gistfile1.txt

git --git-dir /home/pvh/.planemo/gx_repo config remote.origin.fetch '+refs/*:refs/*'
git --git-dir /home/pvh/.planemo/gx_repo config remote.origin.mirror true
git --git-dir /home/pvh/.planemo/gx_repo remote update >/dev/null 2>&1
git clone --branch master /home/pvh/.planemo/gx_repo /tmp/tmp4bznxpwc/galaxy-dev && cd /tmp/tmp4bznxpwc/galaxy-dev && if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/pvh/.planemo/gx_venv; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/pvh/anaconda3/envs/planemo/bin/virtualenv -p /usr/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}
Cloning into '/tmp/tmp4bznxpwc/galaxy-dev'...
done.
Set COMMON_STARTUP_ARGS to --dev-wheels
Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample
Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample
Initializing static/welcome.html from welcome.html.sample
Activating virtualenv at /home/pvh/.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 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. 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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (19.2.1)
WARNING: You are using pip version 19.2.1, however version 20.0.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. 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: adal==1.2.2 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) (0.8.8)
Requirement already satisfied: bz2file==0.98 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) (0.98)
Requirement already satisfied: cachecontrol==0.11.7 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) (0.8.9)
Requirement already satisfied: coloredlogs==10.0 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 43)) (10.0)
Requirement already satisfied: configparser==4.0.2 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) (2.8)
Requirement already satisfied: cwltool==1.0.20191225192155 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) (2.0.7)
Requirement already satisfied: dictobj==0.4 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) (0.4)
Requirement already satisfied: docopt==0.6.2 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) (0.15.0)
Requirement already satisfied: humanfriendly==4.18 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) (4.18)
Requirement already satisfied: idna==2.8 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 77)) (0.9.4)
Requirement already satisfied: jsonpatch==1.24 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 78)) (1.24)
Requirement already satisfied: jsonpointer==2.0 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) (2.0)
Requirement already satisfied: jsonschema==3.2.0 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 87)) (1.1.1)
Requirement already satisfied: mercurial==5.2 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 88)) (5.2)
Requirement already satisfied: mistune==0.8.4 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 89)) (0.8.4)
Requirement already satisfied: monotonic==1.5 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 98)) (0.10.9)
Requirement already satisfied: networkx==1.11 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 99)) (1.11)
Requirement already satisfied: nodeenv==1.3.3 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 114)) (3.42.0)
Requirement already satisfied: packaging==20.0 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 115)) (20.0)
Requirement already satisfied: paramiko==2.7.1 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 116)) (2.7.1)
Requirement already satisfied: parsley==1.3 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 117)) (1.3)
Requirement already satisfied: paste==3.2.3 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 128)) (0.4.8)
Requirement already satisfied: pycparser==2.19 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 129)) (2.19)
Requirement already satisfied: pycryptodome==3.9.6 in /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 131)) (0.1.0)
Requirement already satisfied: pyinotify==0.9.6 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 132)) (0.9.6)
Requirement already satisfied: pyjwt==1.7.1 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 150)) (3.6.0)
Requirement already satisfied: pytz==2019.3 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 162)) (2.4.1)
Requirement already satisfied: rsa==4.0 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 47)) (41.0.1)
WARNING: You are using pip version 19.2.1, however version 20.0.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable.
