comparison nohup.out @ 2:bf36e0afdfb4 draft default tip

"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/optitype commit 703114ab7ad18b1b0e824b103f1df213448c6e97-dirty"

2:bf36e0afdfb4

git --git-dir /Users/jj/.planemo/gx_repo config remote.origin.fetch '+refs/*:refs/*'
git --git-dir /Users/jj/.planemo/gx_repo config remote.origin.mirror true
git --git-dir /Users/jj/.planemo/gx_repo remote update >/dev/null 2>&1
galaxy.tool_util.deps.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
git clone --branch master /Users/jj/.planemo/gx_repo /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev
Cloning into '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev'...
done.
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if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/Users/jj/.planemo/gx_venv; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /Users/jj/.planemo/gx_venv/bin/virtualenv -p /Users/jj/.planemo/gx_venv/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; 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.tool_util.deps.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
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
Unsetting $PYTHONPATH
Activating virtualenv at /Users/jj/.planemo/gx_venv
Galaxy support for Python 2.7 is deprecated, please consider moving to
Python >= 3.5 .
https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions
on how to force Galaxy to use a different version.
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Requirement already satisfied: pip>=8.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (20.0.2)
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Ignoring pyinotify: markers 'sys_platform != "win32" and sys_platform != "darwin" and sys_platform != "sunos5"' don't match your environment
Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple
Requirement already satisfied: adal==1.2.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) (1.2.2)
Requirement already satisfied: amqp==2.5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) (2.5.2)
Requirement already satisfied: appdirs==1.4.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) (1.4.3)
Requirement already satisfied: attrs==19.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) (19.3.0)
Requirement already satisfied: azure-common==1.1.14 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) (1.1.14)
Requirement already satisfied: azure-cosmosdb-nspkg==2.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) (2.0.2)
Requirement already satisfied: azure-cosmosdb-table==1.0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) (1.0.4)
Requirement already satisfied: azure-mgmt-compute==4.0.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 10)) (4.0.1)
Requirement already satisfied: azure-mgmt-devtestlabs==2.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 11)) (2.2.0)
Requirement already satisfied: azure-mgmt-network==2.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 12)) (2.1.0)
Requirement already satisfied: azure-mgmt-nspkg==3.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 13)) (3.0.2)
Requirement already satisfied: azure-mgmt-resource==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 14)) (2.0.0)
Requirement already satisfied: azure-mgmt-storage==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15)) (2.0.0)
Requirement already satisfied: azure-nspkg==3.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) (3.0.2)
Requirement already satisfied: azure-storage-blob==1.3.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) (1.3.1)
Requirement already satisfied: azure-storage-common==1.4.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) (1.4.2)
Requirement already satisfied: azure-storage-nspkg==3.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) (3.1.0)
Requirement already satisfied: babel==2.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) (2.7.0)
Requirement already satisfied: bagit==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) (1.7.0)
Requirement already satisfied: bcrypt==3.1.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) (3.1.7)
Requirement already satisfied: bdbag==1.5.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) (1.5.6)
Requirement already satisfied: beaker==1.11.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) (1.11.0)
Requirement already satisfied: bioblend==0.13.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) (0.13.0)
Requirement already satisfied: bleach==3.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) (3.1.1)
Requirement already satisfied: boltons==19.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) (19.3.0)
Requirement already satisfied: boto3==1.9.114 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) (1.9.114)
Requirement already satisfied: boto==2.49.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) (2.49.0)
Requirement already satisfied: botocore==1.12.253 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) (1.12.253)
Requirement already satisfied: bx-python==0.8.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) (0.8.8)
Requirement already satisfied: bz2file==0.98 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) (0.98)
Requirement already satisfied: cachecontrol==0.11.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) (0.11.7)
Requirement already satisfied: cachetools==3.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) (3.1.1)
Requirement already satisfied: certifi==2019.11.28 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) (2019.11.28)
Requirement already satisfied: cffi==1.13.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) (1.13.2)
Requirement already satisfied: chardet==3.0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) (3.0.4)
Requirement already satisfied: cheetah3==3.2.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 38)) (3.2.4)
Requirement already satisfied: cliff==2.16.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) (2.16.0)
Requirement already satisfied: cloudauthz==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) (0.6.0)
Requirement already satisfied: cloudbridge==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) (2.0.0)
Requirement already satisfied: cmd2==0.8.9 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) (0.8.9)
Requirement already satisfied: coloredlogs==10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 43)) (10.0)
Requirement already satisfied: configparser==4.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) (4.0.2)
Requirement already satisfied: contextlib2==0.6.0.post1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) (0.6.0.post1)
Requirement already satisfied: cryptography==2.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) (2.8)
Requirement already satisfied: cwltool==1.0.20191225192155 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) (1.0.20191225192155)
Requirement already satisfied: debtcollector==1.22.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) (1.22.0)
Requirement already satisfied: decorator==4.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) (4.4.1)
Requirement already satisfied: deprecated==1.2.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) (1.2.7)
Requirement already satisfied: deprecation==2.0.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) (2.0.7)
Requirement already satisfied: dictobj==0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) (0.4)
Requirement already satisfied: docopt==0.6.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) (0.6.2)
Requirement already satisfied: docutils==0.15.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) (0.15.2)
Requirement already satisfied: dogpile.cache==0.9.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) (0.9.0)
Requirement already satisfied: ecdsa==0.14.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) (0.14.1)
Requirement already satisfied: enum34==1.1.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) (1.1.6)
Requirement already satisfied: fabric3==1.14.post1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) (1.14.post1)
Requirement already satisfied: funcsigs==1.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) (1.0.2)
Requirement already satisfied: functools32==3.2.3.post2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) (3.2.3.post2)
Requirement already satisfied: future==0.18.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 61)) (0.18.2)
Requirement already satisfied: futures==3.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 62)) (3.3.0)
Requirement already satisfied: galaxy-sequence-utils==1.1.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) (1.1.4)
Requirement already satisfied: google-api-python-client==1.7.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) (1.7.8)
Requirement already satisfied: google-auth-httplib2==0.0.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) (0.0.3)
Requirement already satisfied: google-auth==1.7.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) (1.7.1)
Requirement already satisfied: gxformat2==0.10.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) (0.10.1)
Requirement already satisfied: h5py==2.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 68)) (2.10.0)
Requirement already satisfied: httplib2==0.15.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) (0.15.0)
Requirement already satisfied: humanfriendly==4.18 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) (4.18)
Requirement already satisfied: idna==2.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) (2.8)
Requirement already satisfied: importlib-metadata==1.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 72)) (1.2.0)
Requirement already satisfied: ipaddress==1.0.23 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 73)) (1.0.23)
Requirement already satisfied: isa-rwval==0.10.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) (0.10.7)
Requirement already satisfied: iso8601==0.1.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) (0.1.12)
Requirement already satisfied: isodate==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) (0.6.0)
Requirement already satisfied: jmespath==0.9.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 77)) (0.9.4)
Requirement already satisfied: jsonpatch==1.24 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 78)) (1.24)
Requirement already satisfied: jsonpointer==2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) (2.0)
Requirement already satisfied: jsonschema==3.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 80)) (3.2.0)
Requirement already satisfied: keystoneauth1==3.18.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 81)) (3.18.0)
Requirement already satisfied: kombu==4.6.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) (4.6.6)
Requirement already satisfied: lockfile==0.12.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 83)) (0.12.2)
Requirement already satisfied: lxml==4.4.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 84)) (4.4.2)
Requirement already satisfied: mako==1.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 85)) (1.1.0)
Requirement already satisfied: markdown==3.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 86)) (3.1.1)
Requirement already satisfied: markupsafe==1.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 87)) (1.1.1)
Requirement already satisfied: mercurial==5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 88)) (5.2)
Requirement already satisfied: mistune==0.8.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 89)) (0.8.4)
Requirement already satisfied: monotonic==1.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 90)) (1.5)
Requirement already satisfied: more-itertools==5.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 91)) (5.0.0)
Requirement already satisfied: msgpack==0.6.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 92)) (0.6.2)
Requirement already satisfied: msrest==0.5.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 93)) (0.5.5)
Requirement already satisfied: msrestazure==0.5.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 94)) (0.5.0)
Requirement already satisfied: munch==2.5.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 95)) (2.5.0)
Requirement already satisfied: mypy-extensions==0.4.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 96)) (0.4.3)
Requirement already satisfied: netaddr==0.7.19 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 97)) (0.7.19)
Requirement already satisfied: netifaces==0.10.9 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 98)) (0.10.9)
Requirement already satisfied: networkx==1.11 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 99)) (1.11)
Requirement already satisfied: nodeenv==1.3.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 100)) (1.3.3)
Requirement already satisfied: nose==1.3.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 101)) (1.3.7)
Requirement already satisfied: numpy==1.16.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 102)) (1.16.5)
Requirement already satisfied: oauth2client==4.1.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 103)) (4.1.3)
Requirement already satisfied: oauthlib==3.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 104)) (3.1.0)
Requirement already satisfied: openstacksdk==0.17.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 105)) (0.17.0)
Requirement already satisfied: os-client-config==1.33.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 106)) (1.33.0)
Requirement already satisfied: os-service-types==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 107)) (1.7.0)
