Galaxy update 19.09

[vloux]

• [x] DB Dump
• [x] Galaxy rep saved
• [x] VM snapshot

git fetch origin
[proteore@proteore galaxy]$ git fetch origin
remote: Enumerating objects: 13998, done.
remote: Counting objects: 100% (13998/13998), done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 49587 (delta 13995), reused 13998 (delta 13995), pack-reused 35589
Receiving objects: 100% (49587/49587), 28.08 MiB | 16.94 MiB/s, done.
Resolving deltas: 100% (39092/39092), completed with 2308 local objects.
From https://github.com/galaxyproject/galaxy
   9aaafd8..359fadc  release_18.09 -> origin/release_18.09
   03acc98..850d483  dev        -> origin/dev
   f2c9baf..f1209e2  master     -> origin/master
   f3ba9e2..8f14121  release_16.01 -> origin/release_16.01
   482f1ea..48510a2  release_16.04 -> origin/release_16.04
   8a1616a..6c02000  release_16.07 -> origin/release_16.07
   809ae58..267037f  release_16.10 -> origin/release_16.10
   fa7f2a4..61e6fd1  release_17.01 -> origin/release_17.01
   c4150d2..e0a06a3  release_17.05 -> origin/release_17.05
   40cecf6..b04b3d9  release_17.09 -> origin/release_17.09
   b5ce8d0..a429433  release_18.01 -> origin/release_18.01
   45e475e..b7a2fdb  release_18.05 -> origin/release_18.05
 * [new branch]      release_19.01 -> origin/release_19.01
 * [new branch]      release_19.05 -> origin/release_19.05
 * [new branch]      release_19.09 -> origin/release_19.09
 + df07b28...4bde91f usegalaxy  -> origin/usegalaxy  (forced update)
From https://github.com/galaxyproject/galaxy
 * [new tag]         galaxy-containers-19.9.0 -> galaxy-containers-19.9.0
 * [new tag]         galaxy-job-metrics-19.9.0 -> galaxy-job-metrics-19.9.0
 * [new tag]         galaxy-objectstore-19.9.0 -> galaxy-objectstore-19.9.0
 * [new tag]         galaxy-tool-util-19.9.0 -> galaxy-tool-util-19.9.0
 * [new tag]         galaxy-util-19.9.0 -> galaxy-util-19.9.0
 * [new tag]         v19.01     -> v19.01
 * [new tag]         v19.05     -> v19.05
 * [new tag]         v19.09     -> v19.09

[proteore@proteore galaxy]$ git checkout release_19.09
error: Your local changes to the following files would be overwritten by checkout:
    config/tool_conf.xml.main
    static/style/blue/base.css
Please, commit your changes or stash them before you can switch branches.
Aborting
[proteore@proteore galaxy]$ less static/style/blue/base.css
[proteore@proteore galaxy]$
[proteore@proteore galaxy]$
[proteore@proteore galaxy]$
[proteore@proteore galaxy]$ mv config/tool_conf.xml.main config/tool_conf.xml.main.20191217
[proteore@proteore galaxy]$ mv static/style/blue/base.css static/style/blue/base.css.20191217
[proteore@proteore galaxy]$
[proteore@proteore galaxy]$
[proteore@proteore galaxy]$ git checkout release_19.09
Branch release_19.09 set up to track remote branch release_19.09 from origin.
Switched to a new branch 'release_19.09'