Testing using galaxy_root /tmp/tmp4bznxpwc/galaxy-dev
Testing tools with command [cd /tmp/tmp4bznxpwc/galaxy-dev && if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/pvh/.planemo/gx_venv; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/pvh/anaconda3/envs/planemo/bin/virtualenv -p /usr/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 /home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/data_managers/data_manager_fetch_refseq/tool_test_output.html --xunit_report_file /tmp/tmp4bznxpwc/xunit.xml --structured_data_report_file /home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/data_managers/data_manager_fetch_refseq/tool_test_output.json functional.test_toolbox]
Activating virtualenv at /home/pvh/.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 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. 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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (19.2.1)
WARNING: You are using pip version 19.2.1, however version 20.0.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. 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: adal==1.2.2 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) (0.8.8)
Requirement already satisfied: bz2file==0.98 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) (0.98)
Requirement already satisfied: cachecontrol==0.11.7 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) (0.8.9)
Requirement already satisfied: coloredlogs==10.0 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 43)) (10.0)
Requirement already satisfied: configparser==4.0.2 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) (2.8)
Requirement already satisfied: cwltool==1.0.20191225192155 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) (2.0.7)
Requirement already satisfied: dictobj==0.4 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) (0.4)
Requirement already satisfied: docopt==0.6.2 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) (0.15.0)
Requirement already satisfied: humanfriendly==4.18 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) (4.18)
Requirement already satisfied: idna==2.8 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 77)) (0.9.4)
Requirement already satisfied: jsonpatch==1.24 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 78)) (1.24)
Requirement already satisfied: jsonpointer==2.0 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) (2.0)
Requirement already satisfied: jsonschema==3.2.0 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 87)) (1.1.1)
Requirement already satisfied: mercurial==5.2 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 88)) (5.2)
Requirement already satisfied: mistune==0.8.4 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 89)) (0.8.4)
Requirement already satisfied: monotonic==1.5 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 98)) (0.10.9)
Requirement already satisfied: networkx==1.11 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 99)) (1.11)
Requirement already satisfied: nodeenv==1.3.3 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 114)) (3.42.0)
Requirement already satisfied: packaging==20.0 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 115)) (20.0)
Requirement already satisfied: paramiko==2.7.1 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 116)) (2.7.1)
Requirement already satisfied: parsley==1.3 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 117)) (1.3)
Requirement already satisfied: paste==3.2.3 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 128)) (0.4.8)
Requirement already satisfied: pycparser==2.19 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 129)) (2.19)
Requirement already satisfied: pycryptodome==3.9.6 in /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 131)) (0.1.0)
Requirement already satisfied: pyinotify==0.9.6 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 132)) (0.9.6)
Requirement already satisfied: pyjwt==1.7.1 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 150)) (3.6.0)
Requirement already satisfied: pytz==2019.3 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 162)) (2.4.1)
Requirement already satisfied: rsa==4.0 in /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.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 /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 47)) (41.0.1)
WARNING: You are using pip version 19.2.1, however version 20.0.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. 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
WARNING: You are using pip version 19.2.1, however version 20.0.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. 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: watchdog in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from -r /dev/stdin (line 1)) (0.9.0)
Requirement already satisfied: argh>=0.24.1 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from watchdog->-r /dev/stdin (line 1)) (0.26.2)
Requirement already satisfied: PyYAML>=3.10 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from watchdog->-r /dev/stdin (line 1)) (5.2)
Requirement already satisfied: pathtools>=0.1.1 in /home/pvh/.planemo/gx_venv/lib/python2.7/site-packages (from watchdog->-r /dev/stdin (line 1)) (0.1.2)
WARNING: You are using pip version 19.2.1, however version 20.0.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable.
Activating virtualenv at /home/pvh/.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.
2020-04-17 15:01:02,702 INFO  [galaxy.queue_worker] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////tmp/tmpF76xX4/tmpg3Enrn/tmpOiyLKC/database/control.sqlite?isolation_level=IMMEDIATE
2020-04-17 15:01:02,783 INFO  [galaxy.model.migrate.check] Migrating 141 -> 142... 
2020-04-17 15:01:03,434 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:03,434 INFO  [galaxy.model.migrate.check] Migration script to change the 'value' column of 'user_preference' table from numeric(22, 7) to numeric(26, 7)
2020-04-17 15:01:03,434 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:03,434 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:03,434 INFO  [galaxy.model.migrate.check] Migrating 142 -> 143... 
2020-04-17 15:01:03,923 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:03,924 INFO  [galaxy.model.migrate.check] Migration script to add a new tables for CloudAuthz (tokens required to access cloud-based resources).
2020-04-17 15:01:03,924 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:03,924 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:03,924 INFO  [galaxy.model.migrate.check] Migrating 143 -> 144... 
