| error +| Dataset Info: +| /tmp/tmpwlal_jyf/job_working_directory/000/2/tool_script.sh: ligne 111: deseq2_preprocess.py : commande introuvable +| Peek: +| *Peek unavilable.* +| Dataset Job Standard Output: +| *Standard output was empty.* +| Dataset Job Standard Error: +| /tmp/tmpwlal_jyf/job_working_directory/000/2/tool_script.sh: ligne 111: deseq2_preprocess.py : commande introuvable +| +-------------------------------------- +| Job 5729865256bc2525 +| State: +| error +| Update Time: +| 2021-04-08T12:18:13.004218 +| Create Time: +| 2021-04-08T12:18:07.583824 +| +-------------------------------------- +| Job 2891970512fa2d5a +| State: +| ok +| Update Time: +| 2021-04-08T12:18:07.294113 +| Create Time: +| 2021-04-08T12:18:00.018829 +| +-------------------------------------- +Problem in history with id 2891970512fa2d5a - summary of history's datasets and jobs below. +-------------------------------------- +| 1 - 16-phylo_import.Rdata (HID - NAME) +| Dataset State: +| ok +| Dataset Blurb: +| 390.5 KB +| Dataset Info: +| The uploaded binary file format cannot be determined automatically, please set the file 'Type' manually +| Peek: +| <table cellspacing="0" cellpadding="3"><tr><td>binary data</td></tr></table> +| Dataset Job Standard Output: +| *Standard output was empty.* +| Dataset Job Standard Error: +| *Standard error was empty.* +| +-------------------------------------- +| 2 - FROGSSTAT DESeq2 Preprocess: dds.Rdata (HID - NAME) +| Dataset State: +| error +| Dataset Blurb: +| error +| Dataset Info: +| /tmp/tmpwlal_jyf/job_working_directory/000/2/tool_script.sh: ligne 111: deseq2_preprocess.py : commande introuvable +| Peek: +| *Peek unavilable.* +| Dataset Job Standard Output: +| *Standard output was empty.* +| Dataset Job Standard Error: +| /tmp/tmpwlal_jyf/job_working_directory/000/2/tool_script.sh: ligne 111: deseq2_preprocess.py : commande introuvable +| +-------------------------------------- +| Job 5729865256bc2525 +| State: +| error +| Update Time: +| 2021-04-08T12:18:13.004218 +| Create Time: +| 2021-04-08T12:18:07.583824 +| +-------------------------------------- +| Job 2891970512fa2d5a +| State: +| ok +| Update Time: +| 2021-04-08T12:18:07.294113 +| Create Time: +| 2021-04-08T12:18:00.018829 +| +-------------------------------------- + +--------------------- >> end captured stdout << ---------------------- + +---------------------------------------------------------------------- +XML: /tmp/tmpwlal_jyf/xunit.xml +---------------------------------------------------------------------- +Ran 1 test in 15.192s + +FAILED (failures=1) +2021-04-08 14:18:14,473 INFO [test_driver] Shutting down +2021-04-08 14:18:14,474 INFO [test_driver] Shutting down embedded galaxy web server +2021-04-08 14:18:14,479 INFO [test_driver] Embedded web server galaxy stopped +2021-04-08 14:18:14,479 INFO [test_driver] Stopping application galaxy +2021-04-08 14:18:15,187 INFO [galaxy.queue_worker] Sending reconfigure_watcher control task. +2021-04-08 14:18:15,223 INFO [galaxy.jobs.handler] sending stop signal to worker thread +2021-04-08 14:18:15,223 INFO [galaxy.jobs.handler] job handler queue stopped +2021-04-08 14:18:15,223 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 job worker threads +2021-04-08 14:18:15,223 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown... +2021-04-08 14:18:15,224 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly +2021-04-08 14:18:15,224 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 job worker threads +2021-04-08 14:18:15,224 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown... +2021-04-08 14:18:15,225 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly +2021-04-08 14:18:15,225 INFO [galaxy.jobs.handler] sending stop signal to worker thread +2021-04-08 14:18:15,225 INFO [galaxy.jobs.handler] job handler stop queue stopped +2021-04-08 14:18:15,225 INFO [test_driver] Application galaxy stopped. +Testing complete. HTML report is in "/home/maria/workspace/FROGS-wrappers_dev/tool_test_output.html". +There were problems with 1 test(s) - out of 1 test(s) executed. See /home/maria/workspace/FROGS-wrappers_dev/tool_test_output.html for detailed breakdown. +FROGSSTAT_DESeq2_Preprocess (Test #1): failed