Galaxy update 18.09 - Githubissues

[proteore@proteore galaxy]$ git fetch origin remote: Enumerating objects: 6550, done. remote: Counting objects: 100% (6550/6550), done. remote: Total 12449 (delta 6549), reused 6550 (delta 6549), pack-reused 5899 Receiving objects: 100% (12449/12449), 5.84 MiB | 1.25 MiB/s, done. Resolving deltas: 100% (9723/9723), completed with 1369 local objects. From https://github.com/galaxyproject/galaxy 03c485e..45e475e release_18.05 -> origin/release_18.05 bb95452..03acc98 dev -> origin/dev ea085b0..f2c9baf master -> origin/master 2207e7f..f3ba9e2 release_16.01 -> origin/release_16.01 dad5563..482f1ea release_16.04 -> origin/release_16.04 9a13a4a..8a1616a release_16.07 -> origin/release_16.07 4a28142..809ae58 release_16.10 -> origin/release_16.10 54b9b09..fa7f2a4 release_17.01 -> origin/release_17.01 d80e60c..c4150d2 release_17.05 -> origin/release_17.05 e25b086..40cecf6 release_17.09 -> origin/release_17.09 6d9df51..b5ce8d0 release_18.01 -> origin/release_18.01

[new branch] release_18.09 -> origin/release_18.09
44fc5d6...df07b28 usegalaxy -> origin/usegalaxy (forced update) From https://github.com/galaxyproject/galaxy
[new tag] v18.09 -> v18.09 [proteore@proteore galaxy]$ git checkout release_18.09 Branch release_18.09 set up to track remote branch release_18.09 from origin. Switched to a new branch 'release_18.09' [proteore@proteore galaxy]$ git pull --ff-only origin release_18.09 From https://github.com/galaxyproject/galaxy
branch release_18.09 -> FETCH_HEAD Already up-to-date. [proteore@proteore galaxy]$ [proteore@proteore galaxy]$ [proteore@proteore galaxy]$ [proteore@proteore galaxy]$ sh run.sh 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 18.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Collecting adal==1.1.0 (from -r requirements.txt (line 3)) Downloading https://files.pythonhosted.org/packages/15/2b/8f674c2a20bb2a55f8f1c8fb7a458c9b513409b2cfc42f73e4cbc1ee757e/adal-1.1.0-py2.py3-none-any.whl (51kB) 100% |████████████████████████████████| 61kB 2.7MB/s Collecting amqp==2.3.2 (from -r requirements.txt (line 4)) Downloading https://files.pythonhosted.org/packages/7f/cf/12d4611fc67babd4ae250c9e8249c5650ae1933395488e9e7e3562b4ff24/amqp-2.3.2-py2.py3-none-any.whl (48kB) 100% |████████████████████████████████| 51kB 9.0MB/s Requirement already satisfied: appdirs==1.4.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: asn1crypto==0.24.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) Collecting azure-common==1.1.14 (from -r requirements.txt (line 7)) Downloading https://files.pythonhosted.org/packages/91/66/6636001c0b6be5423f4bbaffe5febbf9eda39bd1941eb39a73504d8f6f71/azure_common-1.1.14-py2.py3-none-any.whl Collecting azure-cosmosdb-nspkg==2.0.2 (from -r requirements.txt (line 8)) Downloading https://files.pythonhosted.org/packages/58/0d/1329b47e5386b0acf4e42ada2284851eff60ef3337a87e5b2dfedabbfcb1/azure_cosmosdb_nspkg-2.0.2-py2.py3-none-any.whl Collecting azure-cosmosdb-table==1.0.4 (from -r requirements.txt (line 9)) Downloading https://files.pythonhosted.org/packages/ba/b7/bf3b5891ee87fea0568b5f9d199249c9c3b3208fa3f77256adcda6618558/azure_cosmosdb_table-1.0.4-py2.py3-none-any.whl (82kB) 100% |████████████████████████████████| 92kB 5.8MB/s Collecting azure-mgmt-compute==4.0.1 (from -r requirements.txt (line 10)) Downloading https://files.pythonhosted.org/packages/30/ef/4063088399938baef2ea1c2d4a7b0bd09f2d14349828f6c35346cf222d90/azure_mgmt_compute-4.0.1-py2.py3-none-any.whl (2.1MB) 100% |████████████████████████████████| 2.1MB 618kB/s Collecting azure-mgmt-devtestlabs==2.2.0 (from -r requirements.txt (line 11)) Downloading https://files.pythonhosted.org/packages/2f/93/a64abaede2fc6a52476af8ceab9cedb368c49e948d9385cbe7cd4ce5ffff/azure_mgmt_devtestlabs-2.2.0-py2.py3-none-any.whl (194kB) 100% |████████████████████████████████| 194kB 6.0MB/s Collecting azure-mgmt-network==2.1.0 (from -r requirements.txt (line 12)) Downloading https://files.pythonhosted.org/packages/2f/1d/1163b84425f5848e758b4d0bd569fd0ec272b5d8d919c494e6633f844e56/azure_mgmt_network-2.1.0-py2.py3-none-any.whl (6.9MB) 100% |████████████████████████████████| 7.0MB 189kB/s Collecting azure-mgmt-nspkg==2.0.0 (from -r requirements.txt (line 13)) Downloading https://files.pythonhosted.org/packages/c9/e3/48b98f929290b0cd0aaa4707ecabb8aaeb267e8ef628af907f1d1c506ec7/azure_mgmt_nspkg-2.0.0-py2.py3-none-any.whl Collecting azure-mgmt-resource==2.0.0 (from -r requirements.txt (line 14)) Downloading https://files.pythonhosted.org/packages/2b/26/c0cb69dfac2e5b7125db034045b8bcf937cf1e8d3df2009a87c33d0959f5/azure_mgmt_resource-2.0.0-py2.py3-none-any.whl (698kB) 100% |████████████████████████████████| 706kB 1.9MB/s Collecting azure-mgmt-storage==2.0.0 (from -r requirements.txt (line 15)) Downloading https://files.pythonhosted.org/packages/67/5b/15e6a8109af53e4c2228142ea816532036700757d035fc1b9cd0f6a63b02/azure_mgmt_storage-2.0.0-py2.py3-none-any.whl (558kB) 100% |████████████████████████████████| 563kB 2.4MB/s Collecting azure-nspkg==2.0.0 (from -r requirements.txt (line 16)) Downloading https://files.pythonhosted.org/packages/cd/a0/76ca6659ae9afd7567fdbb5b9c85e9c9a0b48238cfcacd92525484408f66/azure_nspkg-2.0.0-py2.py3-none-any.whl Collecting azure-storage-blob==1.3.1 (from -r requirements.txt (line 17)) Downloading https://files.pythonhosted.org/packages/dd/26/45de0cb737aeeeb2fa56cf12ab0042ba64dafd24bcc50bf8c8cdf913a1a6/azure_storage_blob-1.3.1-py2.py3-none-any.whl (77kB) 100% |████████████████████████████████| 81kB 9.8MB/s Collecting azure-storage-common==1.3.0 (from -r requirements.txt (line 18)) Downloading https://files.pythonhosted.org/packages/7b/18/03872177864b7ce4aa0302eae5726e8cb66dbb4f30a3408ed27a6639407f/azure_storage_common-1.3.0-py2.py3-none-any.whl (48kB) 100% |████████████████████████████████| 51kB 9.6MB/s Collecting azure-storage-nspkg==3.0.0 (from -r requirements.txt (line 19)) Downloading https://files.pythonhosted.org/packages/b1/e9/0a11f4feefb9c4c2f7e30d4d448e15b32df3adabe370be70aaf4278fbb52/azure_storage_nspkg-3.0.0-py2.py3-none-any.whl Collecting babel==2.6.0 (from -r requirements.txt (line 20)) Downloading https://files.pythonhosted.org/packages/b8/ad/c6f60602d3ee3d92fbed87675b6fb6a6f9a38c223343ababdb44ba201f10/Babel-2.6.0-py2.py3-none-any.whl (8.1MB) 100% |████████████████████████████████| 8.1MB 147kB/s Requirement already satisfied: bagit==1.6.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied: bcrypt==3.1.