Requirement already satisfied: osc-lib==1.14.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 108)) (1.14.1)
Requirement already satisfied: oslo.config==6.12.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 109)) (6.12.0)
Requirement already satisfied: oslo.context==2.23.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 110)) (2.23.0)
Requirement already satisfied: oslo.i18n==3.25.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 111)) (3.25.0)
Requirement already satisfied: oslo.log==3.45.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 112)) (3.45.0)
Requirement already satisfied: oslo.serialization==2.29.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 113)) (2.29.2)
Requirement already satisfied: oslo.utils==3.42.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 114)) (3.42.0)
Requirement already satisfied: packaging==20.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 115)) (20.0)
Requirement already satisfied: paramiko==2.7.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 116)) (2.7.1)
Requirement already satisfied: parsley==1.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 117)) (1.3)
Requirement already satisfied: paste==3.2.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 118)) (3.2.3)
Requirement already satisfied: pastedeploy==2.0.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 119)) (2.0.1)
Requirement already satisfied: pastescript==3.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 120)) (3.2.0)
Requirement already satisfied: pathlib2==2.3.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 121)) (2.3.5)
Requirement already satisfied: pbr==5.4.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 122)) (5.4.4)
Requirement already satisfied: prettytable==0.7.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 123)) (0.7.2)
Requirement already satisfied: prov==1.5.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 124)) (1.5.1)
Requirement already satisfied: psutil==5.6.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 125)) (5.6.7)
Requirement already satisfied: pulsar-galaxy-lib==0.14.0.dev1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 126)) (0.14.0.dev1)
Requirement already satisfied: pyasn1-modules==0.2.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 127)) (0.2.7)
Requirement already satisfied: pyasn1==0.4.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 128)) (0.4.8)
Requirement already satisfied: pycparser==2.19 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 129)) (2.19)
Requirement already satisfied: pycryptodome==3.9.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 130)) (3.9.6)
Requirement already satisfied: pyeventsystem==0.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 131)) (0.1.0)
Requirement already satisfied: pyjwt==1.7.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 133)) (1.7.1)
Requirement already satisfied: pykwalify==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 134)) (1.7.0)
Requirement already satisfied: pynacl==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 135)) (1.3.0)
Requirement already satisfied: pyopenssl==19.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 136)) (19.1.0)
Requirement already satisfied: pyparsing==2.4.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 137)) (2.4.5)
Requirement already satisfied: pyperclip==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 138)) (1.7.0)
Requirement already satisfied: pyrsistent==0.15.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 139)) (0.15.6)
Requirement already satisfied: pysam==0.15.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 140)) (0.15.2)
Requirement already satisfied: pysftp==0.2.9 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 141)) (0.2.9)
Requirement already satisfied: python-cinderclient==4.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 142)) (4.0.0)
Requirement already satisfied: python-dateutil==2.8.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 143)) (2.8.1)
Requirement already satisfied: python-glanceclient==2.12.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 144)) (2.12.0)
Requirement already satisfied: python-jose==3.0.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 145)) (3.0.1)
Requirement already satisfied: python-keystoneclient==3.17.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 146)) (3.17.0)
Requirement already satisfied: python-neutronclient==6.9.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 147)) (6.9.0)
Requirement already satisfied: python-novaclient==11.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 148)) (11.0.0)
Requirement already satisfied: python-openid==2.2.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 149)) (2.2.5)
Requirement already satisfied: python-swiftclient==3.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 150)) (3.6.0)
Requirement already satisfied: pytz==2019.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 151)) (2019.3)
Requirement already satisfied: pyuwsgi==2.0.18.post0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 152)) (2.0.18.post0)
Requirement already satisfied: pyyaml==5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 153)) (5.2)
Requirement already satisfied: rdflib-jsonld==0.4.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 154)) (0.4.0)
Requirement already satisfied: rdflib==4.2.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 155)) (4.2.2)
Requirement already satisfied: repoze.lru==0.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 156)) (0.7)
Requirement already satisfied: requests-oauthlib==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 157)) (1.3.0)
Requirement already satisfied: requests-toolbelt==0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 158)) (0.9.1)
Requirement already satisfied: requests==2.22.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 159)) (2.22.0)
Requirement already satisfied: requestsexceptions==1.4.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 160)) (1.4.0)
Requirement already satisfied: rfc3986==1.3.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 161)) (1.3.2)
Requirement already satisfied: routes==2.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 162)) (2.4.1)
Requirement already satisfied: rsa==4.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 163)) (4.0)
Requirement already satisfied: ruamel.ordereddict==0.4.14 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 164)) (0.4.14)
Requirement already satisfied: ruamel.yaml.clib==0.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 165)) (0.2.0)
Requirement already satisfied: ruamel.yaml==0.16.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 166)) (0.16.0)
Requirement already satisfied: s3transfer==0.2.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 167)) (0.2.1)
Requirement already satisfied: scandir==1.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 168)) (1.10.0)
Requirement already satisfied: schema-salad==4.5.20191229160203 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 169)) (4.5.20191229160203)
Requirement already satisfied: setuptools-scm==3.3.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 170)) (3.3.3)
Requirement already satisfied: shellescape==3.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 171)) (3.4.1)
Requirement already satisfied: simplejson==3.17.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 172)) (3.17.0)
Requirement already satisfied: six==1.11.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 173)) (1.11.0)
Requirement already satisfied: social-auth-core[openidconnect]==3.1.0+gx0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 174)) (3.1.0+gx0)
Requirement already satisfied: sqlalchemy-migrate==0.13.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 175)) (0.13.0)
Requirement already satisfied: sqlalchemy-utils==0.35.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 176)) (0.35.0)
Requirement already satisfied: sqlalchemy==1.3.11 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 177)) (1.3.11)
Requirement already satisfied: sqlparse==0.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 178)) (0.3.0)
Requirement already satisfied: stevedore==1.31.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 179)) (1.31.0)
Requirement already satisfied: subprocess32==3.5.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 180)) (3.5.4)
Requirement already satisfied: svgwrite==1.3.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 181)) (1.3.1)
Requirement already satisfied: tempita==0.5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 182)) (0.5.2)
Requirement already satisfied: tenacity==4.12.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 183)) (4.12.0)
Requirement already satisfied: typing-extensions==3.7.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 184)) (3.7.4.1)
Requirement already satisfied: typing==3.7.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 185)) (3.7.4.1)
Requirement already satisfied: tzlocal==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 186)) (2.0.0)
Requirement already satisfied: unicodecsv==0.14.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 187)) (0.14.1)
Requirement already satisfied: uritemplate==3.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 188)) (3.0.0)
Requirement already satisfied: urllib3==1.25.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 189)) (1.25.7)
Requirement already satisfied: vine==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 190)) (1.3.0)
Requirement already satisfied: warlock==1.3.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 191)) (1.3.3)
Requirement already satisfied: wcwidth==0.1.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 192)) (0.1.7)
Requirement already satisfied: webencodings==0.5.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 193)) (0.5.1)
Requirement already satisfied: webob==1.8.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 194)) (1.8.5)
Requirement already satisfied: whoosh==2.7.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 195)) (2.7.4)
Requirement already satisfied: wrapt==1.11.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 196)) (1.11.2)
Requirement already satisfied: zipp==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 197)) (0.6.0)
Requirement already satisfied: alabaster==0.7.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (0.7.12)
Requirement already satisfied: argh==0.26.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) (0.26.2)
Requirement already satisfied: atomicwrites==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) (1.3.0)
Requirement already satisfied: commonmark==0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 10)) (0.9.1)
Requirement already satisfied: coverage==4.5.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 13)) (4.5.4)
Requirement already satisfied: gunicorn==19.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 18)) (19.10.0)
Requirement already satisfied: imagesize==1.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (1.1.0)
Requirement already satisfied: jinja2==2.10.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 22)) (2.10.3)
Requirement already satisfied: mirakuru==1.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 26)) (1.1.0)
Requirement already satisfied: mock==3.0.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (3.0.5)
Requirement already satisfied: nosehtml==0.4.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 30)) (0.4.5)
Requirement already satisfied: pathtools==0.1.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 33)) (0.1.2)
Requirement already satisfied: pluggy==0.13.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 34)) (0.13.1)
Requirement already satisfied: port-for==0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 35)) (0.4)
Requirement already satisfied: py==1.8.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 37)) (1.8.0)
Requirement already satisfied: pygithub==1.45 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 38)) (1.45)
Requirement already satisfied: pygments==2.5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 39)) (2.5.2)
Requirement already satisfied: pytest-cov==2.8.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 42)) (2.8.1)
Requirement already satisfied: pytest-html==1.22.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 43)) (1.22.1)
Requirement already satisfied: pytest-metadata==1.8.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (1.8.0)
Requirement already satisfied: pytest-postgresql==1.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 45)) (1.4.1)
Requirement already satisfied: pytest-pythonpath==0.7.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 46)) (0.7.3)
Requirement already satisfied: pytest==4.6.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 47)) (4.6.6)
Requirement already satisfied: recommonmark==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 49)) (0.6.0)
Requirement already satisfied: selenium==3.141.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 52)) (3.141.0)
Requirement already satisfied: snowballstemmer==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 54)) (2.0.0)
Requirement already satisfied: sphinx-markdown-tables==0.0.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55)) (0.0.12)
Requirement already satisfied: sphinx-rtd-theme==0.4.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 56)) (0.4.3)
Requirement already satisfied: sphinx==1.8.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 57)) (1.8.5)
Requirement already satisfied: sphinxcontrib-websupport==1.1.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 58)) (1.1.2)