[proteore@proteore galaxy]$ sh run.sh start
Unsetting $PYTHONPATH
Activating virtualenv at .venv
Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages
You are using pip version 9.0.1, however version 19.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Collecting adal==1.2.2 (from -r requirements.txt (line 3))
  Downloading https://files.pythonhosted.org/packages/4f/b5/3ea9ae3d1096b9ff31e8f1846c47d49f3129a12464ac0a73b602de458298/adal-1.2.2-py2.py3-none-any.whl (53kB)
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Collecting amqp==2.5.1 (from -r requirements.txt (line 4))
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Requirement already satisfied: appdirs==1.4.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))
Collecting attrs==19.1.0 (from -r requirements.txt (line 6))
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Collecting avro==1.8.1 (from -r requirements.txt (line 7))
  Downloading https://files.pythonhosted.org/packages/b8/d4/c0af0dd8e3e6994f3297b7d49aceed2b6b9a6b55e78c4c4c8448683aabba/avro-1.8.1.tar.gz (44kB)
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Requirement already satisfied: azure-common==1.1.14 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))
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Requirement already satisfied: azure-mgmt-compute==4.0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 11))
Requirement already satisfied: azure-mgmt-devtestlabs==2.2.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 12))
Requirement already satisfied: azure-mgmt-network==2.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 13))
Collecting azure-mgmt-nspkg==3.0.2 (from -r requirements.txt (line 14))
  Downloading https://files.pythonhosted.org/packages/a1/6e/464d039ec6184234b188d6a9d199e658cce86b38afe4db0e8edd1629f3f6/azure_mgmt_nspkg-3.0.2-py2-none-any.whl
Requirement already satisfied: azure-mgmt-resource==2.0.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 15))
Requirement already satisfied: azure-mgmt-storage==2.0.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16))
Collecting azure-nspkg==3.0.2 (from -r requirements.txt (line 17))
  Downloading https://files.pythonhosted.org/packages/c2/95/af354f2f415d250dafe26a5d94230558aa8cf733a9dcbf0d26cd61f5a9b8/azure_nspkg-3.0.2-py2-none-any.whl
Requirement already satisfied: azure-storage-blob==1.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18))
Collecting azure-storage-common==1.4.2 (from -r requirements.txt (line 19))
  Downloading https://files.pythonhosted.org/packages/05/6c/b2285bf3687768dbf61b6bc085b0c1be2893b6e2757a9d023263764177f3/azure_storage_common-1.4.2-py2.py3-none-any.whl (47kB)
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Collecting azure-storage-nspkg==3.1.0 (from -r requirements.txt (line 20))
  Downloading https://files.pythonhosted.org/packages/ba/f6/054ace7b01c6c21b3b95a83c3997f7d6539d939a2c08c4f27f779128a030/azure_storage_nspkg-3.1.0-py2.py3-none-any.whl
Collecting babel==2.7.0 (from -r requirements.txt (line 21))
  Downloading https://files.pythonhosted.org/packages/2c/60/f2af68eb046c5de5b1fe6dd4743bf42c074f7141fe7b2737d3061533b093/Babel-2.7.0-py2.py3-none-any.whl (8.4MB)
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Requirement already satisfied: bagit==1.6.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22))
Collecting bcrypt==3.1.7 (from -r requirements.txt (line 23))
  Downloading https://files.pythonhosted.org/packages/ad/36/9a0227d048e98409f012570f7bef8a8c2373b9c9c5dfbf82963cbae05ede/bcrypt-3.1.7-cp27-cp27mu-manylinux1_x86_64.whl (59kB)
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Requirement already satisfied: bdbag==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24))
Collecting beaker==1.10.1 (from -r requirements.txt (line 25))
  Downloading https://files.pythonhosted.org/packages/76/87/ecc1a222f0caaa7ba7b8928737e89b2e91b8c22450c12b8a51ee625a4d87/Beaker-1.10.1.tar.gz (40kB)
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Collecting bioblend==0.13.0 (from -r requirements.txt (line 26))
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Collecting bleach==3.1.0 (from -r requirements.txt (line 27))
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Collecting boltons==19.1.0 (from -r requirements.txt (line 28))
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Collecting boto3==1.9.114 (from -r requirements.txt (line 29))
  Downloading https://files.pythonhosted.org/packages/22/7d/d558ed7f0d916f912cfab65104375e1d7e41972c97284afe43bb6a53dd3c/boto3-1.9.114-py2.py3-none-any.whl (128kB)
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Requirement already satisfied: boto==2.49.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30))
Collecting botocore==1.12.212 (from -r requirements.txt (line 31))
  Downloading https://files.pythonhosted.org/packages/89/aa/c6055e862b9de8462f3d02b011373a86bdef5586e1eb4247f0bde4889d10/botocore-1.12.212-py2.py3-none-any.whl (5.7MB)
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Collecting bx-python==0.8.4 (from -r requirements.txt (line 32))
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Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33))
Collecting cachecontrol==0.11.7 (from -r requirements.txt (line 34))
  Downloading https://files.pythonhosted.org/packages/c5/cb/7a78039c1e0d4e5fd9d8e9edf7ae34df469267e1c58873ca11af16e96bd8/CacheControl-0.11.7.tar.gz
Collecting cachetools==3.1.1 (from -r requirements.txt (line 35))
  Downloading https://files.pythonhosted.org/packages/2f/a6/30b0a0bef12283e83e58c1d6e7b5aabc7acfc4110df81a4471655d33e704/cachetools-3.1.1-py2.py3-none-any.whl
Collecting certifi==2019.6.16 (from -r requirements.txt (line 36))
  Downloading https://files.pythonhosted.org/packages/69/1b/b853c7a9d4f6a6d00749e94eb6f3a041e342a885b87340b79c1ef73e3a78/certifi-2019.6.16-py2.py3-none-any.whl (157kB)
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Collecting cffi==1.12.3 (from -r requirements.txt (line 37))
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Requirement already satisfied: chardet==3.0.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 38))
Collecting cheetah3==3.2.3 (from -r requirements.txt (line 39))
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Collecting cliff==2.15.0 (from -r requirements.txt (line 40))
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Collecting cloudauthz==0.6.0 (from -r requirements.txt (line 41))
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Collecting cloudbridge==2.0.0 (from -r requirements.txt (line 42))
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Requirement already satisfied: cmd2==0.8.9 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 43))
Collecting configparser==3.8.1 (from -r requirements.txt (line 44))
  Downloading https://files.pythonhosted.org/packages/ab/1a/ec151e5e703ac80041eaccef923611bbcec2b667c20383655a06962732e9/configparser-3.8.1-py2.py3-none-any.whl
Requirement already satisfied: contextlib2==0.5.5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45))
Collecting cryptography==2.8 (from -r requirements.txt (line 46))
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Collecting cwltool==1.0.20180721142728 (from -r requirements.txt (line 47))
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Collecting debtcollector==1.21.0 (from -r requirements.txt (line 48))
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Collecting decorator==4.4.0 (from -r requirements.txt (line 49))
  Downloading https://files.pythonhosted.org/packages/5f/88/0075e461560a1e750a0dcbf77f1d9de775028c37a19a346a6c565a257399/decorator-4.4.0-py2.py3-none-any.whl
Collecting deprecated==1.2.6 (from -r requirements.txt (line 50))
  Downloading https://files.pythonhosted.org/packages/88/0e/9d5a1a8cd7130c49334cce7b8167ceda63d6a329c8ea65b626116bc9e9e6/Deprecated-1.2.6-py2.py3-none-any.whl
Collecting deprecation==2.0.7 (from -r requirements.txt (line 51))
  Downloading https://files.pythonhosted.org/packages/b9/2a/d5084a8781398cea745c01237b95d9762c382697c63760a95cc6a814ad3a/deprecation-2.0.7-py2.py3-none-any.whl
Requirement already satisfied: dictobj==0.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 52))
Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 53))
Collecting docutils==0.15.2 (from -r requirements.txt (line 54))
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Collecting dogpile.cache==0.7.1 (from -r requirements.txt (line 55))
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Collecting ecdsa==0.13.2 (from -r requirements.txt (line 56))
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Requirement already satisfied: enum34==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 57))
Requirement already satisfied: fabric3==1.14.post1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 58))
Requirement already satisfied: funcsigs==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59))
Requirement already satisfied: functools32==3.2.3.post2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60))
Collecting future==0.17.1 (from -r requirements.txt (line 61))
  Downloading https://files.pythonhosted.org/packages/90/52/e20466b85000a181e1e144fd8305caf2cf475e2f9674e797b222f8105f5f/future-0.17.1.tar.gz (829kB)
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Collecting futures==3.3.0 (from -r requirements.txt (line 62))
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Requirement already satisfied: galaxy-sequence-utils==1.1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63))
Collecting google-api-python-client==1.7.8 (from -r requirements.txt (line 64))
  Downloading https://files.pythonhosted.org/packages/7a/84/ffde3c95d4162cdc8bae710fecc6873cccb05ac33afc3b2c925c74cc0150/google-api-python-client-1.7.8.tar.gz (141kB)
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Collecting google-auth-httplib2==0.0.3 (from -r requirements.txt (line 65))
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Collecting google-auth==1.6.3 (from -r requirements.txt (line 66))
  Downloading https://files.pythonhosted.org/packages/c5/9b/ed0516cc1f7609fb0217e3057ff4f0f9f3e3ce79a369c6af4a6c5ca25664/google_auth-1.6.3-py2.py3-none-any.whl (73kB)
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Collecting gxformat2==0.9.0 (from -r requirements.txt (line 67))
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Collecting h5py==2.9.0 (from -r requirements.txt (line 68))
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Collecting httplib2==0.13.1 (from -r requirements.txt (line 69))
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Collecting idna==2.8 (from -r requirements.txt (line 70))
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Collecting importlib-metadata==0.19 (from -r requirements.txt (line 71))
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Requirement already satisfied: ipaddress==1.0.22 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 72))
Collecting isa-rwval==0.10.7 (from -r requirements.txt (line 73))
  Downloading https://files.pythonhosted.org/packages/b0/ba/6b84326bf61a9dc2c86ea98c62746b400b48f9eb860ddbcffa712bd0ff5f/isa_rwval-0.10.7-py2.py3-none-any.whl (40kB)
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Requirement already satisfied: iso8601==0.1.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74))
Requirement already satisfied: isodate==0.6.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75))
Collecting jmespath==0.9.4 (from -r requirements.txt (line 76))
  Downloading https://files.pythonhosted.org/packages/83/94/7179c3832a6d45b266ddb2aac329e101367fbdb11f425f13771d27f225bb/jmespath-0.9.4-py2.py3-none-any.whl
Collecting jsonpatch==1.24 (from -r requirements.txt (line 77))
  Downloading https://files.pythonhosted.org/packages/86/7e/035d19a73306278673039f0805b863be8798057cc1b4008b9c8c7d1d32a3/jsonpatch-1.24-py2.py3-none-any.whl
Requirement already satisfied: jsonpointer==2.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 78))
Collecting jsonschema==3.0.2 (from -r requirements.txt (line 79))
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Collecting keystoneauth1==3.17.0 (from -r requirements.txt (line 80))
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Collecting kombu==4.6.4 (from -r requirements.txt (line 81))
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Collecting lockfile==0.12.2 (from -r requirements.txt (line 82))
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Collecting lxml==4.4.1 (from -r requirements.txt (line 83))
  Downloading https://files.pythonhosted.org/packages/e4/f4/65d145cd6917131826050b0479be35aaccba2847b7f80fc4afc6bec6616b/lxml-4.4.1-cp27-cp27mu-manylinux1_x86_64.whl (5.7MB)
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Collecting mako==1.1.0 (from -r requirements.txt (line 84))
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Collecting markupsafe==1.1.1 (from -r requirements.txt (line 85))
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Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 86))
Collecting mistune==0.8.4 (from -r requirements.txt (line 87))
  Downloading https://files.pythonhosted.org/packages/09/ec/4b43dae793655b7d8a25f76119624350b4d65eb663459eb9603d7f1f0345/mistune-0.8.4-py2.py3-none-any.whl
Requirement already satisfied: monotonic==1.5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 88))
Collecting msgpack==0.6.1 (from -r requirements.txt (line 89))
  Downloading https://files.pythonhosted.org/packages/6f/74/06f950e5a4c1fb94b676640b8fea839b80bffdc247144bd054dd5eed250e/msgpack-0.6.1-cp27-cp27mu-manylinux1_x86_64.whl (231kB)
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Requirement already satisfied: msrest==0.5.5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 90))
Requirement already satisfied: msrestazure==0.5.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 91))
Requirement already satisfied: munch==2.3.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 92))
Collecting mypy-extensions==0.4.1 (from -r requirements.txt (line 93))
  Downloading https://files.pythonhosted.org/packages/4d/72/8d54e2b296631b9b14961d583e56e90d9d7fba8a240d5ce7f1113cc5e887/mypy_extensions-0.4.1-py2.py3-none-any.whl
Requirement already satisfied: netaddr==0.7.19 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 94))