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Collecting bdbag==1.4.1 (from -r requirements.txt (line 23)) Downloading https://files.pythonhosted.org/packages/53/c1/c28ec526b699813287f94cd4b9971918881505ecb1e7760a3a0fa8d9bf9c/bdbag-1.4.1-py2.py3-none-any.whl (63kB) 100% |████████████████████████████████| 71kB 9.7MB/s Collecting beaker==1.10.0 (from -r requirements.txt (line 24)) Downloading https://files.pythonhosted.org/packages/c2/21/b052b2fbfee3def06670923d5d34b0d353d4c278013e4a714c3fb663f150/Beaker-1.10.0.tar.gz (41kB) 100% |████████████████████████████████| 51kB 10.7MB/s Collecting bioblend==0.11.0 (from -r requirements.txt (line 25)) Downloading https://files.pythonhosted.org/packages/dc/b0/a396ba582286e23b6687a816cf4aaf6044b800e51ab12a8d78228be21ef7/bioblend-0.11.0-py2.py3-none-any.whl (121kB) 100% |████████████████████████████████| 122kB 8.0MB/s Collecting bleach==2.1.4 (from -r requirements.txt (line 26)) Downloading https://files.pythonhosted.org/packages/94/aa/0f7ce53f8688bb9f80c0cffacc3964ddfe08321c509c0bfe5062848951f9/bleach-2.1.4-py2.py3-none-any.whl Collecting boltons==18.0.1 (from -r requirements.txt (line 27)) Downloading https://files.pythonhosted.org/packages/38/b4/94690b531740f8be7dd853bc3a97bc113ff4adc7aa4a9cc802efac86dc78/boltons-18.0.1-py2.py3-none-any.whl (156kB) 100% |████████████████████████████████| 163kB 6.4MB/s Collecting boto3==1.7.84 (from -r requirements.txt (line 28)) Downloading https://files.pythonhosted.org/packages/ac/6e/faf7c6c3ae59641c75023fb5dcc8a02c33752ac8ccadf9931e8d8364f2fe/boto3-1.7.84-py2.py3-none-any.whl (128kB) 100% |████████████████████████████████| 133kB 7.7MB/s Collecting boto==2.49.0 (from -r requirements.txt (line 29)) Downloading https://files.pythonhosted.org/packages/23/10/c0b78c27298029e4454a472a1919bde20cb182dab1662cec7f2ca1dcc523/boto-2.49.0-py2.py3-none-any.whl (1.4MB) 100% |████████████████████████████████| 1.4MB 804kB/s Collecting botocore==1.10.84 (from -r requirements.txt (line 30)) Downloading https://files.pythonhosted.org/packages/01/b7/cb08cd1af2bb0d0dfb393101a93b6ab6fb80f109ab7b37f2f34386c11351/botocore-1.10.84-py2.py3-none-any.whl (4.5MB) 100% |████████████████████████████████| 4.5MB 275kB/s Requirement already satisfied: bunch==1.0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Collecting bx-python==0.8.2 (from -r requirements.txt (line 32)) Downloading https://wheels.galaxyproject.org/packages/bx_python-0.8.2-cp27-cp27mu-manylinux1_x86_64.whl (3.2MB) 100% |████████████████████████████████| 3.2MB 31.2MB/s Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) Collecting certifi==2018.8.24 (from -r requirements.txt (line 34)) Downloading https://files.pythonhosted.org/packages/df/f7/04fee6ac349e915b82171f8e23cee63644d83663b34c539f7a09aed18f9e/certifi-2018.8.24-py2.py3-none-any.whl (147kB) 100% |████████████████████████████████| 153kB 6.9MB/s Requirement already satisfied: cffi==1.11.5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied: chardet==3.0.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied: cheetah3==3.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) Collecting cliff==2.13.0 (from -r requirements.txt (line 38)) Downloading https://files.pythonhosted.org/packages/06/6d/672b0f1eb3c5f455dff6e9558990c3b0777c70452b8020b62c425035795c/cliff-2.13.0-py2.py3-none-any.whl (71kB) 100% |████████████████████████████████| 81kB 9.9MB/s Collecting cloudbridge==1.0.1 (from -r requirements.txt (line 39)) Downloading https://wheels.galaxyproject.org/packages/cloudbridge-1.0.1-py2.py3-none-any.whl (137kB) 100% |████████████████████████████████| 143kB 36.3MB/s Collecting cmd2==0.8.9 (from -r requirements.txt (line 40)) Downloading https://files.pythonhosted.org/packages/e9/40/a71caa2aaff10c73612a7106e2d35f693e85b8cf6e37ab0774274bca3cf9/cmd2-0.8.9-py2.py3-none-any.whl (53kB) 100% |████████████████████████████████| 61kB 8.1MB/s Requirement already satisfied: contextlib2==0.5.5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Collecting cryptography==2.3.1 (from -r requirements.txt (line 42)) Downloading https://files.pythonhosted.org/packages/87/e6/915a482dbfef98bbdce6be1e31825f591fc67038d4ee09864c1d2c3db371/cryptography-2.3.1-cp27-cp27mu-manylinux1_x86_64.whl (2.1MB) 100% |████████████████████████████████| 2.1MB 600kB/s Collecting debtcollector==1.20.0 (from -r requirements.txt (line 43)) Downloading https://files.pythonhosted.org/packages/9b/01/fbbe8ad43ffebe5cd75476448b17825e31c4fc7b9b26519571ec91972c5c/debtcollector-1.20.0-py2.py3-none-any.whl Collecting decorator==4.3.0 (from -r requirements.txt (line 44)) Downloading https://files.pythonhosted.org/packages/bc/bb/a24838832ba35baf52f32ab1a49b906b5f82fb7c76b2f6a7e35e140bac30/decorator-4.3.0-py2.py3-none-any.whl Collecting deprecation==2.0.5 (from -r requirements.txt (line 45)) Downloading https://files.pythonhosted.org/packages/9e/87/2e497672bf5157740f36233a8d2d59266dd083887ccdc5f3b6979e8c3a46/deprecation-2.0.5-py2-none-any.whl Requirement already satisfied: dictobj==0.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) Requirement already satisfied: docutils==0.14 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Collecting dogpile.cache==0.6.7 (from -r requirements.txt (line 49)) Downloading https://files.pythonhosted.org/packages/ee/bd/440da735a11c6087eed7cc8747fc4b995cbac2464168682f8ee1c8e43844/dogpile.cache-0.6.7.tar.gz (323kB) 100% |████████████████████████████████| 327kB 3.6MB/s Requirement already satisfied: enum34==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) Requirement already satisfied: fabric3==1.14.post1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied: funcsigs==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) Requirement already satisfied: functools32==3.2.3.post2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) Requirement already satisfied: future==0.16.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied: futures==3.2.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) Collecting galaxy-sequence-utils==1.1.3 (from -r requirements.txt (line 56)) Downloading https://files.pythonhosted.org/packages/8c/55/94aec5317a2080133c1c668501f9623721bb3bec69e20d64b493d978d752/galaxy_sequence_utils-1.1.3-py2.py3-none-any.whl Collecting h5py==2.8.0 (from -r requirements.txt (line 57)) Downloading https://files.pythonhosted.org/packages/33/0c/1c5dfa85e05052aa5f50969d87c67a2128dc39a6f8ce459a503717e56bd0/h5py-2.8.0-cp27-cp27mu-manylinux1_x86_64.whl (2.7MB) 100% |████████████████████████████████| 2.7MB 458kB/s Requirement already satisfied: html5lib==1.0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) Collecting idna==2.7 (from -r requirements.txt (line 59)) Downloading https://files.pythonhosted.org/packages/4b/2a/0276479a4b3caeb8a8c1af2f8e4355746a97fab05a372e4a2c6a6b876165/idna-2.7-py2.py3-none-any.whl (58kB) 100% |████████████████████████████████| 61kB 8.0MB/s Collecting ipaddress==1.0.22 (from -r requirements.txt (line 60)) Downloading https://files.pythonhosted.org/packages/fc/d0/7fc3a811e011d4b388be48a0e381db8d990042df54aa4ef4599a31d39853/ipaddress-1.0.22-py2.py3-none-any.whl Requirement already satisfied: iso8601==0.1.