Requirement already satisfied: testfixtures==6.10.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 59)) (6.10.3)
Requirement already satisfied: twill==0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 60)) (0.9.1)
Requirement already satisfied: watchdog==0.9.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 63)) (0.9.0)
Requirement already satisfied: setuptools in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 47)) (28.8.0)
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple
Requirement already satisfied: pykube==0.15.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r /dev/stdin (line 1)) (0.15.0)
Requirement already satisfied: PyYAML in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (5.2)
Requirement already satisfied: requests>=2.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (2.22.0)
Requirement already satisfied: tzlocal in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (2.0.0)
Requirement already satisfied: six>=1.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (1.11.0)
Requirement already satisfied: requests-oauthlib in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (1.3.0)
Requirement already satisfied: oauth2client in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (4.1.3)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (3.0.4)
Requirement already satisfied: idna<2.9,>=2.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (2.8)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (1.25.7)
Requirement already satisfied: certifi>=2017.4.17 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (2019.11.28)
Requirement already satisfied: pytz in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from tzlocal->pykube==0.15.0->-r /dev/stdin (line 1)) (2019.3)
Requirement already satisfied: oauthlib>=3.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests-oauthlib->pykube==0.15.0->-r /dev/stdin (line 1)) (3.1.0)
Requirement already satisfied: pyasn1>=0.1.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (0.4.8)
Requirement already satisfied: pyasn1-modules>=0.0.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (0.2.7)
Requirement already satisfied: httplib2>=0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (0.15.0)
Requirement already satisfied: rsa>=3.1.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (4.0)
The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable.
Testing using galaxy_root /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev
Testing tools with command [cd /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev && if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/Users/jj/.planemo/gx_venv; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /Users/jj/.planemo/gx_venv/bin/virtualenv -p /Users/jj/.planemo/gx_venv/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; fi && sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /Users/jj/gx/gh/jj/galaxytools/optitype/tool_test_output.html --xunit_report_file /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/xunit.xml --structured_data_report_file /Users/jj/gx/gh/jj/galaxytools/optitype/tool_test_output.json functional.test_toolbox]
galaxy.tool_util.deps.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
Unsetting $PYTHONPATH
Activating virtualenv at /Users/jj/.planemo/gx_venv
Galaxy support for Python 2.7 is deprecated, please consider moving to
Python >= 3.5 .
https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions
on how to force Galaxy to use a different version.
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Requirement already satisfied: pip>=8.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (20.0.2)
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Ignoring pyinotify: markers 'sys_platform != "win32" and sys_platform != "darwin" and sys_platform != "sunos5"' don't match your environment
Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple
Requirement already satisfied: adal==1.2.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) (1.2.2)
Requirement already satisfied: amqp==2.5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) (2.5.2)
Requirement already satisfied: appdirs==1.4.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) (1.4.3)
Requirement already satisfied: attrs==19.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) (19.3.0)
Requirement already satisfied: azure-common==1.1.14 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) (1.1.14)
Requirement already satisfied: azure-cosmosdb-nspkg==2.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) (2.0.2)
Requirement already satisfied: azure-cosmosdb-table==1.0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) (1.0.4)
Requirement already satisfied: azure-mgmt-compute==4.0.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 10)) (4.0.1)
Requirement already satisfied: azure-mgmt-devtestlabs==2.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 11)) (2.2.0)
Requirement already satisfied: azure-mgmt-network==2.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 12)) (2.1.0)
Requirement already satisfied: azure-mgmt-nspkg==3.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 13)) (3.0.2)
Requirement already satisfied: azure-mgmt-resource==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 14)) (2.0.0)
Requirement already satisfied: azure-mgmt-storage==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15)) (2.0.0)
Requirement already satisfied: azure-nspkg==3.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) (3.0.2)
Requirement already satisfied: azure-storage-blob==1.3.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) (1.3.1)
Requirement already satisfied: azure-storage-common==1.4.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) (1.4.2)
Requirement already satisfied: azure-storage-nspkg==3.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) (3.1.0)
Requirement already satisfied: babel==2.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) (2.7.0)
Requirement already satisfied: bagit==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) (1.7.0)
Requirement already satisfied: bcrypt==3.1.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) (3.1.7)
Requirement already satisfied: bdbag==1.5.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) (1.5.6)
Requirement already satisfied: beaker==1.11.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) (1.11.0)
Requirement already satisfied: bioblend==0.13.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) (0.13.0)
Requirement already satisfied: bleach==3.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) (3.1.1)
Requirement already satisfied: boltons==19.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) (19.3.0)
Requirement already satisfied: boto3==1.9.114 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) (1.9.114)
Requirement already satisfied: boto==2.49.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) (2.49.0)
Requirement already satisfied: botocore==1.12.253 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) (1.12.253)
Requirement already satisfied: bx-python==0.8.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) (0.8.8)
Requirement already satisfied: bz2file==0.98 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) (0.98)
Requirement already satisfied: cachecontrol==0.11.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) (0.11.7)
Requirement already satisfied: cachetools==3.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) (3.1.1)
Requirement already satisfied: certifi==2019.11.28 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) (2019.11.28)
Requirement already satisfied: cffi==1.13.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) (1.13.2)
Requirement already satisfied: chardet==3.0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) (3.0.4)
Requirement already satisfied: cheetah3==3.2.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 38)) (3.2.4)
Requirement already satisfied: cliff==2.16.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) (2.16.0)
Requirement already satisfied: cloudauthz==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) (0.6.0)
Requirement already satisfied: cloudbridge==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) (2.0.0)
Requirement already satisfied: cmd2==0.8.9 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) (0.8.9)
Requirement already satisfied: coloredlogs==10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 43)) (10.0)
Requirement already satisfied: configparser==4.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) (4.0.2)
Requirement already satisfied: contextlib2==0.6.0.post1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) (0.6.0.post1)
Requirement already satisfied: cryptography==2.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) (2.8)
Requirement already satisfied: cwltool==1.0.20191225192155 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) (1.0.20191225192155)
Requirement already satisfied: debtcollector==1.22.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) (1.22.0)
Requirement already satisfied: decorator==4.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) (4.4.1)
Requirement already satisfied: deprecated==1.2.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) (1.2.7)
Requirement already satisfied: deprecation==2.0.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) (2.0.7)
Requirement already satisfied: dictobj==0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) (0.4)
Requirement already satisfied: docopt==0.6.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) (0.6.2)
Requirement already satisfied: docutils==0.15.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) (0.15.2)
Requirement already satisfied: dogpile.cache==0.9.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) (0.9.0)
Requirement already satisfied: ecdsa==0.14.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) (0.14.1)
Requirement already satisfied: enum34==1.1.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) (1.1.6)
Requirement already satisfied: fabric3==1.14.post1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) (1.14.post1)
Requirement already satisfied: funcsigs==1.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) (1.0.2)
Requirement already satisfied: functools32==3.2.3.post2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) (3.2.3.post2)
Requirement already satisfied: future==0.18.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 61)) (0.18.2)
Requirement already satisfied: futures==3.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 62)) (3.3.0)
Requirement already satisfied: galaxy-sequence-utils==1.1.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) (1.1.4)
Requirement already satisfied: google-api-python-client==1.7.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) (1.7.8)
Requirement already satisfied: google-auth-httplib2==0.0.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) (0.0.3)
Requirement already satisfied: google-auth==1.7.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) (1.7.1)
Requirement already satisfied: gxformat2==0.10.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) (0.10.1)
Requirement already satisfied: h5py==2.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 68)) (2.10.0)
Requirement already satisfied: httplib2==0.15.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) (0.15.0)
Requirement already satisfied: humanfriendly==4.18 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) (4.18)
Requirement already satisfied: idna==2.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) (2.8)
Requirement already satisfied: importlib-metadata==1.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 72)) (1.2.0)
Requirement already satisfied: ipaddress==1.0.23 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 73)) (1.0.23)
Requirement already satisfied: isa-rwval==0.10.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) (0.10.7)
Requirement already satisfied: iso8601==0.1.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) (0.1.12)
Requirement already satisfied: isodate==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) (0.6.0)
Requirement already satisfied: jmespath==0.9.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 77)) (0.9.4)
Requirement already satisfied: jsonpatch==1.24 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 78)) (1.24)
Requirement already satisfied: jsonpointer==2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) (2.0)
Requirement already satisfied: jsonschema==3.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 80)) (3.2.0)
Requirement already satisfied: keystoneauth1==3.18.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 81)) (3.18.0)
Requirement already satisfied: kombu==4.6.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) (4.6.6)
Requirement already satisfied: lockfile==0.12.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 83)) (0.12.2)
Requirement already satisfied: lxml==4.4.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 84)) (4.4.2)
Requirement already satisfied: mako==1.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 85)) (1.1.0)
Requirement already satisfied: markdown==3.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 86)) (3.1.1)
Requirement already satisfied: markupsafe==1.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 87)) (1.1.1)
Requirement already satisfied: mercurial==5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 88)) (5.2)
Requirement already satisfied: mistune==0.8.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 89)) (0.8.4)
Requirement already satisfied: monotonic==1.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 90)) (1.5)