2020-04-17 15:01:04,594 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:04,595 INFO  [galaxy.model.migrate.check] Migration script to add the cleanup_event_user_association table.
2020-04-17 15:01:04,595 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:04,595 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:04,595 INFO  [galaxy.model.migrate.check] Migrating 144 -> 145... 
2020-04-17 15:01:05,695 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:05,695 INFO  [galaxy.model.migrate.check] Migration script for workflow step input table.
2020-04-17 15:01:05,695 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:05,695 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:05,695 INFO  [galaxy.model.migrate.check] Migrating 145 -> 146... 
2020-04-17 15:01:06,265 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:06,265 INFO  [galaxy.model.migrate.check] Migration script for workflow paths.
2020-04-17 15:01:06,265 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:06,265 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:06,265 INFO  [galaxy.model.migrate.check] Migrating 146 -> 147... 
2020-04-17 15:01:08,315 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:08,315 INFO  [galaxy.model.migrate.check] Add structured failure reason column to jobs table
2020-04-17 15:01:08,315 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:08,315 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:08,315 INFO  [galaxy.model.migrate.check] Migrating 147 -> 148... 
2020-04-17 15:01:08,991 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:08,991 INFO  [galaxy.model.migrate.check] Migration script to add dataset source and hash tables.
2020-04-17 15:01:08,991 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:08,991 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:08,991 INFO  [galaxy.model.migrate.check] Migrating 148 -> 149... 
2020-04-17 15:01:10,023 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:10,023 INFO  [galaxy.model.migrate.check] Migration script to add the dynamic_tool table.
2020-04-17 15:01:10,024 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:10,024 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:10,024 INFO  [galaxy.model.migrate.check] Migrating 149 -> 150... 
2020-04-17 15:01:10,454 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:10,454 INFO  [galaxy.model.migrate.check] Adds `create_time` columns to cloudauthz table.
2020-04-17 15:01:10,454 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:10,454 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:10,454 INFO  [galaxy.model.migrate.check] Migrating 150 -> 151... 
2020-04-17 15:01:11,120 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:11,121 INFO  [galaxy.model.migrate.check] Add table for worker processes
2020-04-17 15:01:11,121 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:11,121 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:11,121 INFO  [galaxy.model.migrate.check] Migrating 151 -> 152... 
2020-04-17 15:01:11,641 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:11,641 INFO  [galaxy.model.migrate.check] Adds `uuid` column to MetadataFile table.
2020-04-17 15:01:11,641 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:11,641 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:11,642 INFO  [galaxy.model.migrate.check] Migrating 152 -> 153... 
2020-04-17 15:01:12,177 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:12,177 INFO  [galaxy.model.migrate.check] Migration for adding custos_authnz_token table.
2020-04-17 15:01:12,177 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:12,177 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:12,177 INFO  [galaxy.model.migrate.check] Migrating 153 -> 154... 
2020-04-17 15:01:12,713 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:12,713 INFO  [galaxy.model.migrate.check] Adds created_from_basename to dataset.
2020-04-17 15:01:12,713 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:12,714 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:12,714 INFO  [galaxy.model.migrate.check] Migrating 154 -> 155... 
2020-04-17 15:01:13,172 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:13,173 INFO  [galaxy.model.migrate.check] Add 'galaxy_version' attribute to Job table.
2020-04-17 15:01:13,173 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:13,173 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:13,173 INFO  [galaxy.model.migrate.check] Migrating 155 -> 156... 
2020-04-17 15:01:14,058 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:14,058 INFO  [galaxy.model.migrate.check] Migration script to add new tables for InteractiveTools.
2020-04-17 15:01:14,059 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:14,059 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:14,059 INFO  [galaxy.model.migrate.check] Migrating 156 -> 157... 
2020-04-17 15:01:14,689 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:14,689 INFO  [galaxy.model.migrate.check] Rework dataset validation in database.
2020-04-17 15:01:14,689 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:14,689 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:14,689 INFO  [galaxy.model.migrate.check] Migrating 157 -> 158... 