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 61)) Collecting isodate==0.6.0 (from -r requirements.txt (line 62)) Downloading https://files.pythonhosted.org/packages/9b/9f/b36f7774ff5ea8e428fdcfc4bb332c39ee5b9362ddd3d40d9516a55221b2/isodate-0.6.0-py2.py3-none-any.whl (45kB) 100% |████████████████████████████████| 51kB 8.9MB/s Requirement already satisfied: jmespath==0.9.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) Requirement already satisfied: jsonpatch==1.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) Requirement already satisfied: jsonpointer==2.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) Requirement already satisfied: jsonschema==2.6.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Collecting keystoneauth1==3.10.0 (from -r requirements.txt (line 67)) Downloading https://files.pythonhosted.org/packages/24/23/2b7624d229567cc52cfe6623f9f54a2616ea3ebb0a1e9d42a4358be7266b/keystoneauth1-3.10.0-py2.py3-none-any.whl (289kB) 100% |████████████████████████████████| 296kB 3.9MB/s Collecting kombu==4.2.1 (from -r requirements.txt (line 68)) Downloading https://files.pythonhosted.org/packages/97/61/65838c7da048e56d549e358ac19c0979c892e17dc6186610c49531d35b70/kombu-4.2.1-py2.py3-none-any.whl (177kB) 100% |████████████████████████████████| 184kB 6.1MB/s Requirement already satisfied: mako==1.0.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) Requirement already satisfied: markupsafe==1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) Collecting monotonic==1.5 (from -r requirements.txt (line 72)) Downloading https://files.pythonhosted.org/packages/ac/aa/063eca6a416f397bd99552c534c6d11d57f58f2e94c14780f3bbf818c4cf/monotonic-1.5-py2.py3-none-any.whl Requirement already satisfied: msgpack==0.5.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 73)) Collecting msrest==0.5.5 (from -r requirements.txt (line 74)) Downloading https://files.pythonhosted.org/packages/ad/2a/37b2481fa1a7cd727c07d20cbcb0a3f9bf9dd994930f44dd9770df15c28d/msrest-0.5.5-py2.py3-none-any.whl (47kB) 100% |████████████████████████████████| 51kB 8.2MB/s Collecting msrestazure==0.5.0 (from -r requirements.txt (line 75)) Downloading https://files.pythonhosted.org/packages/a4/48/cfa54772365b4d0b8f3e7af16354db768b0317b3273265b37c14f71b705b/msrestazure-0.5.0-py2.py3-none-any.whl Collecting munch==2.3.2 (from -r requirements.txt (line 76)) Downloading https://files.pythonhosted.org/packages/68/f4/260ec98ea840757a0da09e0ed8135333d59b8dfebe9752a365b04857660a/munch-2.3.2.tar.gz Requirement already satisfied: netaddr==0.7.19 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 77)) Collecting netifaces==0.10.7 (from -r requirements.txt (line 78)) Downloading https://files.pythonhosted.org/packages/70/dd/411bb4cda549136cf9ff5dbd4f33f898fd90b25ac73fd4ea42a3d3e8fd15/netifaces-0.10.7-cp27-cp27mu-manylinux1_x86_64.whl Collecting nodeenv==1.3.2 (from -r requirements.txt (line 79)) Downloading https://files.pythonhosted.org/packages/36/ca/1a635c6cd6049105fadfdc05c8de364f368fcc7aebad3081dd8ccb0c5c7f/nodeenv-1.3.2.tar.gz Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 80)) Collecting numpy==1.15.1 (from -r requirements.txt (line 81)) Downloading https://files.pythonhosted.org/packages/c9/16/1134977cc35d2f72dbe80efa75a8e989ac21289f8e7e2c9005444cd17cd5/numpy-1.15.1-cp27-cp27mu-manylinux1_x86_64.whl (13.8MB) 100% |████████████████████████████████| 13.8MB 85kB/s Collecting oauthlib==2.1.0 (from -r requirements.txt (line 82)) Downloading https://files.pythonhosted.org/packages/e6/d1/ddd9cfea3e736399b97ded5c2dd62d1322adef4a72d816f1ed1049d6a179/oauthlib-2.1.0-py2.py3-none-any.whl (121kB) 100% |████████████████████████████████| 122kB 7.6MB/s Collecting openstacksdk==0.17.0 (from -r requirements.txt (line 83)) Downloading https://files.pythonhosted.org/packages/e3/8c/21f48b5918dce70d8f6c4bc587dcd7a38e5b595032c6af968378ed9057a5/openstacksdk-0.17.0-py2.py3-none-any.whl (1.0MB) 100% |████████████████████████████████| 1.0MB 1.3MB/s Collecting os-client-config==1.31.2 (from -r requirements.txt (line 84)) Downloading https://files.pythonhosted.org/packages/e5/af/2f3bf859a25c98993f85ff1eb17762aa49b2f894630ebe99c389545b0502/os_client_config-1.31.2-py2.py3-none-any.whl Collecting os-service-types==1.3.0 (from -r requirements.txt (line 85)) Downloading https://files.pythonhosted.org/packages/a2/bc/c8bc9cce8ec064558ae9b8ab2dbea9d5bdfbaf5c50f637a19cb120410b10/os-service-types-1.3.0.tar.gz Collecting osc-lib==1.11.1 (from -r requirements.txt (line 86)) Downloading https://files.pythonhosted.org/packages/8d/a8/b63a53baed828a3e46ff2d1ee5cb63f794e9e071f05e99229642edfc46a5/osc-lib-1.11.1.tar.gz (89kB) 100% |████████████████████████████████| 92kB 8.5MB/s Collecting oslo.config==6.4.0 (from -r requirements.txt (line 87)) Downloading https://files.pythonhosted.org/packages/8a/0a/1bcdc4ca2949c8057f9ca86e894b01d6a94de3f33743cec56d04a14d1038/oslo.config-6.4.0-py2.py3-none-any.whl (121kB) 100% |████████████████████████████████| 122kB 7.7MB/s Collecting oslo.context==2.21.0 (from -r requirements.txt (line 88)) Downloading https://files.pythonhosted.org/packages/10/23/dbbb8caf9c4f8b1694dbed31b8e607e4d2f0248681309797e5a398525c6b/oslo.context-2.21.0-py2.py3-none-any.whl Collecting oslo.i18n==3.21.0 (from -r requirements.txt (line 89)) Downloading https://files.pythonhosted.org/packages/37/44/fc8e4466c348e077d116368151a82cd468b8df48f9c0118cef2398bec6f7/oslo.i18n-3.21.0-py2.py3-none-any.whl (40kB) 100% |████████████████████████████████| 40kB 8.9MB/s Collecting oslo.log==3.39.0 (from -r requirements.txt (line 90)) Downloading https://files.pythonhosted.org/packages/e0/55/cc020b81d61b4a12a3d71074776a56955886e42dd2b32f54229adcf0318b/oslo.log-3.39.0-py2.py3-none-any.whl (63kB) 100% |████████████████████████████████| 71kB 10.1MB/s Collecting oslo.serialization==2.27.0 (from -r requirements.txt (line 91)) Downloading https://files.pythonhosted.org/packages/b6/77/5d322fb625f0db2bcca035ff6ff1906c718b31cd371bcf25bc31f7c2075d/oslo.serialization-2.27.0-py2.py3-none-any.whl Collecting oslo.utils==3.37.0 (from -r requirements.txt (line 92)) Downloading https://files.pythonhosted.org/packages/68/8d/7567226f7f2528e481a9beca6afb1859b264fb74a1e562769e8a26ef53f7/oslo.utils-3.37.0-py2.py3-none-any.whl (92kB) 100% |████████████████████████████████| 92kB 8.5MB/s Requirement already satisfied: packaging==17.