Requirement already satisfied: more-itertools==5.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 91)) (5.0.0)
Requirement already satisfied: msgpack==0.6.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 92)) (0.6.2)
Requirement already satisfied: msrest==0.5.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 93)) (0.5.5)
Requirement already satisfied: msrestazure==0.5.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 94)) (0.5.0)
Requirement already satisfied: munch==2.5.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 95)) (2.5.0)
Requirement already satisfied: mypy-extensions==0.4.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 96)) (0.4.3)
Requirement already satisfied: netaddr==0.7.19 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 97)) (0.7.19)
Requirement already satisfied: netifaces==0.10.9 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 98)) (0.10.9)
Requirement already satisfied: networkx==1.11 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 99)) (1.11)
Requirement already satisfied: nodeenv==1.3.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 100)) (1.3.3)
Requirement already satisfied: nose==1.3.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 101)) (1.3.7)
Requirement already satisfied: numpy==1.16.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 102)) (1.16.5)
Requirement already satisfied: oauth2client==4.1.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 103)) (4.1.3)
Requirement already satisfied: oauthlib==3.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 104)) (3.1.0)
Requirement already satisfied: openstacksdk==0.17.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 105)) (0.17.0)
Requirement already satisfied: os-client-config==1.33.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 106)) (1.33.0)
Requirement already satisfied: os-service-types==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 107)) (1.7.0)
Requirement already satisfied: osc-lib==1.14.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 108)) (1.14.1)
Requirement already satisfied: oslo.config==6.12.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 109)) (6.12.0)
Requirement already satisfied: oslo.context==2.23.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 110)) (2.23.0)
Requirement already satisfied: oslo.i18n==3.25.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 111)) (3.25.0)
Requirement already satisfied: oslo.log==3.45.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 112)) (3.45.0)
Requirement already satisfied: oslo.serialization==2.29.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 113)) (2.29.2)
Requirement already satisfied: oslo.utils==3.42.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 114)) (3.42.0)
Requirement already satisfied: packaging==20.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 115)) (20.0)
Requirement already satisfied: paramiko==2.7.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 116)) (2.7.1)
Requirement already satisfied: parsley==1.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 117)) (1.3)
Requirement already satisfied: paste==3.2.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 118)) (3.2.3)
Requirement already satisfied: pastedeploy==2.0.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 119)) (2.0.1)
Requirement already satisfied: pastescript==3.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 120)) (3.2.0)
Requirement already satisfied: pathlib2==2.3.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 121)) (2.3.5)
Requirement already satisfied: pbr==5.4.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 122)) (5.4.4)
Requirement already satisfied: prettytable==0.7.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 123)) (0.7.2)
Requirement already satisfied: prov==1.5.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 124)) (1.5.1)
Requirement already satisfied: psutil==5.6.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 125)) (5.6.7)
Requirement already satisfied: pulsar-galaxy-lib==0.14.0.dev1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 126)) (0.14.0.dev1)
Requirement already satisfied: pyasn1-modules==0.2.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 127)) (0.2.7)
Requirement already satisfied: pyasn1==0.4.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 128)) (0.4.8)
Requirement already satisfied: pycparser==2.19 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 129)) (2.19)
Requirement already satisfied: pycryptodome==3.9.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 130)) (3.9.6)
Requirement already satisfied: pyeventsystem==0.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 131)) (0.1.0)
Requirement already satisfied: pyjwt==1.7.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 133)) (1.7.1)
Requirement already satisfied: pykwalify==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 134)) (1.7.0)
Requirement already satisfied: pynacl==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 135)) (1.3.0)
Requirement already satisfied: pyopenssl==19.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 136)) (19.1.0)
Requirement already satisfied: pyparsing==2.4.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 137)) (2.4.5)
Requirement already satisfied: pyperclip==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 138)) (1.7.0)
Requirement already satisfied: pyrsistent==0.15.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 139)) (0.15.6)
Requirement already satisfied: pysam==0.15.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 140)) (0.15.2)
Requirement already satisfied: pysftp==0.2.9 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 141)) (0.2.9)
Requirement already satisfied: python-cinderclient==4.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 142)) (4.0.0)
Requirement already satisfied: python-dateutil==2.8.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 143)) (2.8.1)
Requirement already satisfied: python-glanceclient==2.12.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 144)) (2.12.0)
Requirement already satisfied: python-jose==3.0.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 145)) (3.0.1)
Requirement already satisfied: python-keystoneclient==3.17.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 146)) (3.17.0)
Requirement already satisfied: python-neutronclient==6.9.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 147)) (6.9.0)
Requirement already satisfied: python-novaclient==11.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 148)) (11.0.0)
Requirement already satisfied: python-openid==2.2.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 149)) (2.2.5)
Requirement already satisfied: python-swiftclient==3.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 150)) (3.6.0)
Requirement already satisfied: pytz==2019.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 151)) (2019.3)
Requirement already satisfied: pyuwsgi==2.0.18.post0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 152)) (2.0.18.post0)
Requirement already satisfied: pyyaml==5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 153)) (5.2)
Requirement already satisfied: rdflib-jsonld==0.4.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 154)) (0.4.0)
Requirement already satisfied: rdflib==4.2.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 155)) (4.2.2)
Requirement already satisfied: repoze.lru==0.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 156)) (0.7)
Requirement already satisfied: requests-oauthlib==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 157)) (1.3.0)
Requirement already satisfied: requests-toolbelt==0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 158)) (0.9.1)
Requirement already satisfied: requests==2.22.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 159)) (2.22.0)
Requirement already satisfied: requestsexceptions==1.4.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 160)) (1.4.0)
Requirement already satisfied: rfc3986==1.3.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 161)) (1.3.2)
Requirement already satisfied: routes==2.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 162)) (2.4.1)
Requirement already satisfied: rsa==4.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 163)) (4.0)
Requirement already satisfied: ruamel.ordereddict==0.4.14 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 164)) (0.4.14)
Requirement already satisfied: ruamel.yaml.clib==0.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 165)) (0.2.0)
Requirement already satisfied: ruamel.yaml==0.16.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 166)) (0.16.0)
Requirement already satisfied: s3transfer==0.2.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 167)) (0.2.1)
Requirement already satisfied: scandir==1.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 168)) (1.10.0)
Requirement already satisfied: schema-salad==4.5.20191229160203 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 169)) (4.5.20191229160203)
Requirement already satisfied: setuptools-scm==3.3.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 170)) (3.3.3)
Requirement already satisfied: shellescape==3.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 171)) (3.4.1)
Requirement already satisfied: simplejson==3.17.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 172)) (3.17.0)
Requirement already satisfied: six==1.11.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 173)) (1.11.0)
Requirement already satisfied: social-auth-core[openidconnect]==3.1.0+gx0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 174)) (3.1.0+gx0)
Requirement already satisfied: sqlalchemy-migrate==0.13.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 175)) (0.13.0)
Requirement already satisfied: sqlalchemy-utils==0.35.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 176)) (0.35.0)
Requirement already satisfied: sqlalchemy==1.3.11 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 177)) (1.3.11)
Requirement already satisfied: sqlparse==0.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 178)) (0.3.0)
Requirement already satisfied: stevedore==1.31.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 179)) (1.31.0)
Requirement already satisfied: subprocess32==3.5.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 180)) (3.5.4)
Requirement already satisfied: svgwrite==1.3.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 181)) (1.3.1)
Requirement already satisfied: tempita==0.5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 182)) (0.5.2)
Requirement already satisfied: tenacity==4.12.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 183)) (4.12.0)
Requirement already satisfied: typing-extensions==3.7.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 184)) (3.7.4.1)
Requirement already satisfied: typing==3.7.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 185)) (3.7.4.1)
Requirement already satisfied: tzlocal==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 186)) (2.0.0)
Requirement already satisfied: unicodecsv==0.14.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 187)) (0.14.1)
Requirement already satisfied: uritemplate==3.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 188)) (3.0.0)
Requirement already satisfied: urllib3==1.25.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 189)) (1.25.7)
Requirement already satisfied: vine==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 190)) (1.3.0)
Requirement already satisfied: warlock==1.3.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 191)) (1.3.3)
Requirement already satisfied: wcwidth==0.1.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 192)) (0.1.7)
Requirement already satisfied: webencodings==0.5.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 193)) (0.5.1)
Requirement already satisfied: webob==1.8.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 194)) (1.8.5)
Requirement already satisfied: whoosh==2.7.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 195)) (2.7.4)
Requirement already satisfied: wrapt==1.11.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 196)) (1.11.2)
Requirement already satisfied: zipp==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 197)) (0.6.0)
Requirement already satisfied: alabaster==0.7.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (0.7.12)
Requirement already satisfied: argh==0.26.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) (0.26.2)
Requirement already satisfied: atomicwrites==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) (1.3.0)
Requirement already satisfied: commonmark==0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 10)) (0.9.1)
Requirement already satisfied: coverage==4.5.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 13)) (4.5.4)
Requirement already satisfied: gunicorn==19.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 18)) (19.10.0)
Requirement already satisfied: imagesize==1.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (1.1.0)
Requirement already satisfied: jinja2==2.10.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 22)) (2.10.3)
Requirement already satisfied: mirakuru==1.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 26)) (1.1.0)
Requirement already satisfied: mock==3.0.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (3.0.5)
Requirement already satisfied: nosehtml==0.4.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 30)) (0.4.5)
Requirement already satisfied: pathtools==0.1.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 33)) (0.1.2)