Collecting netifaces==0.10.9 (from -r requirements.txt (line 95))
  Downloading https://files.pythonhosted.org/packages/7e/02/ad1a92a72620cc17d448fe4dbdfbdf8fe1487ee7bfd82bb48308712c2f3c/netifaces-0.10.9-cp27-cp27mu-manylinux1_x86_64.whl
Collecting networkx==1.11 (from -r requirements.txt (line 96))
  Downloading https://files.pythonhosted.org/packages/d3/2c/e473e54afc9fae58dfa97066ef6709a7e35a1dd1c28c5a3842989322be00/networkx-1.11-py2.py3-none-any.whl (1.3MB)
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Collecting nodeenv==1.3.3 (from -r requirements.txt (line 97))
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Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 98))
Collecting numpy==1.16.4 (from -r requirements.txt (line 99))
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Collecting oauth2client==4.1.3 (from -r requirements.txt (line 100))
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Collecting oauthlib==3.1.0 (from -r requirements.txt (line 101))
  Downloading https://files.pythonhosted.org/packages/05/57/ce2e7a8fa7c0afb54a0581b14a65b56e62b5759dbc98e80627142b8a3704/oauthlib-3.1.0-py2.py3-none-any.whl (147kB)
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Requirement already satisfied: openstacksdk==0.17.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 102))
Collecting os-client-config==1.32.0 (from -r requirements.txt (line 103))
  Downloading https://files.pythonhosted.org/packages/53/c1/0eebf3164bb37c09c0a720c7601d1e3c9bf7ec43cbed7e9e0af7245ba306/os_client_config-1.32.0-py2.py3-none-any.whl
Collecting os-service-types==1.7.0 (from -r requirements.txt (line 104))
  Downloading https://files.pythonhosted.org/packages/10/2d/318b2b631f68e0fc221ba8f45d163bf810cdb795cf242fe85ad3e5d45639/os_service_types-1.7.0-py2.py3-none-any.whl
Collecting osc-lib==1.13.0 (from -r requirements.txt (line 105))
  Downloading https://files.pythonhosted.org/packages/2b/95/d7d88b69287cfef2c0946fe6c454e707abfeffaf53ba53722eaf29b867a1/osc_lib-1.13.0-py2.py3-none-any.whl (87kB)
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Collecting oslo.config==6.11.0 (from -r requirements.txt (line 106))
  Downloading https://files.pythonhosted.org/packages/6f/7c/ebba93a2d3e09fd0220e1adfdb8230142f4e21d1527e5b06aa353dc27719/oslo.config-6.11.0-py2.py3-none-any.whl (131kB)
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Collecting oslo.context==2.22.1 (from -r requirements.txt (line 107))
  Downloading https://files.pythonhosted.org/packages/f1/a9/7922909f3cc999276072a0de71dbcc23d7945d66814feee15c63d0c0cbc5/oslo.context-2.22.1-py2.py3-none-any.whl
Collecting oslo.i18n==3.23.1 (from -r requirements.txt (line 108))
  Downloading https://files.pythonhosted.org/packages/61/eb/4732a0f12850ef5ada812d4920c6801b7e394f14969864a91927ed853a2f/oslo.i18n-3.23.1-py2.py3-none-any.whl (46kB)
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Collecting oslo.log==3.44.0 (from -r requirements.txt (line 109))
  Downloading https://files.pythonhosted.org/packages/98/a9/8ab877f8159b89a4199b5220b524d861f152adad753c4be8764506763eb9/oslo.log-3.44.0-py2.py3-none-any.whl (72kB)
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Collecting oslo.serialization==2.29.1 (from -r requirements.txt (line 110))
  Downloading https://files.pythonhosted.org/packages/bc/ad/7401e409d946469a9ad90aef8c98e5d39abea9c24e4db803285f9c7d726c/oslo.serialization-2.29.1-py2.py3-none-any.whl
Collecting oslo.utils==3.41.0 (from -r requirements.txt (line 111))
  Downloading https://files.pythonhosted.org/packages/9f/87/0f36497a282db6d6e58d1b80a2ab509a0709c4e1cddd44bcb31f054f4d8b/oslo.utils-3.41.0-py2.py3-none-any.whl (99kB)
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Collecting packaging==19.1 (from -r requirements.txt (line 112))
  Downloading https://files.pythonhosted.org/packages/ec/22/630ac83e8f8a9566c4f88038447ed9e16e6f10582767a01f31c769d9a71e/packaging-19.1-py2.py3-none-any.whl
Collecting paramiko==2.6.0 (from -r requirements.txt (line 113))
  Downloading https://files.pythonhosted.org/packages/4b/80/74dace9e48b0ef923633dfb5e48798f58a168e4734bca8ecfaf839ba051a/paramiko-2.6.0-py2.py3-none-any.whl (199kB)
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Requirement already satisfied: parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 114))
Collecting paste==3.1.0 (from -r requirements.txt (line 115))
  Cache entry deserialization failed, entry ignored
  Downloading https://files.pythonhosted.org/packages/97/4c/e451ff04fa9cd64ebad62c442d5c273debd40e295af5b040454a00be2869/Paste-3.1.0-py2.py3-none-any.whl (592kB)
    100% |████████████████████████████████| 593kB 1.9MB/s
Collecting pastedeploy==2.0.1 (from -r requirements.txt (line 116))
  Downloading https://files.pythonhosted.org/packages/67/0c/faa9971b2e5e048b3b30008d04c72e4d5f63b42f48937c169acce2c5e70a/PasteDeploy-2.0.1-py2.py3-none-any.whl
Collecting pastescript==3.1.0 (from -r requirements.txt (line 117))
  Downloading https://files.pythonhosted.org/packages/47/4f/a3e6a848328b2540e73e12a96c17c72637175661470cb852efa2eb9187e3/PasteScript-3.1.0-py2.py3-none-any.whl (73kB)
    100% |████████████████████████████████| 81kB 8.3MB/s
Collecting pathlib2==2.3.2 (from -r requirements.txt (line 118))
  Downloading https://files.pythonhosted.org/packages/66/a7/9f8d84f31728d78beade9b1271ccbfb290c41c1e4dc13dbd4997ad594dcd/pathlib2-2.3.2-py2.py3-none-any.whl
Collecting pbr==5.4.2 (from -r requirements.txt (line 119))
  Downloading https://files.pythonhosted.org/packages/f9/d8/bd657bfa0e89eb71ad5e977ed99a9bb2b44e5db68d9190970637c26501bb/pbr-5.4.2-py2.py3-none-any.whl (110kB)
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Requirement already satisfied: prettytable==0.7.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 120))
Collecting prov==1.5.1 (from -r requirements.txt (line 121))
  Downloading https://files.pythonhosted.org/packages/8e/fb/2c4c618185be2bda327f9dacd16b3122cc938809f19df7be840595d0e584/prov-1.5.1-py2.py3-none-any.whl (426kB)
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Collecting psutil==5.6.3 (from -r requirements.txt (line 122))
  Downloading https://wheels.galaxyproject.org/simple/psutil/psutil-5.6.3-cp27-cp27mu-manylinux1_x86_64.whl (252kB)
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Collecting pulsar-galaxy-lib==0.13.0 (from -r requirements.txt (line 123))
  Downloading https://files.pythonhosted.org/packages/18/af/9176683072a5e8d2a2a80b7d29d56365907472ea5f113cbed6dd22ac9047/pulsar_galaxy_lib-0.13.0-py2.py3-none-any.whl (178kB)
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Collecting pyasn1-modules==0.2.6 (from -r requirements.txt (line 124))
  Downloading https://files.pythonhosted.org/packages/be/70/e5ea8afd6d08a4b99ebfc77bd1845248d56cfcf43d11f9dc324b9580a35c/pyasn1_modules-0.2.6-py2.py3-none-any.whl (95kB)
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Collecting pyasn1==0.4.6 (from -r requirements.txt (line 125))
  Downloading https://files.pythonhosted.org/packages/6a/6e/209351ec34b7d7807342e2bb6ff8a96eef1fd5dcac13bdbadf065c2bb55c/pyasn1-0.4.6-py2.py3-none-any.whl (75kB)
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Collecting pycparser==2.19 (from -r requirements.txt (line 126))
  Downloading https://files.pythonhosted.org/packages/68/9e/49196946aee219aead1290e00d1e7fdeab8567783e83e1b9ab5585e6206a/pycparser-2.19.tar.gz (158kB)
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Collecting pycryptodome==3.8.2 (from -r requirements.txt (line 127))
  Downloading https://files.pythonhosted.org/packages/05/41/36b91c77204f615b640ffd61309b668cec6cbb3a1aff42540ba08c275bbf/pycryptodome-3.8.2-cp27-cp27mu-manylinux1_x86_64.whl (9.6MB)
    100% |████████████████████████████████| 9.6MB 112kB/s
Collecting pyeventsystem==0.1.0 (from -r requirements.txt (line 128))
  Downloading https://files.pythonhosted.org/packages/e5/d3/99dac9569f8e90c21889a6d91d187404eb831ceef4638c98c3ff8915ae44/pyeventsystem-0.1.0-py2.py3-none-any.whl
Requirement already satisfied: pyinotify==0.9.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 129))
Collecting pyjwt==1.7.1 (from -r requirements.txt (line 130))
  Downloading https://files.pythonhosted.org/packages/87/8b/6a9f14b5f781697e51259d81657e6048fd31a113229cf346880bb7545565/PyJWT-1.7.1-py2.py3-none-any.whl
Collecting pykwalify==1.7.0 (from -r requirements.txt (line 131))
  Downloading https://files.pythonhosted.org/packages/36/9f/612de8ca540bd24d604f544248c4c46e9db76f6ea5eb75fb4244da6ebbf0/pykwalify-1.7.0-py2.py3-none-any.whl (40kB)
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Collecting pynacl==1.3.0 (from -r requirements.txt (line 132))
  Downloading https://files.pythonhosted.org/packages/b3/25/e605574f24948a8a53b497744e93f061eb1dbe7c44b6465fc1c172d591aa/PyNaCl-1.3.0-cp27-cp27mu-manylinux1_x86_64.whl (762kB)
    100% |████████████████████████████████| 768kB 1.5MB/s
Collecting pyopenssl==19.0.0 (from -r requirements.txt (line 133))
  Downloading https://files.pythonhosted.org/packages/01/c8/ceb170d81bd3941cbeb9940fc6cc2ef2ca4288d0ca8929ea4db5905d904d/pyOpenSSL-19.0.0-py2.py3-none-any.whl (53kB)
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Collecting pyparsing==2.4.2 (from -r requirements.txt (line 134))
  Downloading https://files.pythonhosted.org/packages/11/fa/0160cd525c62d7abd076a070ff02b2b94de589f1a9789774f17d7c54058e/pyparsing-2.4.2-py2.py3-none-any.whl (65kB)
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Collecting pyperclip==1.7.0 (from -r requirements.txt (line 135))
  Downloading https://files.pythonhosted.org/packages/2d/0f/4eda562dffd085945d57c2d9a5da745cfb5228c02bc90f2c74bbac746243/pyperclip-1.7.0.tar.gz
Collecting pyrsistent==0.15.4 (from -r requirements.txt (line 136))
  Downloading https://files.pythonhosted.org/packages/b9/66/b2638d96a2d128b168d0dba60fdc77b7800a9b4a5340cefcc5fc4eae6295/pyrsistent-0.15.4.tar.gz (107kB)
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Collecting pysam==0.15.2 (from -r requirements.txt (line 137))
  Cache entry deserialization failed, entry ignored
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    100% |████████████████████████████████| 8.9MB 126kB/s
Requirement already satisfied: pysftp==0.2.9 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 138))
Requirement already satisfied: python-cinderclient==4.0.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 139))
Collecting python-dateutil==2.8.0 (from -r requirements.txt (line 140))
  Downloading https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl (226kB)
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Collecting python-genomespaceclient==1.2.0 (from -r requirements.txt (line 141))
  Downloading https://files.pythonhosted.org/packages/a8/7e/a1766c364148114805cb0bf9d517df21e832e6290b8bb3487acb8e0c1f8c/python-genomespaceclient-1.2.0.tar.gz
Requirement already satisfied: python-glanceclient==2.12.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 142))
Collecting python-jose==3.0.1 (from -r requirements.txt (line 143))
  Downloading https://files.pythonhosted.org/packages/96/da/c0dcc5e7a98a53440b8db3cf9771345fa696754f79e8734ea59123f7d734/python_jose-3.0.1-py2.py3-none-any.whl
Requirement already satisfied: python-keystoneclient==3.17.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 144))
Requirement already satisfied: python-neutronclient==6.9.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 145))
Requirement already satisfied: python-novaclient==11.0.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 146))
Requirement already satisfied: python-openid==2.2.5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 147))
Requirement already satisfied: python-swiftclient==3.6.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 148))
Collecting pytz==2019.2 (from -r requirements.txt (line 149))
  Downloading https://files.pythonhosted.org/packages/87/76/46d697698a143e05f77bec5a526bf4e56a0be61d63425b68f4ba553b51f2/pytz-2019.2-py2.py3-none-any.whl (508kB)
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Collecting pyuwsgi==2.0.18.post0 (from -r requirements.txt (line 150))
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Collecting pyyaml==5.1.2 (from -r requirements.txt (line 151))
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Collecting rdflib-jsonld==0.4.0 (from -r requirements.txt (line 152))
  Downloading https://files.pythonhosted.org/packages/ba/48/edaad22fc9de34500699f0c7fc9124385dd425fd18857244f126a6f7df66/rdflib-jsonld-0.4.0.tar.gz (53kB)
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Collecting rdflib==4.2.2 (from -r requirements.txt (line 153))
  Downloading https://files.pythonhosted.org/packages/c5/77/1fa0f4cffd5faad496b1344ab665902bb2609f56e0fb19bcf80cff485da0/rdflib-4.2.2.tar.gz (905kB)
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Requirement already satisfied: repoze.lru==0.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 154))
Collecting requests-oauthlib==1.2.0 (from -r requirements.txt (line 155))
  Downloading https://files.pythonhosted.org/packages/c2/e2/9fd03d55ffb70fe51f587f20bcf407a6927eb121de86928b34d162f0b1ac/requests_oauthlib-1.2.0-py2.py3-none-any.whl
Collecting requests-toolbelt==0.9.1 (from -r requirements.txt (line 156))
  Cache entry deserialization failed, entry ignored
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  Downloading https://files.pythonhosted.org/packages/60/ef/7681134338fc097acef8d9b2f8abe0458e4d87559c689a8c306d0957ece5/requests_toolbelt-0.9.1-py2.py3-none-any.whl (54kB)
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Collecting requests==2.22.0 (from -r requirements.txt (line 157))
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  Downloading https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl (57kB)
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Requirement already satisfied: requestsexceptions==1.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 158))
Collecting rfc3986==1.3.2 (from -r requirements.txt (line 159))
  Downloading https://files.pythonhosted.org/packages/00/8d/9d56bfe43997f1864fe0891be69bc239ded98e69c9f56eb9eaa5b1789660/rfc3986-1.3.2-py2.py3-none-any.whl
Requirement already satisfied: routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 160))
Collecting rsa==4.0 (from -r requirements.txt (line 161))