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 93)) Collecting paramiko==2.4.2 (from -r requirements.txt (line 94)) Downloading https://files.pythonhosted.org/packages/cf/ae/94e70d49044ccc234bfdba20114fa947d7ba6eb68a2e452d89b920e62227/paramiko-2.4.2-py2.py3-none-any.whl (193kB) 100% |████████████████████████████████| 194kB 5.5MB/s Requirement already satisfied: parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 95)) Collecting paste==3.0.4 (from -r requirements.txt (line 96)) Downloading https://files.pythonhosted.org/packages/f8/ef/5882c90866f3cc1b285c75e1a8a8795c2207483c20480afcd9f88b5cfd49/Paste-3.0.4-py2.py3-none-any.whl (592kB) 100% |████████████████████████████████| 593kB 2.1MB/s Requirement already satisfied: pastedeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 97)) Requirement already satisfied: pastescript==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 98)) Collecting pbr==4.2.0 (from -r requirements.txt (line 99)) Downloading https://files.pythonhosted.org/packages/69/1c/98cba002ed975a91a0294863d9c774cc0ebe38e05bbb65e83314550b1677/pbr-4.2.0-py2.py3-none-any.whl (100kB) 100% |████████████████████████████████| 102kB 9.5MB/s Requirement already satisfied: prettytable==0.7.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 100)) Collecting psutil==5.4.7 (from -r requirements.txt (line 101)) Downloading https://wheels.galaxyproject.org/packages/psutil-5.4.7-cp27-cp27mu-manylinux1_x86_64.whl (244kB) 100% |████████████████████████████████| 245kB 1.2MB/s Requirement already satisfied: pulsar-galaxy-lib==0.8.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 102)) Collecting pyasn1==0.4.4 (from -r requirements.txt (line 103)) Downloading https://files.pythonhosted.org/packages/d1/a1/7790cc85db38daa874f6a2e6308131b9953feb1367f2ae2d1123bb93a9f5/pyasn1-0.4.4-py2.py3-none-any.whl (72kB) 100% |████████████████████████████████| 81kB 9.4MB/s Requirement already satisfied: pycparser==2.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 104)) Collecting pycryptodome==3.6.6 (from -r requirements.txt (line 105)) Downloading https://files.pythonhosted.org/packages/40/26/1546cda8b55c08001c9100c031bd1be4c93edb18bee788877f7e23fc1ecd/pycryptodome-3.6.6-cp27-cp27mu-manylinux1_x86_64.whl (7.4MB) 100% |████████████████████████████████| 7.4MB 169kB/s Collecting pycryptodomex==3.6.6 (from -r requirements.txt (line 106)) Downloading https://files.pythonhosted.org/packages/3a/2e/622a647a1204c80f403ef5a49acd8ae1f99a68847c0d9958df337ccf887d/pycryptodomex-3.6.6-cp27-cp27mu-manylinux1_x86_64.whl (7.4MB) 100% |████████████████████████████████| 7.4MB 172kB/s Collecting pyinotify==0.9.6 (from -r requirements.txt (line 107)) Downloading https://files.pythonhosted.org/packages/e3/c0/fd5b18dde17c1249658521f69598f3252f11d9d7a980c5be8619970646e1/pyinotify-0.9.6.tar.gz (60kB) 100% |████████████████████████████████| 61kB 8.7MB/s Requirement already satisfied: pyjwkest==1.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 108)) Collecting pyjwt==1.6.4 (from -r requirements.txt (line 109)) Downloading https://files.pythonhosted.org/packages/93/d1/3378cc8184a6524dc92993090ee8b4c03847c567e298305d6cf86987e005/PyJWT-1.6.4-py2.py3-none-any.whl Requirement already satisfied: pykwalify==1.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 110)) Requirement already satisfied: pynacl==1.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 111)) Collecting pyopenssl==18.0.0 (from -r requirements.txt (line 112)) Downloading https://files.pythonhosted.org/packages/96/af/9d29e6bd40823061aea2e0574ccb2fcf72bfd6130ce53d32773ec375458c/pyOpenSSL-18.0.0-py2.py3-none-any.whl (53kB) 100% |████████████████████████████████| 61kB 8.8MB/s Requirement already satisfied: pyparsing==2.2.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 113)) Collecting pyperclip==1.6.4 (from -r requirements.txt (line 114)) Downloading https://files.pythonhosted.org/packages/2d/9a/23059a00dfd52eb700bd03c4ee3a6954cae60827539c3488026c8742a555/pyperclip-1.6.4.tar.gz Requirement already satisfied: pysam==0.14.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 115)) Collecting pysftp==0.2.9 (from -r requirements.txt (line 116)) Downloading https://files.pythonhosted.org/packages/36/60/45f30390a38b1f92e0a8cf4de178cd7c2bc3f874c85430e40ccf99df8fe7/pysftp-0.2.9.tar.gz Collecting python-cinderclient==4.0.0 (from -r requirements.txt (line 117)) Downloading https://files.pythonhosted.org/packages/ba/d2/50ff8a47087e51464b001cce75822958df344ed355510b7d7406337743c7/python_cinderclient-4.0.0-py2.py3-none-any.whl (319kB) 100% |████████████████████████████████| 327kB 3.6MB/s Collecting python-dateutil==2.7.3 (from -r requirements.txt (line 118)) Downloading https://files.pythonhosted.org/packages/cf/f5/af2b09c957ace60dcfac112b669c45c8c97e32f94aa8b56da4c6d1682825/python_dateutil-2.7.3-py2.py3-none-any.whl (211kB) 100% |████████████████████████████████| 215kB 5.3MB/s Collecting python-genomespaceclient==1.1.0 (from -r requirements.txt (line 119)) Downloading https://files.pythonhosted.org/packages/7e/2c/43e8adae84693b05a08b4b5755bbb8f5d7578f088983d26cfb59dd4c49b2/python_genomespaceclient-1.1.0-py2.py3-none-any.whl Collecting python-glanceclient==2.12.0 (from -r requirements.txt (line 120)) Downloading https://files.pythonhosted.org/packages/b5/3b/6ddd595c3c5bb91ce7184ff6c2fb4cc02222d64c01518c6c33289c39bc4a/python_glanceclient-2.12.0-py2.py3-none-any.whl (184kB) 100% |████████████████████████████████| 184kB 6.2MB/s Collecting python-keystoneclient==3.17.0 (from -r requirements.txt (line 121)) Downloading https://files.pythonhosted.org/packages/b1/bf/c3577dc6f66adc29e573ef31cb348e234059224fae9200b40612b4ab56ce/python_keystoneclient-3.17.0-py2.py3-none-any.whl (382kB) 100% |████████████████████████████████| 389kB 3.2MB/s Collecting python-neutronclient==6.9.0 (from -r requirements.txt (line 122)) Downloading https://files.pythonhosted.org/packages/04/7e/81bdd73893d3709c369b30892f6fa81f04ac8f552dd784b8884713ef407b/python_neutronclient-6.9.0-py2.py3-none-any.whl (418kB) 100% |████████████████████████████████| 419kB 3.0MB/s Collecting python-novaclient==11.0.0 (from -r requirements.txt (line 123)) Downloading https://files.pythonhosted.org/packages/a6/f3/d0aaae716fc5f058330da1e910c779fdae41d0cb8b22581acb209e109256/python_novaclient-11.0.0-py2.py3-none-any.whl (311kB) 100% |████████████████████████████████| 317kB 3.9MB/s Requirement already satisfied: python-openid==2.2.5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 124)) Collecting python-swiftclient==3.6.0 (from -r requirements.txt (line 125)) Downloading https://files.pythonhosted.org/packages/38/82/c0d85ebde493909a53b5984d0567702e53a4b0a5140285f4289510274176/python_swiftclient-3.6.0-py2.py3-none-any.whl (77kB) 100% |████████████████████████████████| 81kB 8.8MB/s Collecting pytz==2018.5 (from -r requirements.txt (line 126)) Downloading https://files.pythonhosted.org/packages/30/4e/27c34b62430286c6d59177a0842ed90dc789ce5d1ed740887653b898779a/pytz-2018.5-py2.py3-none-any.whl (510kB) 100% |████████████████████████████████| 512kB 2.6MB/s Collecting pyyaml==3.13 (from -r requirements.txt (line 127)) Downloading https://wheels.galaxyproject.org/packages/PyYAML-3.13-cp27-cp27mu-manylinux1_x86_64.whl (441kB) 100% |████████████████████████████████| 450kB 43.6MB/s Requirement already satisfied: repoze.lru==0.