2020-04-17 15:01:15,287 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:15,287 INFO  [galaxy.model.migrate.check] Adds reports_config to workflow.
2020-04-17 15:01:15,287 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:15,287 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:15,288 INFO  [galaxy.model.migrate.check] Migrating 158 -> 159... 
2020-04-17 15:01:15,848 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:15,848 INFO  [galaxy.model.migrate.check] Add index for job runner external ID.
2020-04-17 15:01:15,848 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:15,849 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:15,849 INFO  [galaxy.model.migrate.check] Migrating 159 -> 160... 
2020-04-17 15:01:15,879 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:15,879 INFO  [galaxy.model.migrate.check] Migration script to set the 'deleted' column of the
2020-04-17 15:01:15,879 INFO  [galaxy.model.migrate.check] 'history_dataset_association' table to True if 'purged' is True.
2020-04-17 15:01:15,879 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:15,879 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:15,880 INFO  [galaxy.model.migrate.check] Migrating 160 -> 161... 
2020-04-17 15:01:16,588 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:16,588 INFO  [galaxy.model.migrate.check] Migration script to add a new workflow_invocation_output_parameter table to track output parameters.
2020-04-17 15:01:16,588 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:16,588 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:16,588 INFO  [galaxy.model.migrate.check] Migrating 161 -> 162... 
2020-04-17 15:01:17,503 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:17,504 INFO  [galaxy.model.migrate.check] Migration script to allow null workflow_step for PostJobActions.
2020-04-17 15:01:17,504 INFO  [galaxy.model.migrate.check] This enables using PJAs with individual job executions.
2020-04-17 15:01:17,504 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:17,504 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:17,504 INFO  [galaxy.model.migrate.check] Migrating 162 -> 163... 
2020-04-17 15:01:18,011 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:18,011 INFO  [galaxy.model.migrate.check] Adds `pid` column to worker_process table.
2020-04-17 15:01:18,012 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:18,012 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:18,012 INFO  [galaxy.model.migrate.check] Migrating 163 -> 164... 
2020-04-17 15:01:18,443 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:18,443 INFO  [galaxy.model.migrate.check] Adds page content format.
2020-04-17 15:01:18,443 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:18,443 INFO  [galaxy.model.migrate.check] 
2020-04-17 15:01:18,446 INFO  [galaxy.config] Install database targetting Galaxy's database configuration.
2020-04-17 15:01:18,823 INFO  [galaxy.tools.data] Could not find tool data /tmp/tmp4bznxpwc/galaxy-dev/tool-data/all_fasta.loc, reading sample
2020-04-17 15:01:18,827 ERROR [galaxy.visualization.genomes] Error reading twobit.loc
Traceback (most recent call last):
  File "/tmp/tmp4bznxpwc/galaxy-dev/lib/galaxy/visualization/genomes.py", line 212, in reload_genomes
    for line in open(os.path.join(self.app.config.tool_data_path, "twobit.loc")):
IOError: [Errno 2] No such file or directory: '/tmp/tmp4bznxpwc/galaxy-dev/tool-data/twobit.loc'
2020-04-17 15:01:18,855 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
2020-04-17 15:01:18,855 INFO  [galaxy.jobs] Job handler assignment methods set to: db-preassign
2020-04-17 15:01:18,855 INFO  [galaxy.jobs] Tag [_default_] handlers: main
2020-04-17 15:01:19,058 WARNI [galaxy.tools] The default shed tool config file (/tmp/tmp4bznxpwc/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
2020-04-17 15:01:19,058 INFO  [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp4bznxpwc/tool_conf.xml
2020-04-17 15:01:19,134 WARNI [galaxy.tools] The default shed tool config file (/tmp/tmp4bznxpwc/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
2020-04-17 15:01:19,134 INFO  [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp4bznxpwc/shed_tools_conf.xml
2020-04-17 15:01:19,135 WARNI [galaxy.tools] The default shed tool config file (/tmp/tmp4bznxpwc/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
2020-04-17 15:01:19,135 INFO  [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp4bznxpwc/empty_tool_conf.xml
No handlers could be found for logger "galaxy.datatypes.display_applications.application"
2020-04-17 15:01:19,381 INFO  [galaxy.jobs] Handler 'main' will load all configured runner plugins
2020-04-17 15:01:19,411 INFO  [galaxy.jobs.handler] job handler stop queue started
2020-04-17 15:01:19,423 INFO  [galaxy.jobs.handler] job handler queue started
2020-04-17 15:01:19,426 INFO  [galaxy.jobs.handler] job handler stop queue started
2020-04-17 15:01:19,435 INFO  [galaxy.workflow.scheduling_manager] No workflow schedulers plugin config file defined, using default scheduler.