Requirement already satisfied: pluggy==0.13.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 34)) (0.13.1)
Requirement already satisfied: port-for==0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 35)) (0.4)
Requirement already satisfied: py==1.8.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 37)) (1.8.0)
Requirement already satisfied: pygithub==1.45 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 38)) (1.45)
Requirement already satisfied: pygments==2.5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 39)) (2.5.2)
Requirement already satisfied: pytest-cov==2.8.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 42)) (2.8.1)
Requirement already satisfied: pytest-html==1.22.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 43)) (1.22.1)
Requirement already satisfied: pytest-metadata==1.8.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (1.8.0)
Requirement already satisfied: pytest-postgresql==1.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 45)) (1.4.1)
Requirement already satisfied: pytest-pythonpath==0.7.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 46)) (0.7.3)
Requirement already satisfied: pytest==4.6.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 47)) (4.6.6)
Requirement already satisfied: recommonmark==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 49)) (0.6.0)
Requirement already satisfied: selenium==3.141.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 52)) (3.141.0)
Requirement already satisfied: snowballstemmer==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 54)) (2.0.0)
Requirement already satisfied: sphinx-markdown-tables==0.0.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55)) (0.0.12)
Requirement already satisfied: sphinx-rtd-theme==0.4.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 56)) (0.4.3)
Requirement already satisfied: sphinx==1.8.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 57)) (1.8.5)
Requirement already satisfied: sphinxcontrib-websupport==1.1.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 58)) (1.1.2)
Requirement already satisfied: testfixtures==6.10.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 59)) (6.10.3)
Requirement already satisfied: twill==0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 60)) (0.9.1)
Requirement already satisfied: watchdog==0.9.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 63)) (0.9.0)
Requirement already satisfied: setuptools in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 47)) (28.8.0)
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple
Requirement already satisfied: pykube==0.15.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r /dev/stdin (line 1)) (0.15.0)
Requirement already satisfied: watchdog in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r /dev/stdin (line 2)) (0.9.0)
Requirement already satisfied: PyYAML in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (5.2)
Requirement already satisfied: requests>=2.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (2.22.0)
Requirement already satisfied: tzlocal in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (2.0.0)
Requirement already satisfied: six>=1.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (1.11.0)
Requirement already satisfied: requests-oauthlib in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (1.3.0)
Requirement already satisfied: oauth2client in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (4.1.3)
Requirement already satisfied: pathtools>=0.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from watchdog->-r /dev/stdin (line 2)) (0.1.2)
Requirement already satisfied: argh>=0.24.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from watchdog->-r /dev/stdin (line 2)) (0.26.2)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (3.0.4)
Requirement already satisfied: idna<2.9,>=2.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (2.8)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (1.25.7)
Requirement already satisfied: certifi>=2017.4.17 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (2019.11.28)
Requirement already satisfied: pytz in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from tzlocal->pykube==0.15.0->-r /dev/stdin (line 1)) (2019.3)
Requirement already satisfied: oauthlib>=3.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests-oauthlib->pykube==0.15.0->-r /dev/stdin (line 1)) (3.1.0)
Requirement already satisfied: pyasn1>=0.1.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (0.4.8)
Requirement already satisfied: pyasn1-modules>=0.0.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (0.2.7)
Requirement already satisfied: httplib2>=0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (0.15.0)
Requirement already satisfied: rsa>=3.1.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (4.0)
The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable.
Unsetting $PYTHONPATH
Activating virtualenv at /Users/jj/.planemo/gx_venv
Galaxy support for Python 2.7 is deprecated, please consider moving to
Python >= 3.5 .
https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions
on how to force Galaxy to use a different version.
2020-03-19 13:08:41,856 INFO  [galaxy.queue_worker] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmprRkKGz/tmpaHgrap/tmpqqL2uw/database/control.sqlite?isolation_level=IMMEDIATE
2020-03-19 13:08:41,894 INFO  [galaxy.model.migrate.check] Creating database for URI [sqlite:////private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy.sqlite?isolation_level=IMMEDIATE]
2020-03-19 13:08:41,900 INFO  [galaxy.model.migrate.check] Creating new database from scratch, skipping migrations
2020-03-19 13:08:42,531 INFO  [galaxy.config] Install database targetting Galaxy's database configuration.
2020-03-19 13:08:42,829 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/all_fasta.loc, reading sample
2020-03-19 13:08:42,830 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/bfast_indexes.loc, reading sample
2020-03-19 13:08:42,831 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/blastdb.loc, reading sample
2020-03-19 13:08:42,832 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/blastdb_p.loc, reading sample
2020-03-19 13:08:42,832 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/blastdb_d.loc, reading sample
2020-03-19 13:08:42,833 WARNI [galaxy.tools.data] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes'
2020-03-19 13:08:42,833 WARNI [galaxy.tools.data] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color'
2020-03-19 13:08:42,833 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/maf_index.loc, reading sample
2020-03-19 13:08:42,835 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/ngs_sim_fasta.loc, reading sample
2020-03-19 13:08:42,835 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/perm_base_index.loc, reading sample
2020-03-19 13:08:42,836 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/perm_color_index.loc, reading sample
2020-03-19 13:08:42,836 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/picard_index.loc, reading sample
2020-03-19 13:08:42,837 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/picard_index.loc, reading sample
2020-03-19 13:08:42,838 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/mosaik_index.loc, reading sample
2020-03-19 13:08:42,838 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/twobit.loc, reading sample
2020-03-19 13:08:43,014 WARNI [galaxy.tools.data] Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields):
<Server-Side Genome List>
2020-03-19 13:08:43,017 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/liftOver.loc, reading sample
2020-03-19 13:08:43,018 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/bam_iobio.loc, reading sample
2020-03-19 13:08:43,019 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/vcf_iobio.loc, reading sample
2020-03-19 13:08:43,019 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/biom_simple_display.loc, reading sample
2020-03-19 13:08:43,020 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/intermine_simple_display.loc, reading sample
2020-03-19 13:08:43,021 INFO  [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/icn3d_simple_display.loc, reading sample
2020-03-19 13:08:43,093 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
2020-03-19 13:08:43,094 INFO  [galaxy.jobs] Job handler assignment methods set to: db-preassign
2020-03-19 13:08:43,094 INFO  [galaxy.jobs] Tag [_default_] handlers: main
2020-03-19 13:08:43,342 WARNI [galaxy.tools] The default shed tool config file (/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/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
2020-03-19 13:08:43,342 INFO  [galaxy.tools.toolbox.base] Parsing the tool configuration /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/tool_conf.xml
2020-03-19 13:08:43,457 WARNI [galaxy.tools] The default shed tool config file (/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/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
2020-03-19 13:08:43,457 INFO  [galaxy.tools.toolbox.base] Parsing the tool configuration /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/shed_tools_conf.xml
2020-03-19 13:08:43,457 WARNI [galaxy.tools] The default shed tool config file (/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/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
2020-03-19 13:08:43,457 INFO  [galaxy.tools.toolbox.base] Parsing the tool configuration /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/empty_tool_conf.xml
2020-03-19 13:08:44,009 INFO  [galaxy.jobs] Handler 'main' will load all configured runner plugins
2020-03-19 13:08:44,062 INFO  [galaxy.jobs.handler] job handler stop queue started
2020-03-19 13:08:44,076 INFO  [galaxy.jobs.handler] job handler queue started
2020-03-19 13:08:44,079 INFO  [galaxy.jobs.handler] job handler stop queue started
2020-03-19 13:08:44,101 INFO  [galaxy.workflow.scheduling_manager] No workflow schedulers plugin config file defined, using default scheduler.
2020-03-19 13:08:44,125 INFO  [galaxy.app] Galaxy app startup finished (3415.358 ms)
2020-03-19 13:08:45,281 INFO  [galaxy.queue_worker] Binding and starting galaxy control worker for main
2020-03-19 13:08:45,284 INFO  [galaxy.web_stack] Galaxy server instance 'main' is running
/Users/jj/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:666: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.
  "storage." % (dialect.name, dialect.driver)
( optitype ) > Test-1 ... 2020-03-19 13:08:46,121 INFO  [galaxy.tools] Validated and populated state for tool request (22.694 ms)
2020-03-19 13:08:46,334 INFO  [galaxy.tools.actions.upload_common] tool upload1 created job id 1
2020-03-19 13:08:46,394 INFO  [galaxy.web_stack.handlers] Flushed transaction for Job[id=1,tool_id=upload1] (18.226 ms)
2020-03-19 13:08:46,394 INFO  [galaxy.web_stack.handlers] (Job[id=1,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method
2020-03-19 13:08:47,463 INFO  [galaxy.jobs.handler] (1) Job dispatched
2020-03-19 13:08:47,711 INFO  [galaxy.jobs.command_factory] Built script [/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/1/tool_script.sh] for tool command [python '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tools/data_source/upload.py' /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/1/registry.xml /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/1/upload_params.json 1:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/1/working/dataset_eff120a9-00d7-49cb-b499-a1aa4d89b675_files:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/e/f/f/dataset_eff120a9-00d7-49cb-b499-a1aa4d89b675.dat]
2020-03-19 13:08:59,952 INFO  [galaxy.tools] Validated and populated state for tool request (16.296 ms)
2020-03-19 13:09:00,105 INFO  [galaxy.tools.actions.upload_common] tool upload1 created job id 2
2020-03-19 13:09:00,157 INFO  [galaxy.web_stack.handlers] Flushed transaction for Job[id=2,tool_id=upload1] (23.682 ms)
2020-03-19 13:09:00,157 INFO  [galaxy.web_stack.handlers] (Job[id=2,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method
2020-03-19 13:09:01,142 INFO  [galaxy.jobs.handler] (2) Job dispatched
2020-03-19 13:09:01,352 INFO  [galaxy.jobs.command_factory] Built script [/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/2/tool_script.sh] for tool command [python '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tools/data_source/upload.py' /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/2/registry.xml /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/2/upload_params.json 2:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/2/working/dataset_022eddc9-7baf-417f-bf3d-c0ac83dec823_files:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/0/2/2/dataset_022eddc9-7baf-417f-bf3d-c0ac83dec823.dat]
2020-03-19 13:09:06,983 INFO  [galaxy.tools] Validated and populated state for tool request (23.608 ms)
2020-03-19 13:09:07,003 INFO  [galaxy.tools.actions] Handled output named coverage_plot for tool optitype (2.875 ms)
2020-03-19 13:09:07,005 INFO  [galaxy.tools.actions] Handled output named result for tool optitype (2.115 ms)
2020-03-19 13:09:07,036 INFO  [galaxy.tools.actions] Added output datasets to history (30.977 ms)
2020-03-19 13:09:07,038 INFO  [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=optitype] complete, ready to be enqueued (2.073 ms)
2020-03-19 13:09:07,106 INFO  [galaxy.web_stack.handlers] Flushed transaction for Job[id=3,tool_id=optitype] (67.169 ms)
2020-03-19 13:09:07,106 INFO  [galaxy.web_stack.handlers] (Job[id=3,tool_id=optitype]) Handler 'main' assigned using 'db-preassign' assignment method
2020-03-19 13:09:07,511 INFO  [galaxy.jobs.handler] (3) Job dispatched