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 128)) Collecting requests-oauthlib==1.0.0 (from -r requirements.txt (line 129)) Downloading https://files.pythonhosted.org/packages/94/e7/c250d122992e1561690d9c0f7856dadb79d61fd4bdd0e598087dce607f6c/requests_oauthlib-1.0.0-py2.py3-none-any.whl Requirement already satisfied: requests-toolbelt==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 130)) Collecting requests==2.19.1 (from -r requirements.txt (line 131)) Downloading https://files.pythonhosted.org/packages/65/47/7e02164a2a3db50ed6d8a6ab1d6d60b69c4c3fdf57a284257925dfc12bda/requests-2.19.1-py2.py3-none-any.whl (91kB) 100% |████████████████████████████████| 92kB 9.3MB/s Requirement already satisfied: requestsexceptions==1.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 132)) Requirement already satisfied: rfc3986==1.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 133)) Requirement already satisfied: routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 134)) Requirement already satisfied: s3transfer==0.1.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 135)) Collecting simplejson==3.16.0 (from -r requirements.txt (line 136)) Downloading https://files.pythonhosted.org/packages/e3/24/c35fb1c1c315fc0fffe61ea00d3f88e85469004713dab488dee4f35b0aff/simplejson-3.16.0.tar.gz (81kB) 100% |████████████████████████████████| 81kB 8.9MB/s Requirement already satisfied: six==1.11.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 137)) Requirement already satisfied: social-auth-core==1.5.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 138)) Requirement already satisfied: sqlalchemy-migrate==0.11.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 139)) Collecting sqlalchemy-utils==0.33.3 (from -r requirements.txt (line 140)) Downloading https://files.pythonhosted.org/packages/28/17/fedf5a8b2492a7d12986273b7d661419970b1866f3be3f897114aa3c7195/SQLAlchemy-Utils-0.33.3.tar.gz (126kB) 100% |████████████████████████████████| 133kB 6.8MB/s Collecting sqlalchemy==1.2.11 (from -r requirements.txt (line 141)) Downloading https://files.pythonhosted.org/packages/aa/cc/348eec885d81f7260b07d961b3ececfc0aa82f7d4a8f45ff997e0d3f44ba/SQLAlchemy-1.2.11.tar.gz (5.6MB) 100% |████████████████████████████████| 5.6MB 222kB/s Requirement already satisfied: sqlparse==0.2.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 142)) Collecting stevedore==1.29.0 (from -r requirements.txt (line 143)) Downloading https://files.pythonhosted.org/packages/a1/d9/93a975469c53a9ee85de9ec0deb12345aa777748b4c263860668592344fe/stevedore-1.29.0-py2.py3-none-any.whl Collecting subprocess32==3.5.2 (from -r requirements.txt (line 144)) Downloading https://wheels.galaxyproject.org/packages/subprocess32-3.5.2-cp27-cp27mu-manylinux1_x86_64.whl (43kB) 100% |████████████████████████████████| 51kB 617kB/s Requirement already satisfied: svgwrite==1.1.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 145)) Requirement already satisfied: tempita==0.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 146)) Collecting tenacity==4.12.0 (from -r requirements.txt (line 147)) Downloading https://files.pythonhosted.org/packages/75/1b/46a6a7b7c2b16811665ea09b7e63e7e6b7f9b5dedf2d0ba67e029668403c/tenacity-4.12.0-py2.py3-none-any.whl Collecting typing==3.6.6 (from -r requirements.txt (line 148)) Downloading https://files.pythonhosted.org/packages/cc/3e/29f92b7aeda5b078c86d14f550bf85cff809042e3429ace7af6193c3bc9f/typing-3.6.6-py2-none-any.whl Requirement already satisfied: tzlocal==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 149)) Requirement already satisfied: unicodecsv==0.14.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 150)) Collecting urllib3==1.23 (from -r requirements.txt (line 151)) Downloading https://files.pythonhosted.org/packages/bd/c9/6fdd990019071a4a32a5e7cb78a1d92c53851ef4f56f62a3486e6a7d8ffb/urllib3-1.23-py2.py3-none-any.whl (133kB) 100% |████████████████████████████████| 143kB 7.4MB/s Collecting uwsgi==2.0.17.1 (from -r requirements.txt (line 152)) Downloading https://wheels.galaxyproject.org/packages/uWSGI-2.0.17.1-cp27-cp27mu-manylinux1_x86_64.whl (649kB) 100% |████████████████████████████████| 655kB 38.9MB/s Requirement already satisfied: vine==1.1.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 153)) Collecting warlock==1.3.0 (from -r requirements.txt (line 154)) Downloading https://files.pythonhosted.org/packages/2d/40/9f01a5e1574dab946598793351d59c86f58209d182d229aaa545abb98894/warlock-1.3.0.tar.gz Requirement already satisfied: wcwidth==0.1.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 155)) Requirement already satisfied: webencodings==0.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 156)) Collecting webob==1.8.2 (from -r requirements.txt (line 157)) Downloading https://files.pythonhosted.org/packages/d2/df/9b3b374ea2a82b875a90d1fdcf2c4a652d48f0d1e7c2d1034d636551d4d2/WebOb-1.8.2-py2.py3-none-any.whl (115kB) 100% |████████████████████████████████| 122kB 7.9MB/s Requirement already satisfied: whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 158)) Requirement already satisfied: wrapt==1.10.