2020-04-17 15:01:19,456 INFO  [galaxy.app] Galaxy app startup finished (18252.443 ms)
2020-04-17 15:01:20,643 INFO  [galaxy.queue_worker] Binding and starting galaxy control worker for main
2020-04-17 15:01:20,651 INFO  [galaxy.web_stack] Galaxy server instance 'main' is running
/home/pvh/.planemo/gx_venv/local/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)
( data_manager_fetch_refseq ) > Test-1 ... 2020-04-17 15:01:21,349 INFO  [galaxy.tools] Validated and populated state for tool request (0.139 ms)
2020-04-17 15:01:21,370 INFO  [galaxy.tools.actions] Handled output named output_file for tool data_manager_fetch_refseq (0.655 ms)
2020-04-17 15:01:21,412 INFO  [galaxy.tools.actions] Added output datasets to history (41.527 ms)
2020-04-17 15:01:21,414 INFO  [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=data_manager_fetch_refseq] complete, ready to be enqueued (1.791 ms)
2020-04-17 15:01:21,454 INFO  [galaxy.web_stack.handlers] Flushed transaction for Job[id=1,tool_id=data_manager_fetch_refseq] (40.255 ms)
2020-04-17 15:01:21,454 INFO  [galaxy.web_stack.handlers] (Job[id=1,tool_id=data_manager_fetch_refseq]) Handler 'main' assigned using 'db-preassign' assignment method
2020-04-17 15:01:21,749 INFO  [galaxy.jobs.handler] (1) Job dispatched
2020-04-17 15:01:22,098 INFO  [galaxy.jobs.command_factory] Built script [/tmp/tmp4bznxpwc/job_working_directory/000/1/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/pvh/miniconda3/envs/mulled-v1-c81d2d869008a5a47043a145fb52118d872ce729363c2243d23dd911ff10b108')" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
    . '/home/pvh/miniconda3/bin/activate' '/home/pvh/miniconda3/envs/mulled-v1-c81d2d869008a5a47043a145fb52118d872ce729363c2243d23dd911ff10b108' > conda_activate.log 2>&1
    if [ $? -eq 0 ];then
        break
    else
        let COUNT=COUNT+1
        if [ $COUNT -eq $MAX_TRIES ];then
            echo "Failed to activate conda environment! Error was:"
            cat conda_activate.log
            exit 1
        fi
        sleep 10s
    fi
done ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/pvh/miniconda3/envs/mulled-v1-c81d2d869008a5a47043a145fb52118d872ce729363c2243d23dd911ff10b108')" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
    . '/home/pvh/miniconda3/bin/activate' '/home/pvh/miniconda3/envs/mulled-v1-c81d2d869008a5a47043a145fb52118d872ce729363c2243d23dd911ff10b108' > conda_activate.log 2>&1
    if [ $? -eq 0 ];then
        break
    else
        let COUNT=COUNT+1
        if [ $COUNT -eq $MAX_TRIES ];then
            echo "Failed to activate conda environment! Error was:"
            cat conda_activate.log
            exit 1
        fi
        sleep 10s
    fi
done ; python '/home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/data_managers/data_manager_fetch_refseq/data_manager/fetch_refseq.py' --galaxy_datamanager_filename '/tmp/tmp4bznxpwc/files/5/7/3/dataset_57356ca4-38b9-4212-a5e5-9ec7da23f430.dat' --division_names plastid --mol_types protein --pin_date '2018-03-14']
2020-04-17 15:04:38,104 ERROR [galaxy.jobs.runners] (1/) Job wrapper finish method failed
Traceback (most recent call last):
  File "/tmp/tmp4bznxpwc/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 540, in _finish_or_resubmit_job
    job_wrapper.finish(tool_stdout, tool_stderr, exit_code, check_output_detected_state=check_output_detected_state, job_stdout=job_stdout, job_stderr=job_stderr)
  File "/tmp/tmp4bznxpwc/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1692, in finish
    self.tool.exec_after_process(self.app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state)
  File "/tmp/tmp4bznxpwc/galaxy-dev/lib/galaxy/tools/__init__.py", line 2559, in exec_after_process
    assert data_manager is not None, "Invalid data manager (%s) requested. It may have been removed before the job completed." % (data_manager_id)
AssertionError: Invalid data manager (data_manager_fetch_refseq) requested. It may have been removed before the job completed.