  Downloading https://files.pythonhosted.org/packages/02/e5/38518af393f7c214357079ce67a317307936896e961e35450b70fad2a9cf/rsa-4.0-py2.py3-none-any.whl
Collecting ruamel.ordereddict==0.4.14 (from -r requirements.txt (line 162))
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Collecting ruamel.yaml==0.15.100 (from -r requirements.txt (line 163))
  Downloading https://files.pythonhosted.org/packages/18/7d/58c8c0f216660226588691b2ccb19884a171539d45ed7f49855b8226c9e6/ruamel.yaml-0.15.100-cp27-cp27mu-manylinux1_x86_64.whl (600kB)
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Collecting s3transfer==0.2.1 (from -r requirements.txt (line 164))
  Downloading https://files.pythonhosted.org/packages/16/8a/1fc3dba0c4923c2a76e1ff0d52b305c44606da63f718d14d3231e21c51b0/s3transfer-0.2.1-py2.py3-none-any.whl (70kB)
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Collecting scandir==1.10.0 (from -r requirements.txt (line 165))
  Downloading https://files.pythonhosted.org/packages/df/f5/9c052db7bd54d0cbf1bc0bb6554362bba1012d03e5888950a4f5c5dadc4e/scandir-1.10.0.tar.gz
Collecting schema-salad==2.7.20181126142424 (from -r requirements.txt (line 166))
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Collecting shellescape==3.4.1 (from -r requirements.txt (line 167))
  Downloading https://files.pythonhosted.org/packages/51/b6/986c99a10040beaaefca1ad6c93bd7738cb8e4f52f6caed13d3ed1caa7e4/shellescape-3.4.1-py2.py3-none-any.whl
Requirement already satisfied: simplejson==3.16.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 168))
Requirement already satisfied: six==1.11.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 169))
Collecting social-auth-core[openidconnect]==3.1.0+gx0 (from -r requirements.txt (line 170))
  Downloading https://wheels.galaxyproject.org/simple/social-auth-core/social_auth_core-3.1.0%2Bgx0-py2-none-any.whl (314kB)
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Collecting sqlalchemy-migrate==0.12.0 (from -r requirements.txt (line 171))
  Downloading https://files.pythonhosted.org/packages/b5/99/92c4c90d5a22aac19554effd04789b78b5549c62fefbda1f42cc549b31b1/sqlalchemy_migrate-0.12.0-py2.py3-none-any.whl (108kB)
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Collecting sqlalchemy-utils==0.34.2 (from -r requirements.txt (line 172))
  Downloading https://files.pythonhosted.org/packages/45/61/3bdd2931e86253fa7df6445a26929fbcc9bc43ad6b27a10f991eb6ecde75/SQLAlchemy-Utils-0.34.2.tar.gz (129kB)
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Collecting sqlalchemy==1.3.7 (from -r requirements.txt (line 173))
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Collecting sqlparse==0.3.0 (from -r requirements.txt (line 174))
  Downloading https://files.pythonhosted.org/packages/ef/53/900f7d2a54557c6a37886585a91336520e5539e3ae2423ff1102daf4f3a7/sqlparse-0.3.0-py2.py3-none-any.whl
Collecting stevedore==1.30.1 (from -r requirements.txt (line 175))
  Downloading https://files.pythonhosted.org/packages/c6/dc/6ee92bccfe3c0448786b30b693e6060d62ec8c4a3ec9a287bac1c1a8d8c9/stevedore-1.30.1-py2.py3-none-any.whl (42kB)
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Collecting subprocess32==3.5.4 (from -r requirements.txt (line 176))
  Downloading https://wheels.galaxyproject.org/simple/subprocess32/subprocess32-3.5.4-cp27-cp27mu-manylinux1_x86_64.whl (43kB)
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Collecting svgwrite==1.3.1 (from -r requirements.txt (line 177))
  Downloading https://files.pythonhosted.org/packages/4f/2e/f36cfec1da6162055b884e6366074cff18475a9538559ceae0c0bc58e186/svgwrite-1.3.1-py2.py3-none-any.whl (67kB)
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Requirement already satisfied: tempita==0.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 178))
Requirement already satisfied: tenacity==4.12.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 179))
Collecting typing-extensions==3.7.4 (from -r requirements.txt (line 180))
  Downloading https://files.pythonhosted.org/packages/b8/4d/eddc8b3c539cd79a31987ffc96ccd62ecc35f637d5d4fdaa37e4b64a2e5b/typing_extensions-3.7.4-py2-none-any.whl
Collecting typing==3.7.4 (from -r requirements.txt (line 181))
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Collecting tzlocal==2.0.0 (from -r requirements.txt (line 182))
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Requirement already satisfied: unicodecsv==0.14.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 183))
Collecting uritemplate==3.0.0 (from -r requirements.txt (line 184))
  Downloading https://files.pythonhosted.org/packages/f6/25/66a49231b44409d7f07cfcf2506a8b070ce3c99fc47cc256bea833f24791/uritemplate-3.0.0-py2-none-any.whl
Collecting urllib3==1.25.3 (from -r requirements.txt (line 185))
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Collecting vine==1.3.0 (from -r requirements.txt (line 186))
  Downloading https://files.pythonhosted.org/packages/7f/60/82c03047396126c8331ceb64da1dc52d4f1317209f32e8fe286d0c07365a/vine-1.3.0-py2.py3-none-any.whl
Collecting warlock==1.3.3 (from -r requirements.txt (line 187))
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Requirement already satisfied: wcwidth==0.1.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 188))
Requirement already satisfied: webencodings==0.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 189))
Collecting webob==1.8.5 (from -r requirements.txt (line 190))
  Cache entry deserialization failed, entry ignored
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  Downloading https://files.pythonhosted.org/packages/06/e1/4acd2b4327fceb4c6446bdbca515f807ab83188526fd654940c00bcf8cc3/WebOb-1.8.5-py2.py3-none-any.whl (113kB)
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Requirement already satisfied: whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 191))
Collecting wrapt==1.11.2 (from -r requirements.txt (line 192))
  Downloading https://wheels.galaxyproject.org/simple/wrapt/wrapt-1.11.2-cp27-cp27mu-manylinux1_x86_64.whl (67kB)
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Collecting zipp==0.5.2 (from -r requirements.txt (line 193))
  Downloading https://files.pythonhosted.org/packages/da/bd/1a5fdf15aa44231fd09f63ecf175b60f057ae37ec65b343bb009364923f3/zipp-0.5.2-py2.py3-none-any.whl
Requirement already satisfied: setuptools in ./.venv/lib/python2.7/site-packages (from cwltool==1.0.20180721142728->-r requirements.txt (line 47))
Building wheels for collected packages: avro, beaker, cachecontrol, dogpile.cache, future, google-api-python-client, httplib2, mako, nodeenv, pycparser, pyperclip, pyrsistent, python-genomespaceclient, rdflib-jsonld, rdflib, scandir, sqlalchemy-utils, sqlalchemy, warlock
  Running setup.py bdist_wheel for avro ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/25/89/a2/b91aa12c50a01170300ff61b56f13a1dbb3cc7f4a59121c99b
  Running setup.py bdist_wheel for beaker ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/f1/d3/d7/0a3b096b700cac34307a512eddd9bcd4e649ede32848648d39
  Running setup.py bdist_wheel for cachecontrol ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/66/46/36/bc94397c815ad29e5c41ffa5b870d666b1f2ab68b54135c007
  Running setup.py bdist_wheel for dogpile.cache ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/6b/80/a0/87d93729f5cac879a2561ef73cf8036940787bd5734a0f2b82
  Running setup.py bdist_wheel for future ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/0c/61/d2/d6b7317325828fbb39ee6ad559dbe4664d0896da4721bf379e
  Running setup.py bdist_wheel for google-api-python-client ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/47/59/2a/99d7513987cb500f6efa2866caf027a1b69793156f5052bc64
  Running setup.py bdist_wheel for httplib2 ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/f4/82/e5/32e48c9506525103a5ea623ada8452739e56b4ec4d71708827
  Running setup.py bdist_wheel for mako ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/98/32/7b/a291926643fc1d1e02593e0d9e247c5a866a366b8343b7aa27
  Running setup.py bdist_wheel for nodeenv ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/7b/6c/23/eb26369b77904c8963fae9e64338b0f0b948b4d59710760834
  Running setup.py bdist_wheel for pycparser ... done
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  Running setup.py bdist_wheel for pyperclip ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/92/f0/ac/2ba2972034e98971c3654ece337ac61e546bdeb34ca960dc8c
  Running setup.py bdist_wheel for pyrsistent ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/bb/46/00/6d471ef0b813e3621f0abe6cb723c20d529d39a061de3f7c51
  Running setup.py bdist_wheel for python-genomespaceclient ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/29/ad/b8/c24e40f2610a52c0ed4114038b5fffbc049c8d1739c3ac2f4a
  Running setup.py bdist_wheel for rdflib-jsonld ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/9f/31/d2/ac7f9fea93b5440274e5c67336e35f1c0f9d38e49c71e35b6d
  Running setup.py bdist_wheel for rdflib ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/8d/f6/b7/f5e9501d0f006fc9fd497c930206952856b2191ab5c836cb97
  Running setup.py bdist_wheel for scandir ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/91/95/75/19c98a91239878abbc7c59970abd3b4e0438a7dd5b61778335
  Running setup.py bdist_wheel for sqlalchemy-utils ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/74/73/55/6d2e33ae4013e904a81b7458a50732134b45956d923a050999
  Running setup.py bdist_wheel for sqlalchemy ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/80/e0/68/3d11cc7209b5bd2c7d55cbb56c6bda843cc82f77c8387468ea
  Running setup.py bdist_wheel for warlock ... done
  Stored in directory: /home//proteore/.cache/pip/wheels/07/5b/7f/aa3d5f762792f7e8f1d1fa6f03585da96b78f2cb9fe23f514a
Successfully built avro beaker cachecontrol dogpile.cache future google-api-python-client httplib2 mako nodeenv pycparser pyperclip pyrsistent python-genomespaceclient rdflib-jsonld rdflib scandir sqlalchemy-utils sqlalchemy warlock
Installing collected packages: pyjwt, pycparser, cffi, cryptography, urllib3, certifi, idna, requests, python-dateutil, adal, vine, amqp, attrs, avro, azure-nspkg, azure-mgmt-nspkg, azure-storage-nspkg, azure-storage-common, pytz, babel, bcrypt, beaker, requests-toolbelt, pyyaml, bioblend, bleach, boltons, futures, docutils, jmespath, botocore, s3transfer, boto3, numpy, bx-python, cachecontrol, cachetools, cheetah3, pbr, stevedore, pyparsing, cliff, cloudauthz, httplib2, pyasn1, rsa, pyasn1-modules, google-auth, google-auth-httplib2, uritemplate, google-api-python-client, pyeventsystem, oauth2client, wrapt, deprecated, cloudbridge, configparser, rdflib, typing, lockfile, typing-extensions, mistune, ruamel.ordereddict, ruamel.yaml, rdflib-jsonld, schema-salad, scandir, pathlib2, subprocess32, psutil, decorator, networkx, lxml, prov, mypy-extensions, shellescape, cwltool, debtcollector, packaging, deprecation, dogpile.cache, ecdsa, future, gxformat2, h5py, zipp, importlib-metadata, isa-rwval, jsonpatch, pyrsistent, jsonschema, os-service-types, keystoneauth1, kombu, markupsafe, mako, msgpack, netifaces, nodeenv, oauthlib, os-client-config, oslo.i18n, oslo.utils, osc-lib, rfc3986, oslo.config, oslo.context, oslo.serialization, oslo.log, pynacl, paramiko, paste, pastedeploy, pastescript, webob, pulsar-galaxy-lib, pycryptodome, pykwalify, pyopenssl, pyperclip, pysam, python-genomespaceclient, python-jose, pyuwsgi, requests-oauthlib, social-auth-core, sqlparse, sqlalchemy, sqlalchemy-migrate, sqlalchemy-utils, svgwrite, tzlocal, warlock
  Found existing installation: PyJWT 1.6.4
    Uninstalling PyJWT-1.6.4:
      Successfully uninstalled PyJWT-1.6.4
  Found existing installation: pycparser 2.18
    Uninstalling pycparser-2.18:
      Successfully uninstalled pycparser-2.18
  Found existing installation: cffi 1.11.5
    Uninstalling cffi-1.11.5:
      Successfully uninstalled cffi-1.11.5
  Found existing installation: cryptography 2.3.1
    Uninstalling cryptography-2.3.1:
      Successfully uninstalled cryptography-2.3.1
  Found existing installation: urllib3 1.23
    Uninstalling urllib3-1.23:
      Successfully uninstalled urllib3-1.23
  Found existing installation: certifi 2018.8.24
    Uninstalling certifi-2018.8.24:
      Successfully uninstalled certifi-2018.8.24
  Found existing installation: idna 2.7
    Uninstalling idna-2.7:
      Successfully uninstalled idna-2.7
  Found existing installation: requests 2.19.1
    Uninstalling requests-2.19.1:
      Successfully uninstalled requests-2.19.1
  Found existing installation: python-dateutil 2.7.3
    Uninstalling python-dateutil-2.7.3:
      Successfully uninstalled python-dateutil-2.7.3
  Found existing installation: adal 1.1.0
    Uninstalling adal-1.1.0:
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      Successfully uninstalled vine-1.1.4
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    Uninstalling amqp-2.3.2:
      Successfully uninstalled amqp-2.3.2
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    Uninstalling azure-nspkg-2.0.0:
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    Uninstalling azure-mgmt-nspkg-2.0.0:
      Successfully uninstalled azure-mgmt-nspkg-2.0.0
  Found existing installation: azure-storage-nspkg 3.0.0
    Uninstalling azure-storage-nspkg-3.0.0:
      Successfully uninstalled azure-storage-nspkg-3.0.0
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    Uninstalling azure-storage-common-1.3.0:
      Successfully uninstalled azure-storage-common-1.3.0
  Found existing installation: pytz 2018.5
    Uninstalling pytz-2018.5:
      Successfully uninstalled pytz-2018.5
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    Uninstalling Babel-2.6.0:
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    Uninstalling bcrypt-3.1.4:
      Successfully uninstalled bcrypt-3.1.4
  Found existing installation: Beaker 1.10.0
    Uninstalling Beaker-1.10.0:
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  Found existing installation: requests-toolbelt 0.8.0
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  Found existing installation: PyYAML 3.13
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    Uninstalling bioblend-0.11.0:
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  Found existing installation: bleach 2.1.4
    Uninstalling bleach-2.1.4:
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    Uninstalling futures-3.2.0:
      Successfully uninstalled futures-3.2.0
  Found existing installation: docutils 0.14
    Uninstalling docutils-0.14:
      Successfully uninstalled docutils-0.14
  Found existing installation: jmespath 0.9.3
    Uninstalling jmespath-0.9.3:
      Successfully uninstalled jmespath-0.9.3
  Found existing installation: botocore 1.10.84
    Uninstalling botocore-1.10.84:
      Successfully uninstalled botocore-1.10.84
  Found existing installation: s3transfer 0.1.13
    Uninstalling s3transfer-0.1.13:
      Successfully uninstalled s3transfer-0.1.13
  Found existing installation: boto3 1.7.84
    Uninstalling boto3-1.7.84:
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  Found existing installation: numpy 1.15.1
    Uninstalling numpy-1.15.1:
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  Found existing installation: bx-python 0.8.2
    Uninstalling bx-python-0.8.2:
      Successfully uninstalled bx-python-0.8.2
  Found existing installation: Cheetah3 3.1.0
    Uninstalling Cheetah3-3.1.0:
      Successfully uninstalled Cheetah3-3.1.0
  Found existing installation: pbr 4.2.0
    Uninstalling pbr-4.2.0:
      Successfully uninstalled pbr-4.2.0
  Found existing installation: stevedore 1.29.0
    Uninstalling stevedore-1.29.0:
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  Found existing installation: pyparsing 2.2.0
    Uninstalling pyparsing-2.2.0:
      Successfully uninstalled pyparsing-2.2.0
  Found existing installation: cliff 2.13.0
    Uninstalling cliff-2.13.0:
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  Found existing installation: pyasn1 0.4.4
    Uninstalling pyasn1-0.4.4:
      Successfully uninstalled pyasn1-0.4.4
  Found existing installation: wrapt 1.10.11
    Uninstalling wrapt-1.10.11:
      Successfully uninstalled wrapt-1.10.11
  Found existing installation: cloudbridge 1.0.1
    Uninstalling cloudbridge-1.0.1:
      Successfully uninstalled cloudbridge-1.0.1
  Found existing installation: typing 3.6.6
    Uninstalling typing-3.6.6:
      Successfully uninstalled typing-3.6.6
  Found existing installation: subprocess32 3.5.2
    Uninstalling subprocess32-3.5.2:
      Successfully uninstalled subprocess32-3.5.2
  Found existing installation: psutil 5.4.7
    Uninstalling psutil-5.4.7:
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  Found existing installation: decorator 4.3.0
    Uninstalling decorator-4.3.0:
      Successfully uninstalled decorator-4.3.0
  Found existing installation: debtcollector 1.20.0
    Uninstalling debtcollector-1.20.0:
      Successfully uninstalled debtcollector-1.20.0
  Found existing installation: packaging 17.1
    Uninstalling packaging-17.1:
      Successfully uninstalled packaging-17.1
  Found existing installation: deprecation 2.0.5
    Uninstalling deprecation-2.0.5:
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  Found existing installation: dogpile.cache 0.6.7
    Uninstalling dogpile.cache-0.6.7:
      Successfully uninstalled dogpile.cache-0.6.7
  Found existing installation: ecdsa 0.13
    Uninstalling ecdsa-0.13:
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  Found existing installation: future 0.16.0
    Uninstalling future-0.16.0:
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  Found existing installation: h5py 2.8.0
    Uninstalling h5py-2.8.0:
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  Found existing installation: jsonpatch 1.23
    Uninstalling jsonpatch-1.23:
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  Found existing installation: jsonschema 2.6.0
    Uninstalling jsonschema-2.6.0:
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  Found existing installation: os-service-types 1.3.0
    Uninstalling os-service-types-1.3.0:
      Successfully uninstalled os-service-types-1.3.0
  Found existing installation: keystoneauth1 3.10.0
    Uninstalling keystoneauth1-3.10.0:
      Successfully uninstalled keystoneauth1-3.10.0
  Found existing installation: kombu 4.2.1
    Uninstalling kombu-4.2.1:
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  Found existing installation: MarkupSafe 1.0
    Uninstalling MarkupSafe-1.0:
      Successfully uninstalled MarkupSafe-1.0
  Found existing installation: Mako 1.0.7
    Uninstalling Mako-1.0.7:
      Successfully uninstalled Mako-1.0.7
  Found existing installation: msgpack 0.5.6
    Uninstalling msgpack-0.5.6:
      Successfully uninstalled msgpack-0.5.6
  Found existing installation: netifaces 0.10.7
    Uninstalling netifaces-0.10.7:
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  Found existing installation: nodeenv 1.3.2
    Uninstalling nodeenv-1.3.2:
      Successfully uninstalled nodeenv-1.3.2
  Found existing installation: oauthlib 2.1.0
    Uninstalling oauthlib-2.1.0:
      Successfully uninstalled oauthlib-2.1.0
  Found existing installation: os-client-config 1.31.2
    Uninstalling os-client-config-1.31.2:
      Successfully uninstalled os-client-config-1.31.2
  Found existing installation: oslo.i18n 3.21.0
    Uninstalling oslo.i18n-3.21.0:
      Successfully uninstalled oslo.i18n-3.21.0
  Found existing installation: oslo.utils 3.37.0
    Uninstalling oslo.utils-3.37.0:
      Successfully uninstalled oslo.utils-3.37.0
  Found existing installation: osc-lib 1.11.1
    Uninstalling osc-lib-1.11.1:
      Successfully uninstalled osc-lib-1.11.1
  Found existing installation: rfc3986 1.1.0
    Uninstalling rfc3986-1.1.0:
      Successfully uninstalled rfc3986-1.1.0
  Found existing installation: oslo.config 6.4.0
    Uninstalling oslo.config-6.4.0:
      Successfully uninstalled oslo.config-6.4.0
  Found existing installation: oslo.context 2.21.0
    Uninstalling oslo.context-2.21.0:
      Successfully uninstalled oslo.context-2.21.0
  Found existing installation: oslo.serialization 2.27.0
    Uninstalling oslo.serialization-2.27.0:
      Successfully uninstalled oslo.serialization-2.27.0
  Found existing installation: oslo.log 3.39.0
    Uninstalling oslo.log-3.39.0:
      Successfully uninstalled oslo.log-3.39.0
  Found existing installation: PyNaCl 1.2.1
    Uninstalling PyNaCl-1.2.1:
      Successfully uninstalled PyNaCl-1.2.1
  Found existing installation: paramiko 2.4.2
    Uninstalling paramiko-2.4.2:
      Successfully uninstalled paramiko-2.4.2
  Found existing installation: Paste 3.0.4
    Uninstalling Paste-3.0.4:
      Successfully uninstalled Paste-3.0.4
  Found existing installation: PasteDeploy 1.5.2
    Uninstalling PasteDeploy-1.5.2:
      Successfully uninstalled PasteDeploy-1.5.2
  Found existing installation: PasteScript 2.0.2
    Uninstalling PasteScript-2.0.2:
      Successfully uninstalled PasteScript-2.0.2
  Found existing installation: WebOb 1.8.2
    Uninstalling WebOb-1.8.2:
      Successfully uninstalled WebOb-1.8.2
  Found existing installation: pulsar-galaxy-lib 0.8.3
    Uninstalling pulsar-galaxy-lib-0.8.3:
      Successfully uninstalled pulsar-galaxy-lib-0.8.3
  Found existing installation: pycryptodome 3.6.6
    Uninstalling pycryptodome-3.6.6:
      Successfully uninstalled pycryptodome-3.6.6
  Found existing installation: pykwalify 1.6.1
    Uninstalling pykwalify-1.6.1:
      Successfully uninstalled pykwalify-1.6.1
  Found existing installation: pyOpenSSL 18.0.0
    Uninstalling pyOpenSSL-18.0.0:
      Successfully uninstalled pyOpenSSL-18.0.0
  Found existing installation: pyperclip 1.6.4
    Uninstalling pyperclip-1.6.4:
      Successfully uninstalled pyperclip-1.6.4
  Found existing installation: pysam 0.14.1
    Uninstalling pysam-0.14.1:
      Successfully uninstalled pysam-0.14.1
  Found existing installation: python-genomespaceclient 1.1.0
    Uninstalling python-genomespaceclient-1.1.0:
      Successfully uninstalled python-genomespaceclient-1.1.0
  Found existing installation: requests-oauthlib 1.0.0
    Uninstalling requests-oauthlib-1.0.0:
      Successfully uninstalled requests-oauthlib-1.0.0
  Found existing installation: social-auth-core 1.5.0
    Uninstalling social-auth-core-1.5.0:
      Successfully uninstalled social-auth-core-1.5.0
  Found existing installation: sqlparse 0.2.4
    Uninstalling sqlparse-0.2.4:
      Successfully uninstalled sqlparse-0.2.4
  Found existing installation: SQLAlchemy 1.2.11
    Uninstalling SQLAlchemy-1.2.11:
      Successfully uninstalled SQLAlchemy-1.2.11
  Found existing installation: sqlalchemy-migrate 0.11.0
    Uninstalling sqlalchemy-migrate-0.11.0:
      Successfully uninstalled sqlalchemy-migrate-0.11.0
  Found existing installation: SQLAlchemy-Utils 0.33.3
    Uninstalling SQLAlchemy-Utils-0.33.3:
      Successfully uninstalled SQLAlchemy-Utils-0.33.3
  Found existing installation: svgwrite 1.1.12
    Uninstalling svgwrite-1.1.12:
      Successfully uninstalled svgwrite-1.1.12
  Found existing installation: tzlocal 1.5.1
    Uninstalling tzlocal-1.5.1:
      Successfully uninstalled tzlocal-1.5.1
  Found existing installation: warlock 1.3.0
    Uninstalling warlock-1.3.0:
      Successfully uninstalled warlock-1.3.0
Successfully installed adal-1.2.2 amqp-2.5.1 attrs-19.1.0 avro-1.8.1 azure-mgmt-nspkg-3.0.2 azure-nspkg-3.0.2 azure-storage-common-1.4.2 azure-storage-nspkg-3.1.0 babel-2.7.0 bcrypt-3.1.7 beaker-1.10.1 bioblend-0.13.0 bleach-3.1.0 boltons-19.1.0 boto3-1.9.114 botocore-1.12.212 bx-python-0.8.4 cachecontrol-0.11.7 cachetools-3.1.1 certifi-2019.6.16 cffi-1.12.3 cheetah3-3.2.3 cliff-2.15.0 cloudauthz-0.6.0 cloudbridge-2.0.0 configparser-3.8.1 cryptography-2.8 cwltool-1.0.20180721142728 debtcollector-1.21.0 decorator-4.4.0 deprecated-1.2.6 deprecation-2.0.7 docutils-0.15.2 dogpile.cache-0.7.1 ecdsa-0.13.2 future-0.17.1 futures-3.3.0 google-api-python-client-1.7.8 google-auth-1.6.3 google-auth-httplib2-0.0.3 gxformat2-0.9.0 h5py-2.9.0 httplib2-0.13.1 idna-2.8 importlib-metadata-0.19 isa-rwval-0.10.7 jmespath-0.9.4 jsonpatch-1.24 jsonschema-3.0.2 keystoneauth1-3.17.0 kombu-4.6.4 lockfile-0.12.2 lxml-4.4.1 mako-1.1.0 markupsafe-1.1.1 mistune-0.8.4 msgpack-0.6.1 mypy-extensions-0.4.1 netifaces-0.10.9 networkx-1.11 nodeenv-1.3.3 numpy-1.16.4 oauth2client-4.1.3 oauthlib-3.1.0 os-client-config-1.32.0 os-service-types-1.7.0 osc-lib-1.13.0 oslo.config-6.11.0 oslo.context-2.22.1 oslo.i18n-3.23.1 oslo.log-3.44.0 oslo.serialization-2.29.1 oslo.utils-3.41.0 packaging-19.1 paramiko-2.6.0 paste-3.1.0 pastedeploy-2.0.1 pastescript-3.1.0 pathlib2-2.3.2 pbr-5.4.2 prov-1.5.1 psutil-5.6.3 pulsar-galaxy-lib-0.13.0 pyasn1-0.4.6 pyasn1-modules-0.2.6 pycparser-2.19 pycryptodome-3.8.2 pyeventsystem-0.1.0 pyjwt-1.7.1 pykwalify-1.7.0 pynacl-1.3.0 pyopenssl-19.0.0 pyparsing-2.4.2 pyperclip-1.7.0 pyrsistent-0.15.4 pysam-0.15.2 python-dateutil-2.8.0 python-genomespaceclient-1.2.0 python-jose-3.0.1 pytz-2019.2 pyuwsgi-2.0.18.post0 pyyaml-5.1.2 rdflib-4.2.2 rdflib-jsonld-0.4.0 requests-2.22.0 requests-oauthlib-1.2.0 requests-toolbelt-0.9.1 rfc3986-1.3.2 rsa-4.0 ruamel.ordereddict-0.4.14 ruamel.yaml-0.15.100 s3transfer-0.2.1 scandir-1.10.0 schema-salad-2.7.20181126142424 shellescape-3.4.1 social-auth-core-3.1.0+gx0 sqlalchemy-1.3.7 sqlalchemy-migrate-0.12.0 sqlalchemy-utils-0.34.2 sqlparse-0.3.0 stevedore-1.30.1 subprocess32-3.5.4 svgwrite-1.3.1 typing-3.7.4 typing-extensions-3.7.4 tzlocal-2.0.0 uritemplate-3.0.0 urllib3-1.25.3 vine-1.3.0 warlock-1.3.3 webob-1.8.5 wrapt-1.11.2 zipp-0.5.2
You are using pip version 9.0.1, however version 19.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
You are using pip version 9.0.1, however version 19.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Collecting psycopg2-binary==2.8.4 (from -r /dev/stdin (line 1))
  Downloading https://files.pythonhosted.org/packages/97/2a/b854019bcb9b925cd10ff245dbc9448a82fe7fdb40127e5cf1733ad0765c/psycopg2_binary-2.8.4-cp27-cp27mu-manylinux1_x86_64.whl (2.9MB)
    100% |████████████████████████████████| 2.9MB 282kB/s
Installing collected packages: psycopg2-binary
  Found existing installation: psycopg2-binary 2.7.4
    Uninstalling psycopg2-binary-2.7.4:
      Successfully uninstalled psycopg2-binary-2.7.4
Successfully installed psycopg2-binary-2.8.4
You are using pip version 9.0.1, however version 19.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
The Galaxy client is out of date and will be built now.
Installing node into /home/proteore/galaxy/.venv with nodeenv.
 * Install prebuilt node (10.15.3) ..... done.
yarn install v1.12.3
[1/4] Resolving packages...
[2/4] Fetching packages...
info fsevents@1.2.4: The platform "linux" is incompatible with this module.
info "fsevents@1.2.4" is an optional dependency and failed compatibility check. Excluding it from installation.
[3/4] Linking dependencies...
warning " > @handsontable/vue@2.0.0" has incorrect peer dependency "handsontable@^4.0.0".
[4/4] Building fresh packages...
warning Your current version of Yarn is out of date. The latest version is "1.21.1", while you're on "1.12.3".
info To upgrade, run the following command:
$ curl --compressed -o- -L https://yarnpkg.com/install.sh | bash
Done in 53.72s.
yarn run v1.12.3
$ NODE_ENV=production gulp && yarn run webpack-production-maps && yarn run save-build-hash
[09:24:38] Using gulpfile /home/proteore/galaxy/client/gulpfile.js
[09:24:38] Starting 'default'...
[09:24:38] Starting 'stageLibs'...
[09:24:38] Starting 'fonts'...
[09:24:38] Finished 'stageLibs' after 12 ms
[09:24:38] Starting 'cleanPlugins'...
[09:24:38] Finished 'cleanPlugins' after 54 ms
[09:24:38] Starting 'buildPlugins'...
[09:24:38] Finished 'buildPlugins' after 2.18 ms
[09:24:38] Starting 'stagePlugins'...
Building  /home/proteore/galaxy/config/plugins/visualizations/annotate_image/
info No lockfile found.
[1/4] Resolving packages...
warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.11: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
warning parcel-bundler > core-js@2.6.11: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
[2/4] Fetching packages...
info fsevents@1.2.11: The platform "linux" is incompatible with this module.
info "fsevents@1.2.11" is an optional dependency and failed compatibility check. Excluding it from installation.
[3/4] Linking dependencies...
[4/4] Building fresh packages...
success Saved lockfile.
$ parcel build src/script.js -d static --no-source-maps
✨  Built in 12.37s.