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 159)) Building wheels for collected packages: beaker, dogpile.cache, munch, nodeenv, os-service-types, osc-lib, pyinotify, pyperclip, pysftp, simplejson, sqlalchemy-utils, sqlalchemy, warlock Running setup.py bdist_wheel for beaker ... done Stored in directory: /home//proteore/.cache/pip/wheels/84/60/af/4908e410dd9d066ab1cceebcb9461ef691106b7beeff97abe9 Running setup.py bdist_wheel for dogpile.cache ... done Stored in directory: /home//proteore/.cache/pip/wheels/db/67/7d/4e809c5161474aea07951b22d3cfbca90ca477237064d4cc2a Running setup.py bdist_wheel for munch ... done Stored in directory: /home//proteore/.cache/pip/wheels/db/bf/bc/06a3e1bfe0ab27d2e720ceb3cff3159398d92644c0cec2c125 Running setup.py bdist_wheel for nodeenv ... done Stored in directory: /home//proteore/.cache/pip/wheels/f3/91/e8/836a7b82342fbb2925f1022678a857970820595faae108182f Running setup.py bdist_wheel for os-service-types ... done Stored in directory: /home//proteore/.cache/pip/wheels/58/05/2e/6efc77b404e32b9608f2e4cd63d35d43d324e83bd332935496 Running setup.py bdist_wheel for osc-lib ... done Stored in directory: /home//proteore/.cache/pip/wheels/bd/f2/54/855abb6408f8b051a69405ef22159b477325aabd945fd8b6df Running setup.py bdist_wheel for pyinotify ... done Stored in directory: /home//proteore/.cache/pip/wheels/e0/62/fe/a68c26dff6ed01a86d8a5aa8e01d7687a5a29c7d765af383cb Running setup.py bdist_wheel for pyperclip ... done Stored in directory: /home//proteore/.cache/pip/wheels/73/8c/77/a973e2fbf4808af077582b1740b4cbf9e100262da0166e90d8 Running setup.py bdist_wheel for pysftp ... done Stored in directory: /home//proteore/.cache/pip/wheels/d4/53/02/181ea4f6c795b40c4f1d2022ba2ed15cf811d22975eb2e5968 Running setup.py bdist_wheel for simplejson ... done Stored in directory: /home//proteore/.cache/pip/wheels/5d/1a/1e/0350bb3df3e74215cd91325344cc86c2c691f5306eb4d22c77 Running setup.py bdist_wheel for sqlalchemy-utils ... done Stored in directory: /home//proteore/.cache/pip/wheels/eb/2b/fa/a7b34d1ebfc759948b471948616b8bb159d62ea0447cc2933c Running setup.py bdist_wheel for sqlalchemy ... done Stored in directory: /home//proteore/.cache/pip/wheels/2b/e7/bc/03c832ebc5c8f34a4ddab35f1bc812feb1e606d1147d6af2c9 Running setup.py bdist_wheel for warlock ... done Stored in directory: /home//proteore/.cache/pip/wheels/f8/24/32/3984959f3aa50c103729a8a5eab58331c65a3506d84012a271 Successfully built beaker dogpile.cache munch nodeenv os-service-types osc-lib pyinotify pyperclip pysftp simplejson sqlalchemy-utils sqlalchemy warlock Installing collected packages: pyjwt, idna, ipaddress, cryptography, certifi, urllib3, requests, python-dateutil, adal, amqp, azure-nspkg, azure-common, azure-cosmosdb-nspkg, azure-storage-nspkg, azure-storage-common, azure-cosmosdb-table, azure-mgmt-nspkg, isodate, oauthlib, requests-oauthlib, typing, msrest, msrestazure, azure-mgmt-compute, azure-mgmt-devtestlabs, azure-mgmt-network, azure-mgmt-resource, azure-mgmt-storage, azure-storage-blob, pytz, babel, bdbag, beaker, boto, pyyaml, bioblend, bleach, boltons, botocore, boto3, numpy, bx-python, pyperclip, subprocess32, cmd2, pbr, stevedore, cliff, monotonic, tenacity, debtcollector, oslo.i18n, netifaces, oslo.utils, oslo.serialization, os-service-types, keystoneauth1, oslo.config, python-keystoneclient, pyasn1, paramiko, pysftp, warlock, pyopenssl, python-glanceclient, simplejson, python-cinderclient, python-swiftclient, munch, dogpile.cache, decorator, deprecation, openstacksdk, python-novaclient, os-client-config, pyinotify, oslo.context, oslo.log, osc-lib, python-neutronclient, cloudbridge, galaxy-sequence-utils, h5py, kombu, nodeenv, paste, psutil, pycryptodome, pycryptodomex, python-genomespaceclient, sqlalchemy, sqlalchemy-utils, uwsgi, webob Found existing installation: PyJWT 1.6.1 Uninstalling PyJWT-1.6.1: Successfully uninstalled PyJWT-1.6.1 Found existing installation: idna 2.6 Uninstalling idna-2.6: Successfully uninstalled idna-2.6 Found existing installation: ipaddress 1.0.19 Uninstalling ipaddress-1.0.19: Successfully uninstalled ipaddress-1.0.19 Found existing installation: cryptography 2.2.2 Uninstalling cryptography-2.2.2: Successfully uninstalled cryptography-2.2.2 Found existing installation: certifi 2018.1.18 Uninstalling certifi-2018.1.18: Successfully uninstalled certifi-2018.1.18 Found existing installation: urllib3 1.22 Uninstalling urllib3-1.22: Successfully uninstalled urllib3-1.22 Found existing installation: requests 2.18.4 Uninstalling requests-2.18.4: Successfully uninstalled requests-2.18.4 Found existing installation: python-dateutil 2.7.2 Uninstalling python-dateutil-2.7.2: Successfully uninstalled python-dateutil-2.7.2 Found existing installation: amqp 2.2.2 Uninstalling amqp-2.2.2: Successfully uninstalled amqp-2.2.2 Found existing installation: oauthlib 2.0.7 Uninstalling oauthlib-2.0.7: Successfully uninstalled oauthlib-2.0.7 Found existing installation: requests-oauthlib 0.8.0 Uninstalling requests-oauthlib-0.8.0: Successfully uninstalled requests-oauthlib-0.8.0 Found existing installation: pytz 2018.4 Uninstalling pytz-2018.4: Successfully uninstalled pytz-2018.4 Found existing installation: Babel 2.5.3 Uninstalling Babel-2.5.3: Successfully uninstalled Babel-2.5.3 Found existing installation: bdbag 1.2.4 Uninstalling bdbag-1.2.4: Successfully uninstalled bdbag-1.2.4 Found existing installation: Beaker 1.9.1 Uninstalling Beaker-1.9.1: Successfully uninstalled Beaker-1.9.1 Found existing installation: boto 2.46.1 Uninstalling boto-2.46.1: Successfully uninstalled boto-2.46.1 Found existing installation: PyYAML 3.12 Uninstalling PyYAML-3.12: Successfully uninstalled PyYAML-3.12 Found existing installation: bioblend 0.10.0 Uninstalling bioblend-0.10.0: Successfully uninstalled bioblend-0.10.0 Found existing installation: bleach 2.1.3 Uninstalling bleach-2.1.3: Successfully uninstalled bleach-2.1.3 Found existing installation: boltons 18.0.0 Uninstalling boltons-18.0.0: Successfully uninstalled boltons-18.0.0 Found existing installation: botocore 1.8.44 Uninstalling botocore-1.8.44: Successfully uninstalled botocore-1.8.44 Found existing installation: boto3 1.5.30 Uninstalling boto3-1.5.30: Successfully uninstalled boto3-1.5.30 Found existing installation: numpy 1.14.2 Uninstalling numpy-1.14.2: Successfully uninstalled numpy-1.14.2 Found existing installation: bx-python 0.8.1 Uninstalling bx-python-0.8.1: Successfully uninstalled bx-python-0.8.1 Found existing installation: pyperclip 1.6.0 Uninstalling pyperclip-1.6.0: Successfully uninstalled pyperclip-1.6.0 Found existing installation: subprocess32 3.5.0 Uninstalling subprocess32-3.5.0: Successfully uninstalled subprocess32-3.5.0 Found existing installation: cmd2 0.8.4 Uninstalling cmd2-0.8.4: Successfully uninstalled cmd2-0.8.4 Found existing installation: pbr 4.0.2 Uninstalling pbr-4.0.2: Successfully uninstalled pbr-4.0.2 Found existing installation: stevedore 1.28.0 Uninstalling stevedore-1.28.0: Successfully uninstalled stevedore-1.28.0 Found existing installation: cliff 2.11.0 Uninstalling cliff-2.11.0: Successfully uninstalled cliff-2.11.0 Found existing installation: monotonic 1.4 Uninstalling monotonic-1.4: Successfully uninstalled monotonic-1.4 Found existing installation: debtcollector 1.19.0 Uninstalling debtcollector-1.19.0: Successfully uninstalled debtcollector-1.19.0 Found existing installation: oslo.i18n 3.20.0 Uninstalling oslo.i18n-3.20.0: Successfully uninstalled oslo.i18n-3.20.0 Found existing installation: netifaces 0.10.6 Uninstalling