FAIL
( data_manager_fetch_refseq ) > Test-2 ... 2020-04-17 15:04:48,163 INFO  [galaxy.tools] Validated and populated state for tool request (0.204 ms)
2020-04-17 15:04:48,198 INFO  [galaxy.tools.actions] Handled output named output_file for tool data_manager_fetch_refseq (1.462 ms)
2020-04-17 15:04:48,252 INFO  [galaxy.tools.actions] Added output datasets to history (54.082 ms)
2020-04-17 15:04:48,254 INFO  [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=data_manager_fetch_refseq] complete, ready to be enqueued (1.527 ms)
2020-04-17 15:04:48,292 INFO  [galaxy.web_stack.handlers] Flushed transaction for Job[id=2,tool_id=data_manager_fetch_refseq] (38.040 ms)
2020-04-17 15:04:48,292 INFO  [galaxy.web_stack.handlers] (Job[id=2,tool_id=data_manager_fetch_refseq]) Handler 'main' assigned using 'db-preassign' assignment method
2020-04-17 15:04:48,615 INFO  [galaxy.jobs.handler] (2) Job dispatched
2020-04-17 15:04:48,809 INFO  [galaxy.jobs.command_factory] Built script [/tmp/tmp4bznxpwc/job_working_directory/000/2/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/pvh/miniconda3/envs/mulled-v1-c81d2d869008a5a47043a145fb52118d872ce729363c2243d23dd911ff10b108')" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
    . '/home/pvh/miniconda3/bin/activate' '/home/pvh/miniconda3/envs/mulled-v1-c81d2d869008a5a47043a145fb52118d872ce729363c2243d23dd911ff10b108' > conda_activate.log 2>&1
    if [ $? -eq 0 ];then
        break
    else
        let COUNT=COUNT+1
        if [ $COUNT -eq $MAX_TRIES ];then
            echo "Failed to activate conda environment! Error was:"
            cat conda_activate.log
            exit 1
        fi
        sleep 10s
    fi
done ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/pvh/miniconda3/envs/mulled-v1-c81d2d869008a5a47043a145fb52118d872ce729363c2243d23dd911ff10b108')" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
    . '/home/pvh/miniconda3/bin/activate' '/home/pvh/miniconda3/envs/mulled-v1-c81d2d869008a5a47043a145fb52118d872ce729363c2243d23dd911ff10b108' > conda_activate.log 2>&1
    if [ $? -eq 0 ];then
        break
    else
        let COUNT=COUNT+1
        if [ $COUNT -eq $MAX_TRIES ];then
            echo "Failed to activate conda environment! Error was:"
            cat conda_activate.log
            exit 1
        fi
        sleep 10s
    fi
done ; python '/home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/data_managers/data_manager_fetch_refseq/data_manager/fetch_refseq.py'  --galaxy_datamanager_filename '/tmp/tmp4bznxpwc/files/e/4/c/dataset_e4c1e215-8ba3-46d9-bfa4-139d3622c500.dat' --division_names plastid --mol_types protein --pin_date '2018-03-14']