PackagesNotFoundError: The following packages are not available from current channels:

  - optitype=1.3.2

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



PackagesNotFoundError: The following packages are not available from current channels:

  - optitype=1.3.2

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



PackagesNotFoundError: The following packages are not available from current channels:

  - optitype

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



PackagesNotFoundError: The following packages are not available from current channels:

  - optitype

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



PackagesNotFoundError: The following packages are not available from current channels:

  - optitype=1.3.2

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



PackagesNotFoundError: The following packages are not available from current channels:

  - optitype=1.3.2

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



PackagesNotFoundError: The following packages are not available from current channels:

  - optitype

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



PackagesNotFoundError: The following packages are not available from current channels:

  - optitype

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.


2020-03-19 13:10:02,015 INFO  [galaxy.jobs.command_factory] Built script [/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/3/tool_script.sh] for tool command [ln -s '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/e/f/f/dataset_eff120a9-00d7-49cb-b499-a1aa4d89b675.dat' reads_1.fastq && ln -s '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/0/2/2/dataset_022eddc9-7baf-417f-bf3d-c0ac83dec823.dat' reads_2.fastq && RAZERS3=`which razers3` && sed "s#path_to_razers3#$RAZERS3#" '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/3/configs/tmpTaGSuA' | sed "s/threads=16/threads=$GALAXY_SLOTS/" > config.ini && OptiTypePipeline.py --rna --input    reads_1.fastq reads_2.fastq --config "`pwd`/config.ini" --outdir output_dir && cp output_dir/*/*_coverage_plot.pdf /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/d/5/f/dataset_d5ff36fd-e6ca-4e61-89ee-dc626fb865fe.dat && cp output_dir/*/*_result.tsv /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/1/0/7/dataset_10776cbe-d39b-419d-9014-c8b440e96190.dat]
2020-03-19 13:10:05,636 INFO  [galaxy.tool_util.output_checker] Job 3: {'code_desc': '', 'error_level': 3, 'type': 'exit_code', 'exit_code': 1, 'desc': 'Fatal error: Exit code 1 ()'}
FAIL
( optitype ) > Test-2 ... 2020-03-19 13:10:51,885 INFO  [galaxy.tools] Validated and populated state for tool request (22.757 ms)
2020-03-19 13:10:52,059 INFO  [galaxy.tools.actions.upload_common] tool upload1 created job id 4
2020-03-19 13:10:52,103 INFO  [galaxy.web_stack.handlers] Flushed transaction for Job[id=4,tool_id=upload1] (16.285 ms)
2020-03-19 13:10:52,104 INFO  [galaxy.web_stack.handlers] (Job[id=4,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method
2020-03-19 13:10:52,739 INFO  [galaxy.jobs.handler] (4) Job dispatched
2020-03-19 13:10:52,939 INFO  [galaxy.jobs.command_factory] Built script [/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/4/tool_script.sh] for tool command [python '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tools/data_source/upload.py' /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/4/registry.xml /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/4/upload_params.json 5:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/4/working/dataset_e0780a69-3eba-44ba-a023-0167344a63fd_files:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/e/0/7/dataset_e0780a69-3eba-44ba-a023-0167344a63fd.dat]
2020-03-19 13:10:58,904 INFO  [galaxy.tools] Validated and populated state for tool request (19.855 ms)
2020-03-19 13:10:59,090 INFO  [galaxy.tools.actions.upload_common] tool upload1 created job id 5
2020-03-19 13:10:59,135 INFO  [galaxy.web_stack.handlers] Flushed transaction for Job[id=5,tool_id=upload1] (15.200 ms)
2020-03-19 13:10:59,135 INFO  [galaxy.web_stack.handlers] (Job[id=5,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method
2020-03-19 13:11:00,120 INFO  [galaxy.jobs.handler] (5) Job dispatched
2020-03-19 13:11:00,313 INFO  [galaxy.jobs.command_factory] Built script [/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/5/tool_script.sh] for tool command [python '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tools/data_source/upload.py' /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/5/registry.xml /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/5/upload_params.json 6:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/5/working/dataset_5d34cb9a-478f-46a2-8a64-3534234ee2d3_files:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/5/d/3/dataset_5d34cb9a-478f-46a2-8a64-3534234ee2d3.dat]
2020-03-19 13:11:05,958 INFO  [galaxy.tools] Validated and populated state for tool request (21.036 ms)
2020-03-19 13:11:05,975 INFO  [galaxy.tools.actions] Handled output named coverage_plot for tool optitype (0.857 ms)
2020-03-19 13:11:05,976 INFO  [galaxy.tools.actions] Handled output named result for tool optitype (0.626 ms)
2020-03-19 13:11:06,008 INFO  [galaxy.tools.actions] Added output datasets to history (31.926 ms)
2020-03-19 13:11:06,010 INFO  [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=optitype] complete, ready to be enqueued (1.959 ms)
2020-03-19 13:11:06,082 INFO  [galaxy.web_stack.handlers] Flushed transaction for Job[id=6,tool_id=optitype] (71.447 ms)
2020-03-19 13:11:06,082 INFO  [galaxy.web_stack.handlers] (Job[id=6,tool_id=optitype]) Handler 'main' assigned using 'db-preassign' assignment method
2020-03-19 13:11:06,400 INFO  [galaxy.jobs.handler] (6) Job dispatched

PackagesNotFoundError: The following packages are not available from current channels:

  - optitype=1.3.2

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



PackagesNotFoundError: The following packages are not available from current channels:

  - optitype=1.3.2

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



PackagesNotFoundError: The following packages are not available from current channels:

  - optitype

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



PackagesNotFoundError: The following packages are not available from current channels:

  - optitype

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



PackagesNotFoundError: The following packages are not available from current channels:

  - optitype=1.3.2

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



PackagesNotFoundError: The following packages are not available from current channels:

  - optitype=1.3.2

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



PackagesNotFoundError: The following packages are not available from current channels:

  - optitype

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



PackagesNotFoundError: The following packages are not available from current channels:

  - optitype

Current channels:

  - https://conda.anaconda.org/iuc/osx-64
  - https://conda.anaconda.org/iuc/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.