netifaces-0.10.6: Successfully uninstalled netifaces-0.10.6 Found existing installation: oslo.utils 3.36.0 Uninstalling oslo.utils-3.36.0: Successfully uninstalled oslo.utils-3.36.0 Found existing installation: oslo.serialization 2.25.0 Uninstalling oslo.serialization-2.25.0: Successfully uninstalled oslo.serialization-2.25.0 Found existing installation: os-service-types 1.2.0 Uninstalling os-service-types-1.2.0: Successfully uninstalled os-service-types-1.2.0 Found existing installation: keystoneauth1 3.4.0 Uninstalling keystoneauth1-3.4.0: Successfully uninstalled keystoneauth1-3.4.0 Found existing installation: oslo.config 6.0.2 Uninstalling oslo.config-6.0.2: Successfully uninstalled oslo.config-6.0.2 Found existing installation: python-keystoneclient 3.10.0 Uninstalling python-keystoneclient-3.10.0: Successfully uninstalled python-keystoneclient-3.10.0 Found existing installation: pyasn1 0.4.2 Uninstalling pyasn1-0.4.2: Successfully uninstalled pyasn1-0.4.2 Found existing installation: paramiko 2.4.1 Uninstalling paramiko-2.4.1: Successfully uninstalled paramiko-2.4.1 Found existing installation: warlock 1.2.0 Uninstalling warlock-1.2.0: Successfully uninstalled warlock-1.2.0 Found existing installation: python-glanceclient 2.6.0 Uninstalling python-glanceclient-2.6.0: Successfully uninstalled python-glanceclient-2.6.0 Found existing installation: simplejson 3.13.2 Uninstalling simplejson-3.13.2: Successfully uninstalled simplejson-3.13.2 Found existing installation: python-cinderclient 2.0.1 Uninstalling python-cinderclient-2.0.1: Successfully uninstalled python-cinderclient-2.0.1 Found existing installation: python-swiftclient 3.3.0 Uninstalling python-swiftclient-3.3.0: Successfully uninstalled python-swiftclient-3.3.0 Found existing installation: munch 2.3.1 Uninstalling munch-2.3.1: Successfully uninstalled munch-2.3.1 Found existing installation: dogpile.cache 0.6.5 Uninstalling dogpile.cache-0.6.5: Successfully uninstalled dogpile.cache-0.6.5 Found existing installation: decorator 4.2.1 Uninstalling decorator-4.2.1: Successfully uninstalled decorator-4.2.1 Found existing installation: deprecation 2.0.1 Uninstalling deprecation-2.0.1: Successfully uninstalled deprecation-2.0.1 Found existing installation: openstacksdk 0.12.0 Uninstalling openstacksdk-0.12.0: Successfully uninstalled openstacksdk-0.12.0 Found existing installation: python-novaclient 7.0.0 Uninstalling python-novaclient-7.0.0: Successfully uninstalled python-novaclient-7.0.0 Found existing installation: os-client-config 1.29.0 Uninstalling os-client-config-1.29.0: Successfully uninstalled os-client-config-1.29.0 Found existing installation: osc-lib 1.10.0 Uninstalling osc-lib-1.10.0: Successfully uninstalled osc-lib-1.10.0 Found existing installation: python-neutronclient 6.1.0 Uninstalling python-neutronclient-6.1.0: Successfully uninstalled python-neutronclient-6.1.0 Found existing installation: cloudbridge 0.3.3 Uninstalling cloudbridge-0.3.3: Successfully uninstalled cloudbridge-0.3.3 Found existing installation: galaxy-sequence-utils 1.1.2 Uninstalling galaxy-sequence-utils-1.1.2: Successfully uninstalled galaxy-sequence-utils-1.1.2 Found existing installation: h5py 2.6.0 Uninstalling h5py-2.6.0: Successfully uninstalled h5py-2.6.0 Found existing installation: kombu 4.1.0 Uninstalling kombu-4.1.0: Successfully uninstalled kombu-4.1.0 Found existing installation: Paste 2.0.3 Uninstalling Paste-2.0.3: Successfully uninstalled Paste-2.0.3 Found existing installation: psutil 5.4.3 Uninstalling psutil-5.4.3: Successfully uninstalled psutil-5.4.3 Found existing installation: pycryptodomex 3.6.0 Uninstalling pycryptodomex-3.6.0: Successfully uninstalled pycryptodomex-3.6.0 Found existing installation: python-genomespaceclient 0.2 Uninstalling python-genomespaceclient-0.2: Successfully uninstalled python-genomespaceclient-0.2 Found existing installation: SQLAlchemy 1.2.6 Uninstalling SQLAlchemy-1.2.6: Successfully uninstalled SQLAlchemy-1.2.6 Found existing installation: SQLAlchemy-Utils 0.33.2 Uninstalling SQLAlchemy-Utils-0.33.2: Successfully uninstalled SQLAlchemy-Utils-0.33.2 Found existing installation: uWSGI 2.0.17 Uninstalling uWSGI-2.0.17: Successfully uninstalled uWSGI-2.0.17 Found existing installation: WebOb 1.4.2 Uninstalling WebOb-1.4.2: Successfully uninstalled WebOb-1.4.2 Successfully installed adal-1.1.0 amqp-2.3.2 azure-common-1.1.14 azure-cosmosdb-nspkg-2.0.2 azure-cosmosdb-table-1.0.4 azure-mgmt-compute-4.0.1 azure-mgmt-devtestlabs-2.2.0 azure-mgmt-network-2.1.0 azure-mgmt-nspkg-2.0.0 azure-mgmt-resource-2.0.0 azure-mgmt-storage-2.0.0 azure-nspkg-2.0.0 azure-storage-blob-1.3.1 azure-storage-common-1.3.0 azure-storage-nspkg-3.0.0 babel-2.6.0 bdbag-1.4.1 beaker-1.10.0 bioblend-0.11.0 bleach-2.1.4 boltons-18.0.1 boto-2.49.0 boto3-1.7.84 botocore-1.10.84 bx-python-0.8.2 certifi-2018.8.24 cliff-2.13.0 cloudbridge-1.0.1 cmd2-0.8.9 cryptography-2.3.1 debtcollector-1.20.0 decorator-4.3.0 deprecation-2.0.5 dogpile.cache-0.6.7 galaxy-sequence-utils-1.1.3 h5py-2.8.0 idna-2.7 ipaddress-1.0.22 isodate-0.6.0 keystoneauth1-3.10.0 kombu-4.2.1 monotonic-1.5 msrest-0.5.5 msrestazure-0.5.0 munch-2.3.2 netifaces-0.10.7 nodeenv-1.3.2 numpy-1.15.1 oauthlib-2.1.0 openstacksdk-0.17.0 os-client-config-1.31.2 os-service-types-1.3.0 osc-lib-1.11.1 oslo.config-6.4.0 oslo.context-2.21.0 oslo.i18n-3.21.0 oslo.log-3.39.0 oslo.serialization-2.27.0 oslo.utils-3.37.0 paramiko-2.4.2 paste-3.0.4 pbr-4.2.0 psutil-5.4.7 pyasn1-0.4.4 pycryptodome-3.6.6 pycryptodomex-3.6.6 pyinotify-0.9.6 pyjwt-1.6.4 pyopenssl-18.0.0 pyperclip-1.6.4 pysftp-0.2.9 python-cinderclient-4.0.0 python-dateutil-2.7.3 python-genomespaceclient-1.1.0 python-glanceclient-2.12.0 python-keystoneclient-3.17.0 python-neutronclient-6.9.0 python-novaclient-11.0.0 python-swiftclient-3.6.0 pytz-2018.5 pyyaml-3.13 requests-2.19.1 requests-oauthlib-1.0.0 simplejson-3.16.0 sqlalchemy-1.2.11 sqlalchemy-utils-0.33.3 stevedore-1.29.0 subprocess32-3.5.2 tenacity-4.12.0 typing-3.6.6 urllib3-1.23 uwsgi-2.0.17.1 warlock-1.3.0 webob-1.8.2 You are using pip version 9.0.1, however version 18.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. You are using pip version 9.0.1, however version 18.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Requirement already satisfied: psycopg2-binary==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r /dev/stdin (line 1)) You are using pip version 9.0.1, however version 18.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. The Galaxy client has not yet been built and will be built now. Installing node into /home/proteore/galaxy/.venv with nodeenv.
Install prebuilt node (9.11.1) ..... done.