static/script.js    352.02 KB    11.84s
Building  /home/proteore/galaxy/config/plugins/visualizations/openlayers/
info No lockfile found.
[1/4] Resolving packages...
warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.11: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
warning parcel-bundler > core-js@2.6.11: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
[2/4] Fetching packages...
info fsevents@1.2.11: The platform "linux" is incompatible with this module.
info "fsevents@1.2.11" is an optional dependency and failed compatibility check. Excluding it from installation.
[3/4] Linking dependencies...
[4/4] Building fresh packages...
success Saved lockfile.
$ parcel build src/script.js -d static --no-source-maps
npm ERR! asyncWrite is not a function
npm ERR! pna.nextTick is not a function

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/proteore/.npm/_logs/2019-12-17T08_25_45_092Z-debug.log
⚠️  Could not infer babel version. Defaulting to babel 7. Please add either babel-core or @babel/core as a dependency.
npm ERR! asyncWrite is not a function
npm ERR! pna.nextTick is not a function

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/proteore/.npm/_logs/2019-12-17T08_32_25_962Z-debug.log
🚨  /home/proteore/galaxy/config/plugins/visualizations/openlayers/node_modules/wkt-parser/index.js: Failed to install @babel/core.
    at PromiseQueue.install [as process] (/home/proteore/galaxy/config/plugins/visualizations/openlayers/node_modules/parcel-bundler/src/utils/installPackage.js:46:11)
    at process._tickCallback (internal/process/next_tick.js:68:7)
error Command failed with exit code 1.
info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command.
[09:32:26] Finished 'fonts' after 7.78 min
[09:32:26] Finished 'stagePlugins' after 7.78 min
[09:32:26] Finished 'default' after 7.78 min
$ GXY_BUILD_SOURCEMAPS=1 webpack -p
Browserslist: caniuse-lite is outdated. Please run next command `yarn upgrade caniuse-lite browserslist`
Browserslist: caniuse-lite is outdated. Please run next command `yarn upgrade`
[BABEL] Note: The code generator has deoptimised the styling of /home/proteore/galaxy/client/node_modules/handsontable/dist/handsontable.js as it exceeds the max of 500KB.