2020-03-19 13:11:40,443 INFO  [galaxy.jobs.command_factory] Built script [/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/6/tool_script.sh] for tool command [ln -s '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/e/0/7/dataset_e0780a69-3eba-44ba-a023-0167344a63fd.dat' reads_1.fastq && ln -s '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/5/d/3/dataset_5d34cb9a-478f-46a2-8a64-3534234ee2d3.dat' reads_2.fastq && RAZERS3=`which razers3` && sed "s#path_to_razers3#$RAZERS3#" '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/6/configs/tmpn4N9W7' | sed "s/threads=16/threads=$GALAXY_SLOTS/" > config.ini && OptiTypePipeline.py --dna --input    reads_1.fastq reads_2.fastq --config "`pwd`/config.ini" --outdir output_dir && cp output_dir/*/*_coverage_plot.pdf /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/2/5/b/dataset_25b6ea5d-79fd-4cee-947a-fefbcba3f2e4.dat && cp output_dir/*/*_result.tsv /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/0/1/b/dataset_01b4e0c5-2563-4dc1-8557-411da38239fe.dat]
2020-03-19 13:11:43,559 INFO  [galaxy.tool_util.output_checker] Job 6: {'code_desc': '', 'error_level': 3, 'type': 'exit_code', 'exit_code': 1, 'desc': 'Fatal error: Exit code 1 ()'}
FAIL

======================================================================
FAIL: ( optitype ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/test/functional/test_toolbox.py", line 99, in test_tool
    self.do_it(tool_version=tool_version, test_index=test_index)
  File "/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/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 "/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 789, in verify_tool
    raise e
JobOutputsError: Job in error state.
Job in error state.
-------------------- >> begin captured stdout << ---------------------
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Problem in history with id 2891970512fa2d5a - summary of history's datasets and jobs below.
--------------------------------------
| 1 - CRC_81_N_1_fished.fastq (HID - NAME) 
| Dataset State:
|  ok
| Dataset Blurb:
|  1,569 sequences
| Dataset Info:
|  uploaded fastqsanger file
| Peek:
|  <table cellspacing="0" cellpadding="3"><tr><td>@SRR397217.2404</td></tr><tr><td>TCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGAGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACAT</td></tr><tr><td>+SRR397217.2404</td></tr><tr><td>9FEEBF?DDEE?F?ECFHDHHHHHHHEAFFF@FFHHFHHFFFHDHFHFHHFHHHHFHFHFHFHHHHHHHHHHHHHHHEHHHHHHHHHHHHHHGGHHHHHHH</td></tr><tr><td>@SRR397217.3931</td></tr></table>
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| 2 - CRC_81_N_2_fished.fastq (HID - NAME) 
| Dataset State:
|  ok
| Dataset Blurb:
|  1,515 sequences
| Dataset Info:
|  uploaded fastqsanger file
| Peek:
|  <table cellspacing="0" cellpadding="3"><tr><td>@SRR397217.1805</td></tr><tr><td>GGAAACAGTTCCTCGGAGTGGAGAGGTTTACACCTGCCAAGTGGAGCACCCAAGCCTGACGAGCCCTCTCACAGTGGAATGGAGAGCACGGTCTGAATCTG</td></tr><tr><td>+SRR397217.1805</td></tr><tr><td>HHHHHHHHHHHHHHHHFHEHHHHFHHFHFEHHHHHFFHHFHHHHEFHFHCIGCGIHHHFHHHHFFHFHHHFHAHEHHFFHH@HEED.@EEFBGFE@EFDEA</td></tr><tr><td>@SRR397217.2316</td></tr></table>
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| 3 - OptiType on data 2 and data 1 coverage_plot.pdf (HID - NAME) 
| Dataset State:
|  error
| Dataset Blurb:
|  error
| Dataset Info:
|  *Dataset info is empty.*
| Peek:
|  None
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| 4 - OptiType on data 2 and data 1 result.tsv (HID - NAME) 
| Dataset State:
|  error
| Dataset Blurb:
|  error
| Dataset Info:
|  *Dataset info is empty.*
| Peek:
|  None
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| Job 54f2a3a23292eb07
| State: 
|  error
| Update Time:
|  2020-03-19T18:10:05.914678
| Create Time:
|  2020-03-19T18:09:07.093093
|
--------------------------------------
| Job 5729865256bc2525
| State: 
|  ok
| Update Time:
|  2020-03-19T18:09:06.049350
| Create Time:
|  2020-03-19T18:09:00.092142
|
--------------------------------------
| Job 2891970512fa2d5a
| State: 
|  ok
| Update Time:
|  2020-03-19T18:08:53.411645
| Create Time:
|  2020-03-19T18:08:46.307862
|
--------------------------------------
Problem in history with id 2891970512fa2d5a - summary of history's datasets and jobs below.
--------------------------------------
| 1 - CRC_81_N_1_fished.fastq (HID - NAME) 
| Dataset State:
|  ok
| Dataset Blurb:
|  1,569 sequences
| Dataset Info:
|  uploaded fastqsanger file
| Peek:
|  <table cellspacing="0" cellpadding="3"><tr><td>@SRR397217.2404</td></tr><tr><td>TCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGAGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACAT</td></tr><tr><td>+SRR397217.2404</td></tr><tr><td>9FEEBF?DDEE?F?ECFHDHHHHHHHEAFFF@FFHHFHHFFFHDHFHFHHFHHHHFHFHFHFHHHHHHHHHHHHHHHEHHHHHHHHHHHHHHGGHHHHHHH</td></tr><tr><td>@SRR397217.3931</td></tr></table>
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| 2 - CRC_81_N_2_fished.fastq (HID - NAME) 
| Dataset State:
|  ok
| Dataset Blurb:
|  1,515 sequences
| Dataset Info:
|  uploaded fastqsanger file
| Peek:
|  <table cellspacing="0" cellpadding="3"><tr><td>@SRR397217.1805</td></tr><tr><td>GGAAACAGTTCCTCGGAGTGGAGAGGTTTACACCTGCCAAGTGGAGCACCCAAGCCTGACGAGCCCTCTCACAGTGGAATGGAGAGCACGGTCTGAATCTG</td></tr><tr><td>+SRR397217.1805</td></tr><tr><td>HHHHHHHHHHHHHHHHFHEHHHHFHHFHFEHHHHHFFHHFHHHHEFHFHCIGCGIHHHFHHHHFFHFHHHFHAHEHHFFHH@HEED.@EEFBGFE@EFDEA</td></tr><tr><td>@SRR397217.2316</td></tr></table>
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| 3 - OptiType on data 2 and data 1 coverage_plot.pdf (HID - NAME) 
| Dataset State:
|  error
| Dataset Blurb:
|  error
| Dataset Info:
|  *Dataset info is empty.*
| Peek:
|  None
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| 4 - OptiType on data 2 and data 1 result.tsv (HID - NAME) 
| Dataset State:
|  error
| Dataset Blurb:
|  error
| Dataset Info:
|  *Dataset info is empty.*
| Peek:
|  None
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| Job 54f2a3a23292eb07
| State: 
|  error
| Update Time:
|  2020-03-19T18:10:05.914678
| Create Time:
|  2020-03-19T18:09:07.093093
|
--------------------------------------
| Job 5729865256bc2525
| State: 
|  ok
| Update Time:
|  2020-03-19T18:09:06.049350
| Create Time:
|  2020-03-19T18:09:00.092142
|
--------------------------------------
| Job 2891970512fa2d5a
| State: 
|  ok
| Update Time:
|  2020-03-19T18:08:53.411645
| Create Time:
|  2020-03-19T18:08:46.307862
|
--------------------------------------