Appending data to /home/proteore/galaxy/.venv/bin/activate
Appending data to /home/proteore/galaxy/.venv/bin/activate.fish Installing yarn into /home/proteore/galaxy/.venv with npm. /home/proteore/galaxy/.venv/bin/yarn -> /home/proteore/galaxy/.venv/lib/node_modules/yarn/bin/yarn.js /home/proteore/galaxy/.venv/bin/yarnpkg -> /home/proteore/galaxy/.venv/lib/node_modules/yarn/bin/yarn.js
- yarn@1.12.3 added 1 package in 0.524s cd client && yarn install --network-timeout 120000 --check-files yarn install v1.12.3 [1/4] Resolving packages... [2/4] Fetching packages... info fsevents@1.1.2: The platform "linux" is incompatible with this module. info "fsevents@1.1.2" is an optional dependency and failed compatibility check. Excluding it from installation. 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-beta1" has incorrect peer dependency "handsontable@^0.38.1". [4/4] Building fresh packages... Done in 52.62s. cd client && yarn run build-production-maps yarn run v1.12.3 $ NODE_ENV=production gulp staging && concurrently "yarn run style" "yarn run webpack-production-maps" "yarn run gulp clean && yarn run gulp-production-maps" && yarn run save-build-hash [17:27:23] Using gulpfile /home/proteore/galaxy/client/gulpfile.js [17:27:23] Starting 'stage-libs'... [17:27:23] Starting 'fonts'... [17:27:23] Finished 'fonts' after 72 ms $ gulp clean $ grunt && gulp style $ GXY_BUILD_SOURCEMAPS=1 webpack -p [0] Running "sprite:history-buttons" (sprite) task [2] [17:27:24] Using gulpfile /home/proteore/galaxy/client/gulpfile.js [2] [17:27:24] Starting 'clean'... [2] [17:27:24] Finished 'clean' after 22 ms $ GXY_BUILD_SOURCEMAPS=1 NODE_ENV=production gulp [0] Files "./galaxy/style/scss/sprite-history-buttons.scss", "../static/style/blue/sprite-history-buttons.png" created. [0] [0] Running "sprite:history-states" (sprite) task [0] Files "./galaxy/style/scss/sprite-history-states.scss", "../static/style/blue/sprite-history-states.png" created. [0] [0] Running "sprite:fugue" (sprite) task [0] Files "./galaxy/style/scss/sprite-fugue.scss", "../static/style/blue/sprite-fugue.png" created. [0] [0] Done, without errors. [2] [17:27:26] Using gulpfile /home/proteore/galaxy/client/gulpfile.js [2] [17:27:26] Starting 'scripts'... [2] [17:27:26] Starting 'libs'... [0] [17:27:26] Using gulpfile /home/proteore/galaxy/client/gulpfile.js [0] [17:27:26] Starting 'style'... [0] [17:27:28] Finished 'style' after 1.89 s [0] yarn run style exited with code 0 [2] [17:27:43] Finished 'libs' after 17 s [1] [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". [2] [17:28:10] Finished 'scripts' after 44 s [2] [17:28:10] Starting 'default'... [2] [17:28:10] Finished 'default' after 39 μs [2] yarn run gulp clean && yarn run gulp-production-maps exited with code 0 [1] Hash: cd688a07ed9b57a02780 [1] Version: webpack 3.10.0 [1] Time: 99696ms [1] Asset Size Chunks Chunk Names [1] analysis.bundled.js.map 4.32 MB 0 [emitted] analysis [1] analysis.bundled.js 691 kB 0 [emitted] [big] analysis [1] admin.bundled.js 379 kB 2 [emitted] [big] admin [1] login.bundled.js 358 kB 3 [emitted] [big] login [1] chart.bundled.js 180 kB 4 [emitted] chart [1] libs.bundled.js 2 MB 5 [emitted] [big] libs [1] extended.bundled.js 1.35 MB 1 [emitted] [big] extended [1] extended.bundled.js.map 8.17 MB 1 [emitted] extended [1] admin.bundled.js.map 2.55 MB 2 [emitted] admin [1] login.bundled.js.map 2.41 MB 3 [emitted] login [1] chart.bundled.js.map 1.13 MB 4 [emitted] chart [1] libs.bundled.js.map 12.7 MB 5 [emitted] libs [1] [11] ./galaxy/scripts/mvc/ui/ui-misc.js 12 kB {5} [built] [1] [15] ./galaxy/scripts/mvc/dataset/data.js 18.8 kB {0} {1} {2} {3} [built] [1] [19] ./galaxy/scripts/mvc/ui/ui-modal.js 5.67 kB {5} [built] [1] [25] ./galaxy/scripts/libs/toastr.js 7.74 kB {5} [built] [1] [28] ./galaxy/scripts/mvc/grid/grid-view.js 24 kB {0} {1} {2} {3} [built] [1] [452] multi polyfills jquery libs/jquery/jquery.migrate libs/jquery/jquery.autocomplete libs/jquery/jquery.event.hover libs/jquery/jquery.event.drag libs/jquery/jquery.mousewheel libs/jquery/jquery.form libs/jquery/jquery.rating libs/jquery/select2 libs/jquery.sparklines libs/jquery/jquery-ui libs/jquery/jstorage libs/jquery/jquery.complexify libs/farbtastic bootstrap bootstrap-tour vue libs/underscore libs/backbone libs/toastr ui/autocom_tagging layout/modal layout/panel onload 316 bytes {5} [built] [1] [463] ./galaxy/scripts/apps/login.js 1.89 kB {3} [built] [1] [682] ./galaxy/scripts/apps/analysis.js 18.5 kB {0} [built] [1] [730] ./galaxy/scripts/apps/admin.js 8.46 kB {2} [built] [1] [748] ./galaxy/scripts/apps/chart.js 1.43 kB {4} [built] [1] [762] ./galaxy/scripts/apps/extended.js 6.33 kB {1} [built] [1] [793] ./galaxy/scripts/galaxy.pages.js 24.4 kB {1} [built] [1] [795] ./galaxy/scripts/mvc/history/multi-panel.js 47.1 kB {1} [built] [1] [796] ./galaxy/scripts/mvc/history/history-view-annotated.js 4.76 kB {1} [built] [1] [797] ./galaxy/scripts/legacy/grid/grid-view.js 24.1 kB {1} [built] [1] + 790 hidden modules [1] yarn run webpack-production-maps exited with code 0 $ (git rev-parse HEAD 2>/dev/null || echo '') >../static/client_build_hash.txt Done in 102.96s. Unsetting $PYTHONPATH Activating virtualenv at .venv galaxy.tools.deps DEBUG 2018-11-26 17:29:06,680 Unable to find config file './dependency_resolvers_conf.xml' Executing: python ./scripts/paster.py serve "/home/proteore/galaxy/config/galaxy.ini" DEBUG:galaxy.app:python path is: /home/proteore/galaxy/scripts, /home/proteore/galaxy/lib, /home/proteore/galaxy/.venv/lib64/python27.zip, /home/proteore/galaxy/.venv/lib64/python2.7, /home/proteore/galaxy/.venv/lib64/python2.7/plat-linux2, /home/proteore/galaxy/.venv/lib64/python2.7/lib-tk, /home/proteore/galaxy/.venv/lib64/python2.7/lib-old, /home/proteore/galaxy/.venv/lib64/python2.7/lib-dynload, /usr/lib64/python2.7, /usr/lib/python2.7, /home/proteore/galaxy/.venv/lib/python2.7/site-packages DEBUG:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config galaxy.web.stack DEBUG 2018-11-26 17:29:08,806 server_name set to: main galaxy.queue_worker INFO 2018-11-26 17:29:08,806 Initializing main Galaxy Queue Worker on sqlalchemy+postgresql://proteore:****@localhost/galaxy_proteore galaxy.app DEBUG 2018-11-26 17:29:08,835 Using "galaxy.ini" config file: /home/proteore/galaxy/config/galaxy.ini Traceback (most recent call last): 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 86, in init self._configure_models(check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file) File "/home/proteore/galaxy/lib/galaxy/config.py", line 1130, in _configure_models create_or_verify_database(db_url, config_file, self.config.database_engine_options, app=self) File "/home/proteore/galaxy/lib/galaxy/model/migrate/check.py", line 121, in create_or_verify_database raise Exception("%s. %s%s" % (expect_msg, instructions, backup_msg)) Exception: Your database has version '141' but this code expects version '142'. Please backup your database and then migrate the database schema by running 'sh manage_db.sh upgrade'.

vloux / ProteoRE

Galaxy update 18.09 #157