Hash: 31c6a63ee63f8fbf6753
Version: webpack 4.29.6
Time: 138606ms
Built at: 12/17/2019 9:34:47 AM
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assets/af7ae505a9eed503f8b8e6982036873e.woff2   75.4 KiB          [emitted]
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 assets/fee66e712a8a08eef5805a46892932ad.woff   95.7 KiB          [emitted]
                                base.chunk.js  100 bytes       0  [emitted]         base
                            base.chunk.js.map   90 bytes       0  [emitted]         base
                                     base.css    436 KiB       0  [emitted]  [big]  base
                                 base.css.map   1.41 MiB          [emitted]
                           generic.bundled.js    969 KiB       4  [emitted]  [big]  generic
                       generic.bundled.js.map   3.17 MiB       4  [emitted]         generic
                                libs.chunk.js   1.84 MiB       1  [emitted]  [big]  libs
                            libs.chunk.js.map   7.04 MiB       1  [emitted]         libs
                             login.bundled.js    994 KiB       5  [emitted]  [big]  login
                         login.bundled.js.map   3.25 MiB       5  [emitted]         login
               ruleCollectionBuilder.chunk.js   68.4 KiB       6  [emitted]         ruleCollectionBuilder
           ruleCollectionBuilder.chunk.js.map    215 KiB       6  [emitted]         ruleCollectionBuilder
       vendors~ruleCollectionBuilder.chunk.js   1.03 MiB       7  [emitted]  [big]  vendors~ruleCollectionBuilder
   vendors~ruleCollectionBuilder.chunk.js.map   3.37 MiB       7  [emitted]         vendors~ruleCollectionBuilder
Entrypoint login [big] = base.css base.chunk.js base.chunk.js.map libs.chunk.js libs.chunk.js.map login.bundled.js login.bundled.js.map
Entrypoint analysis [big] = base.css base.chunk.js base.chunk.js.map libs.chunk.js libs.chunk.js.map analysis.bundled.js analysis.bundled.js.map
Entrypoint admin [big] = base.css base.chunk.js base.chunk.js.map libs.chunk.js libs.chunk.js.map admin.bundled.js admin.bundled.js.map
Entrypoint generic [big] = base.css base.chunk.js base.chunk.js.map libs.chunk.js libs.chunk.js.map generic.bundled.js generic.bundled.js.map
  [8] ./galaxy/scripts/utils/utils.js 10.4 KiB {2} {3} {4} {5} [built]
 [35] ./galaxy/scripts/onload/index.js + 12 modules 15.4 KiB {2} {3} {4} {5} [built]
      | ./galaxy/scripts/onload/index.js 590 bytes [built]
      | ./galaxy/scripts/onload/standardInit.js 3.3 KiB [built]
      | ./galaxy/scripts/onload/defaultAppFactory.js 679 bytes [built]
      | ./galaxy/scripts/onload/globalInits/index.js 1.22 KiB [built]
      | ./galaxy/scripts/utils/installMonitor.js 4.54 KiB [built]
      | ./galaxy/scripts/onload/globalInits/initSentry.js 617 bytes [built]
      | ./galaxy/scripts/onload/globalInits/initTooltips.js 494 bytes [built]
      | ./galaxy/scripts/onload/globalInits/iframesAreTerrible.js 1.11 KiB [built]
      | ./galaxy/scripts/onload/globalInits/onloadWebhooks.js 497 bytes [built]
      | ./galaxy/scripts/onload/globalInits/replace_big_select_inputs.js 1.57 KiB [built]
      | ./galaxy/scripts/onload/globalInits/initTours.js 182 bytes [built]
      | ./galaxy/scripts/onload/globalInits/initModals.js 225 bytes [built]
      | ./galaxy/scripts/utils/mock.js 348 bytes [built]
 [85] (webpack)/buildin/global.js 472 bytes {1} [built]
[177] ./galaxy/scripts/layout/page.js + 19 modules 29.6 KiB {2} {3} {5} [built]
      | ./galaxy/scripts/layout/page.js 6.82 KiB [built]
      | ./galaxy/scripts/layout/data.js 3.17 KiB [built]
      |     + 18 hidden modules
[187] ./galaxy/scripts/polyfills.js 2.98 KiB {2} {3} {4} {5} [built]
[198] ./galaxy/scripts/bundleEntries.js-exposed 75 bytes {2} {3} {4} {5} [built]
[211] ./galaxy/scripts/bundleEntries.js + 75 modules 672 KiB {2} {3} {4} {5} [built]
      | ./galaxy/scripts/bundleEntries.js 3.99 KiB [built]
      | ./galaxy/scripts/layout/modal.js 3.97 KiB [built]
      | ./galaxy/scripts/mvc/workflow/workflow-view.js 32.2 KiB [built]
      | ./galaxy/scripts/viz/circster.js 35.9 KiB [built]
      | ./galaxy/scripts/viz/phyloviz.js 30.5 KiB [built]
      | ./galaxy/scripts/viz/sweepster.js 29.4 KiB [built]
      | ./galaxy/scripts/galaxy.library.js 9.37 KiB [built]
      | ./galaxy/scripts/galaxy.pages.js 886 bytes [built]
      | ./galaxy/scripts/mvc/history/multi-panel.js 41.2 KiB [built]
      | ./galaxy/scripts/mvc/history/history-view-annotated.js 3.85 KiB [built]
      | ./galaxy/scripts/legacy/grid/grid-view.js 20.2 KiB [built]
      | ./galaxy/scripts/reports/run_stats.js 16.2 KiB [built]
      | ./galaxy/scripts/toolshed/toolshed.groups.js 1.14 KiB [built]
      | ./galaxy/scripts/galaxy.interactive_environments.js 9.07 KiB [built]
      | ./galaxy/scripts/mvc/visualization/chart/chart-client.js 1.94 KiB [built]
      |     + 61 hidden modules
[450] multi polyfills bundleEntries entry/login 52 bytes {5} [built]
[843] multi polyfills bundleEntries entry/analysis 52 bytes {3} [built]
[906] multi polyfills bundleEntries entry/admin 52 bytes {2} [built]
[912] multi polyfills bundleEntries entry/generic 52 bytes {4} [built]
[913] ./galaxy/scripts/entry/generic.js 122 bytes {4} [built]
[975] ./galaxy/scripts/entry/analysis/index.js + 145 modules 390 KiB {3} [built]
      | ./galaxy/scripts/entry/analysis/index.js 855 bytes [built]
      | ./galaxy/scripts/entry/analysis/AnalysisRouter.js 14.3 KiB [built]
      | ./galaxy/scripts/entry/panels/tool-panel.js 7.84 KiB [built]
      | ./galaxy/scripts/entry/panels/history-panel.js 3.64 KiB [built]
      | ./galaxy/scripts/mvc/tool/tool-form.js 16.5 KiB [built]
      | ./galaxy/scripts/mvc/user/user-preferences.js 8.71 KiB [built]
      | ./galaxy/scripts/mvc/user/user-custom-builds.js 7.96 KiB [built]
      | ./galaxy/scripts/mvc/entrypoints/view.js 1.04 KiB [built]
      | ./galaxy/scripts/mvc/grid/grid-shared.js 2.2 KiB [built]
      | ./galaxy/scripts/mvc/workflow/workflow.js 13.8 KiB [built]
      | ./galaxy/scripts/mvc/history/history-list.js 4.26 KiB [built]
      | ./galaxy/scripts/mvc/tool/tool-form-composite.js 26.7 KiB [built]
      | ./galaxy/scripts/mvc/dataset/dataset-error.js 9.44 KiB [built]
      | ./galaxy/scripts/mvc/dataset/dataset-edit-attributes.js 6.44 KiB [built]
      | ./galaxy/scripts/mvc/upload/upload-view.js 6.04 KiB [built]
      |     + 131 hidden modules
[976] ./galaxy/scripts/entry/admin/index.js + 132 modules 153 KiB {2} [built]
      | ./galaxy/scripts/entry/admin/index.js 692 bytes [built]
      | ./galaxy/scripts/entry/admin/AdminRouter.js 7.72 KiB [built]
      | ./galaxy/scripts/entry/panels/admin-panel.js 4.89 KiB [built]
      |     + 130 hidden modules
[977] ./galaxy/scripts/entry/login/index.js + 15 modules 14.3 KiB {5} [built]
      | ./galaxy/scripts/entry/login/index.js 1.07 KiB [built]
      |     + 15 hidden modules
    + 1386 hidden modules