--------------------- >> end captured stdout << ----------------------

======================================================================
FAIL: ( optitype ) > Test-2
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/test/functional/test_toolbox.py", line 99, in test_tool
    self.do_it(tool_version=tool_version, test_index=test_index)
  File "/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/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 "/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 789, in verify_tool
    raise e
JobOutputsError: Job in error state.
Job in error state.
-------------------- >> begin captured stdout << ---------------------
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Collecting package metadata: ...working... done
Solving environment: ...working... failed
Problem in history with id 5729865256bc2525 - summary of history's datasets and jobs below.
--------------------------------------
| 1 - NA11995_SRR766010_1_fished.fastq (HID - NAME) 
| Dataset State:
|  ok
| Dataset Blurb:
|  1,000 sequences
| Dataset Info:
|  uploaded fastqsanger file
| Peek:
|  <table cellspacing="0" cellpadding="3"><tr><td>@SRR766010.692</td></tr><tr><td>TACAAAAAAATTAGCTGGGCGTGGTGGCACATGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATTGCTTGAATCTGGGAGGCAGAGCTTGCA</td></tr><tr><td>+SRR766010.692</td></tr><tr><td>3BBBCCC&gt;&gt;::CABB@?====66.)B@C?ECCIGEA=ECF=IHGGGHDDHDFDDGHHHBGGGF&lt;GEIG?4HGEGGEIGIIHDGEHFEFFHHHHDDA+D&lt;@@</td></tr><tr><td>@SRR766010.944</td></tr></table>
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| 2 - NA11995_SRR766010_2_fished.fastq (HID - NAME) 
| Dataset State:
|  ok
| Dataset Blurb:
|  1,000 sequences
| Dataset Info:
|  uploaded fastqsanger file
| Peek:
|  <table cellspacing="0" cellpadding="3"><tr><td>@SRR766010.600</td></tr><tr><td>TCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGTTGCGACTACAGGCGCCCACCACCACGCCCAGCTAATTTTTTTTTTTTTTTTT</td></tr><tr><td>+SRR766010.600</td></tr><tr><td>CCCFFFFFHHHHHIIJJJJJJGJJIJJJJJJJJJJJFIJJJJGAHFGGFFFIIGGFFFFEDDDDDBBDDBDDDDDDDDBBDD@CDEDDDDDDDDDBDBDB5</td></tr><tr><td>@SRR766010.666</td></tr></table>
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| 3 - OptiType on data 2 and data 1 coverage_plot.pdf (HID - NAME) 
| Dataset State:
|  error
| Dataset Blurb:
|  error
| Dataset Info:
|  *Dataset info is empty.*
| Peek:
|  None
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| 4 - OptiType on data 2 and data 1 result.tsv (HID - NAME) 
| Dataset State:
|  error
| Dataset Blurb:
|  error
| Dataset Info:
|  *Dataset info is empty.*
| Peek:
|  None
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| Job fa6d20d0fb68383f
| State: 
|  error
| Update Time:
|  2020-03-19T18:11:43.802965
| Create Time:
|  2020-03-19T18:11:06.066886
|
--------------------------------------
| Job 7b55dbb89df8f4e5
| State: 
|  ok
| Update Time:
|  2020-03-19T18:11:05.241405
| Create Time:
|  2020-03-19T18:10:59.076071
|
--------------------------------------
| Job 8155e4b4bf1581ff
| State: 
|  ok
| Update Time:
|  2020-03-19T18:10:58.105973
| Create Time:
|  2020-03-19T18:10:52.045196
|
--------------------------------------
Problem in history with id 5729865256bc2525 - summary of history's datasets and jobs below.
--------------------------------------
| 1 - NA11995_SRR766010_1_fished.fastq (HID - NAME) 
| Dataset State:
|  ok
| Dataset Blurb:
|  1,000 sequences
| Dataset Info:
|  uploaded fastqsanger file
| Peek:
|  <table cellspacing="0" cellpadding="3"><tr><td>@SRR766010.692</td></tr><tr><td>TACAAAAAAATTAGCTGGGCGTGGTGGCACATGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATTGCTTGAATCTGGGAGGCAGAGCTTGCA</td></tr><tr><td>+SRR766010.692</td></tr><tr><td>3BBBCCC&gt;&gt;::CABB@?====66.)B@C?ECCIGEA=ECF=IHGGGHDDHDFDDGHHHBGGGF&lt;GEIG?4HGEGGEIGIIHDGEHFEFFHHHHDDA+D&lt;@@</td></tr><tr><td>@SRR766010.944</td></tr></table>
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| 2 - NA11995_SRR766010_2_fished.fastq (HID - NAME) 
| Dataset State:
|  ok
| Dataset Blurb:
|  1,000 sequences
| Dataset Info:
|  uploaded fastqsanger file
| Peek:
|  <table cellspacing="0" cellpadding="3"><tr><td>@SRR766010.600</td></tr><tr><td>TCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGTTGCGACTACAGGCGCCCACCACCACGCCCAGCTAATTTTTTTTTTTTTTTTT</td></tr><tr><td>+SRR766010.600</td></tr><tr><td>CCCFFFFFHHHHHIIJJJJJJGJJIJJJJJJJJJJJFIJJJJGAHFGGFFFIIGGFFFFEDDDDDBBDDBDDDDDDDDBBDD@CDEDDDDDDDDDBDBDB5</td></tr><tr><td>@SRR766010.666</td></tr></table>
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| 3 - OptiType on data 2 and data 1 coverage_plot.pdf (HID - NAME) 
| Dataset State:
|  error
| Dataset Blurb:
|  error
| Dataset Info:
|  *Dataset info is empty.*
| Peek:
|  None
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| 4 - OptiType on data 2 and data 1 result.tsv (HID - NAME) 
| Dataset State:
|  error
| Dataset Blurb:
|  error
| Dataset Info:
|  *Dataset info is empty.*
| Peek:
|  None
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------
| Job fa6d20d0fb68383f
| State: 
|  error
| Update Time:
|  2020-03-19T18:11:43.802965
| Create Time:
|  2020-03-19T18:11:06.066886
|
--------------------------------------
| Job 7b55dbb89df8f4e5
| State: 
|  ok
| Update Time:
|  2020-03-19T18:11:05.241405
| Create Time:
|  2020-03-19T18:10:59.076071
|
--------------------------------------
| Job 8155e4b4bf1581ff
| State: 
|  ok
| Update Time:
|  2020-03-19T18:10:58.105973
| Create Time:
|  2020-03-19T18:10:52.045196
|
--------------------------------------

--------------------- >> end captured stdout << ----------------------

----------------------------------------------------------------------
XML: /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/xunit.xml
----------------------------------------------------------------------
Ran 2 tests in 193.479s

FAILED (failures=2)
2020-03-19 13:11:59,384 INFO  [test_driver] Shutting down
2020-03-19 13:11:59,384 INFO  [test_driver] Shutting down embedded galaxy web server
2020-03-19 13:11:59,387 INFO  [test_driver] Embedded web server galaxy stopped
2020-03-19 13:11:59,387 INFO  [test_driver] Stopping application galaxy
Exception in thread Thread-6:
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 801, in __bootstrap_inner
    self.run()
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 754, in run
    self.__target(*self.__args, **self.__kwargs)
  File "/Users/jj/.planemo/gx_venv/lib/python2.7/site-packages/paste/httpserver.py", line 1107, in serve_forever
    self.handle_request()
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 274, in handle_request
    fd_sets = _eintr_retry(select.select, [self], [], [], timeout)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 150, in _eintr_retry
    return func(*args)
error: (9, 'Bad file descriptor')

2020-03-19 13:11:59,957 INFO  [galaxy.queue_worker] Sending reconfigure_watcher control task.
2020-03-19 13:12:00,046 INFO  [galaxy.jobs.handler] sending stop signal to worker thread
2020-03-19 13:12:00,047 INFO  [galaxy.jobs.handler] job handler queue stopped
2020-03-19 13:12:00,048 INFO  [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 job worker threads
2020-03-19 13:12:00,048 INFO  [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown...
2020-03-19 13:12:00,050 INFO  [galaxy.jobs.runners] All job worker threads shutdown cleanly
2020-03-19 13:12:00,050 INFO  [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 job worker threads
2020-03-19 13:12:00,050 INFO  [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown...
2020-03-19 13:12:00,052 INFO  [galaxy.jobs.runners] All job worker threads shutdown cleanly
2020-03-19 13:12:00,052 INFO  [galaxy.jobs.handler] sending stop signal to worker thread
2020-03-19 13:12:00,122 INFO  [galaxy.jobs.handler] job handler stop queue stopped
2020-03-19 13:12:00,123 INFO  [test_driver] Application galaxy stopped.
Testing complete. HTML report is in "/Users/jj/gx/gh/jj/galaxytools/optitype/tool_test_output.html".
There were problems with 2 test(s) - out of 2 test(s) executed. See /Users/jj/gx/gh/jj/galaxytools/optitype/tool_test_output.html for detailed breakdown.
optitype[0]: failed
optitype[1]: failed