WARNING in moment
  Multiple versions of moment found:
    2.20.1 ./~/moment
    2.22.2 ./~/pikaday/~/moment

Check how you can resolve duplicate packages:
https://github.com/darrenscerri/duplicate-package-checker-webpack-plugin#resolving-duplicate-packages-in-your-bundle

WARNING in asset size limit: The following asset(s) exceed the recommended size limit (244 KiB).
This can impact web performance.
Assets:
  assets/912ec66d7572ff821749319396470bde.svg (434 KiB)
  base.css (436 KiB)
  libs.chunk.js (1.84 MiB)
  admin.bundled.js (1.05 MiB)
  analysis.bundled.js (1.18 MiB)
  generic.bundled.js (969 KiB)
  login.bundled.js (994 KiB)
  vendors~ruleCollectionBuilder.chunk.js (1.03 MiB)

WARNING in entrypoint size limit: The following entrypoint(s) combined asset size exceeds the recommended limit (244 KiB). This can impact web performance.
Entrypoints:
  login (3.23 MiB)
      base.css
      base.chunk.js
      libs.chunk.js
      login.bundled.js
  analysis (3.44 MiB)
      base.css
      base.chunk.js
      libs.chunk.js
      analysis.bundled.js
  admin (3.31 MiB)
      base.css
      base.chunk.js
      libs.chunk.js
      admin.bundled.js
  generic (3.21 MiB)
      base.css
      base.chunk.js
      libs.chunk.js
      generic.bundled.js

Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/handsontable/dist/handsontable.full.css?vue&type=style&index=0&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/Citations.vue?vue&type=style&index=0&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/DataDialog/DataDialog.vue?vue&type=style&index=0&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/DisplayStructured.vue?vue&type=style&index=0&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/HistoryView.vue?vue&type=style&index=0&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/JobParameters/JobParameters.vue?vue&type=style&index=0&id=1aba2ddb&scoped=true&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/Markdown/MarkdownEditor.vue?vue&type=style&index=0&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/RuleCollectionBuilder.vue?vue&type=style&index=1&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/SidePanel.vue?vue&type=style&index=0&id=f007ce9e&scoped=true&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/ToolBox.vue?vue&type=style&index=0&id=dec91d48&scoped=true&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/ToolSearch.vue?vue&type=style&index=0&id=c5940e74&scoped=true&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/ToolSection.vue?vue&type=style&index=0&id=49bbe06a&scoped=true&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/Toolshed/ServerSelection.vue?vue&type=style&index=0&id=6a36fdbc&scoped=true&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/WorkflowInvocationState/WorkflowInvocationState.vue?vue&type=style&index=0&id=b86df0d0&scoped=true&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/admin/BaseGrid.vue?vue&type=style&index=0&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/admin/DataManager/DataManagerJob.vue?vue&type=style&index=0&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue?vue&type=style&index=0&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--7-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/admin/Jobs.vue?vue&type=style&index=0&lang=css&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/sass-loader/lib/loader.js??ref--8-2!galaxy/style/scss/base.scss:
    Entrypoint mini-css-extract-plugin = *
     [6] ./node_modules/css-loader/dist/cjs.js??ref--8-1!./node_modules/sass-loader/lib/loader.js??ref--8-2!./galaxy/style/scss/base.scss 1.51 MiB {0} [built]
     [9] ./galaxy/images/select2.png 82 bytes {0} [built]
    [10] ./galaxy/images/select2-spinner.gif 82 bytes {0} [built]
    [11] ./galaxy/images/select2x2.png 82 bytes {0} [built]
    [12] ./galaxy/images/delete.gif 82 bytes {0} [built]
    [13] ./galaxy/images/star.gif 82 bytes {0} [built]
    [14] ./galaxy/images/fugue/magnifier-zoom-out.png 82 bytes {0} [built]
    [15] ./galaxy/images/fugue/magnifier-zoom.png 82 bytes {0} [built]
    [16] ./galaxy/images/visualization/draggable_horizontal.png 82 bytes {0} [built]
    [17] ./galaxy/images/tracks/block.png 82 bytes {0} [built]
    [18] ./galaxy/images/tracks/diag_bg.gif 82 bytes {0} [built]
    [19] ./galaxy/images/fugue/exclamation.png 82 bytes {0} [built]
    [20] ./galaxy/images/fugue/bookmarks-bw.png 82 bytes {0} [built]
    [21] ./galaxy/images/fugue/bookmarks.png 82 bytes {0} [built]
    [22] ./galaxy/images/fugue/layers-stack-bw.png 82 bytes {0} [built]
        + 60 hidden modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/sass-loader/lib/loader.js??ref--8-2!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/Markdown/Markdown.vue?vue&type=style&index=0&lang=scss&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/sass-loader/lib/loader.js??ref--8-2!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/Masthead/index.vue?vue&type=style&index=0&lang=scss&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/sass-loader/lib/loader.js??ref--8-2!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/Nametags/Nametag.vue?vue&type=style&index=0&lang=scss&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/sass-loader/lib/loader.js??ref--8-2!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/Nametags/Nametags.vue?vue&type=style&index=0&lang=scss&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/sass-loader/lib/loader.js??ref--8-2!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/PageEditor/PageEditorHtml.vue?vue&type=style&index=0&lang=scss&:
    Entrypoint mini-css-extract-plugin = *
       2 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/sass-loader/lib/loader.js??ref--8-2!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/Tags/StatelessTags.vue?vue&type=style&index=0&lang=scss&:
    Entrypoint mini-css-extract-plugin = *
       9 modules
Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/sass-loader/lib/loader.js??ref--8-2!node_modules/vue-loader/lib/index.js??vue-loader-options!galaxy/scripts/components/User/CloudAuth/CloudAuth.vue?vue&type=style&index=0&lang=scss&:
    Entrypoint mini-css-extract-plugin = *
       9 modules
$ (git rev-parse HEAD 2>/dev/null || echo '') >../static/client_build_hash.txt
Done in 609.99s.
/home/proteore/galaxy
Unsetting $PYTHONPATH
Activating virtualenv at .venv
Executing: python ./script

tail *log
  File "/home/proteore/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory
    app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs)
  File "/home/proteore/galaxy/lib/galaxy/app.py", line 89, in __init__
    self._configure_models(check_migrate_databases=self.config.check_migrate_databases, check_migrate_tools=check_migrate_tools, config_file=config_file)
  File "/home/proteore/galaxy/lib/galaxy/config/__init__.py", line 1232, in _configure_models
    create_or_verify_database(db_url, config_file, self.config.database_engine_options, app=self, map_install_models=combined_install_database)
  File "/home/proteore/galaxy/lib/galaxy/model/migrate/check.py", line 132, in create_or_verify_database
    raise Exception("%s. %s%s" % (expect_msg, instructions, backup_msg))
Exception: Your database has version '142' but this code expects version '158'. Please backup your database and then migrate the database schema by running 'sh manage_db.sh upgrade'.
Removing PID file galaxy.pid

[proteore@proteore galaxy]$ sh manage_db.sh upgrade
Unsetting $PYTHONPATH
Activating virtualenv at .venv
INFO:migrate.versioning.api:142 -> 143...
142 -> 143...

Migration script to add a new tables for CloudAuthz (tokens required to access cloud-based resources).

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:143 -> 144...
143 -> 144...

Migration script to add the cleanup_event_user_association table.

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:144 -> 145...
144 -> 145...

Migration script for workflow step input table.

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:145 -> 146...
145 -> 146...

Migration script for workflow paths.

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:146 -> 147...
146 -> 147...

Add structured failure reason column to jobs table

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:147 -> 148...
147 -> 148...

Migration script to add dataset source and hash tables.

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:148 -> 149...
148 -> 149...

Migration script to add the dynamic_tool table.

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:149 -> 150...
149 -> 150...

Adds `create_time` columns to cloudauthz table.

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:150 -> 151...
150 -> 151...

Add table for worker processes

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:151 -> 152...
151 -> 152...

Adds `uuid` column to MetadataFile table.

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:152 -> 153...
152 -> 153...

Migration for adding custos_authnz_token table.

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:153 -> 154...
153 -> 154...

Adds created_from_basename to dataset.

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:154 -> 155...
154 -> 155...

Add 'galaxy_version' attribute to Job table.

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:155 -> 156...
155 -> 156...

Migration script to add new tables for InteractiveTools.

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:156 -> 157...
156 -> 157...

Rework dataset validation in database.

INFO:migrate.versioning.api:done
done
INFO:migrate.versioning.api:157 -> 158...
157 -> 158...

Adds reports_config to workflow.

INFO:migrate.versioning.api:done
done

http://www.proteore.org/api/version
{"extra": {}, "version_major": "19.09"}

[vloux]

Proteore tools available in workflows / histories … but not visible in tool panel. Related to https://docs.galaxyproject.org/en/master/releases/19.09_announce.html#tool-configuration-file-handling-changes ?

Stop / rm integrated_tool_panel.xml / Start allow Proteore tools to be visible, but with problem in ordering / section / labels

[vloux]

@davidchristiany found the solution :

• Stop galaxy
• Uncomment tool_config_file parameter in galaxy.ini : tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml
• Start Galaxy

Looks like a known bug , default config file does not seem to be taken into account.