Mercurial > repos > jjohnson > optitype
comparison nohup.out @ 2:bf36e0afdfb4 draft default tip
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/optitype commit 703114ab7ad18b1b0e824b103f1df213448c6e97-dirty"
author | jjohnson |
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date | Tue, 09 Feb 2021 15:41:49 +0000 |
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1:54c9c71dabe8 | 2:bf36e0afdfb4 |
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1 git --git-dir /Users/jj/.planemo/gx_repo config remote.origin.fetch '+refs/*:refs/*' | |
2 git --git-dir /Users/jj/.planemo/gx_repo config remote.origin.mirror true | |
3 git --git-dir /Users/jj/.planemo/gx_repo remote update >/dev/null 2>&1 | |
4 galaxy.tool_util.deps.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input | |
5 git clone --branch master /Users/jj/.planemo/gx_repo /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev | |
6 Cloning into '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev'... | |
7 done. | |
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31 Checking out files: 100% (4988/4988), done. | |
32 if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/Users/jj/.planemo/gx_venv; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /Users/jj/.planemo/gx_venv/bin/virtualenv -p /Users/jj/.planemo/gx_venv/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; fi && COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}" && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS} | |
33 galaxy.tool_util.deps.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input | |
34 Set COMMON_STARTUP_ARGS to --dev-wheels | |
35 Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample | |
36 Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample | |
37 Initializing static/welcome.html from welcome.html.sample | |
38 Unsetting $PYTHONPATH | |
39 Activating virtualenv at /Users/jj/.planemo/gx_venv | |
40 Galaxy support for Python 2.7 is deprecated, please consider moving to | |
41 Python >= 3.5 . | |
42 https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions | |
43 on how to force Galaxy to use a different version. | |
44 DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support | |
45 Requirement already satisfied: pip>=8.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (20.0.2) | |
46 DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support | |
47 Ignoring pyinotify: markers 'sys_platform != "win32" and sys_platform != "darwin" and sys_platform != "sunos5"' don't match your environment | |
48 Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple | |
49 Requirement already satisfied: adal==1.2.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) (1.2.2) | |
50 Requirement already satisfied: amqp==2.5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) (2.5.2) | |
51 Requirement already satisfied: appdirs==1.4.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) (1.4.3) | |
52 Requirement already satisfied: attrs==19.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) (19.3.0) | |
53 Requirement already satisfied: azure-common==1.1.14 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) (1.1.14) | |
54 Requirement already satisfied: azure-cosmosdb-nspkg==2.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) (2.0.2) | |
55 Requirement already satisfied: azure-cosmosdb-table==1.0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) (1.0.4) | |
56 Requirement already satisfied: azure-mgmt-compute==4.0.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 10)) (4.0.1) | |
57 Requirement already satisfied: azure-mgmt-devtestlabs==2.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 11)) (2.2.0) | |
58 Requirement already satisfied: azure-mgmt-network==2.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 12)) (2.1.0) | |
59 Requirement already satisfied: azure-mgmt-nspkg==3.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 13)) (3.0.2) | |
60 Requirement already satisfied: azure-mgmt-resource==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 14)) (2.0.0) | |
61 Requirement already satisfied: azure-mgmt-storage==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15)) (2.0.0) | |
62 Requirement already satisfied: azure-nspkg==3.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) (3.0.2) | |
63 Requirement already satisfied: azure-storage-blob==1.3.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) (1.3.1) | |
64 Requirement already satisfied: azure-storage-common==1.4.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) (1.4.2) | |
65 Requirement already satisfied: azure-storage-nspkg==3.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) (3.1.0) | |
66 Requirement already satisfied: babel==2.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) (2.7.0) | |
67 Requirement already satisfied: bagit==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) (1.7.0) | |
68 Requirement already satisfied: bcrypt==3.1.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) (3.1.7) | |
69 Requirement already satisfied: bdbag==1.5.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) (1.5.6) | |
70 Requirement already satisfied: beaker==1.11.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) (1.11.0) | |
71 Requirement already satisfied: bioblend==0.13.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) (0.13.0) | |
72 Requirement already satisfied: bleach==3.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) (3.1.1) | |
73 Requirement already satisfied: boltons==19.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) (19.3.0) | |
74 Requirement already satisfied: boto3==1.9.114 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) (1.9.114) | |
75 Requirement already satisfied: boto==2.49.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) (2.49.0) | |
76 Requirement already satisfied: botocore==1.12.253 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) (1.12.253) | |
77 Requirement already satisfied: bx-python==0.8.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) (0.8.8) | |
78 Requirement already satisfied: bz2file==0.98 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) (0.98) | |
79 Requirement already satisfied: cachecontrol==0.11.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) (0.11.7) | |
80 Requirement already satisfied: cachetools==3.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) (3.1.1) | |
81 Requirement already satisfied: certifi==2019.11.28 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) (2019.11.28) | |
82 Requirement already satisfied: cffi==1.13.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) (1.13.2) | |
83 Requirement already satisfied: chardet==3.0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) (3.0.4) | |
84 Requirement already satisfied: cheetah3==3.2.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 38)) (3.2.4) | |
85 Requirement already satisfied: cliff==2.16.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) (2.16.0) | |
86 Requirement already satisfied: cloudauthz==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) (0.6.0) | |
87 Requirement already satisfied: cloudbridge==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) (2.0.0) | |
88 Requirement already satisfied: cmd2==0.8.9 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) (0.8.9) | |
89 Requirement already satisfied: coloredlogs==10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 43)) (10.0) | |
90 Requirement already satisfied: configparser==4.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) (4.0.2) | |
91 Requirement already satisfied: contextlib2==0.6.0.post1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) (0.6.0.post1) | |
92 Requirement already satisfied: cryptography==2.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) (2.8) | |
93 Requirement already satisfied: cwltool==1.0.20191225192155 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) (1.0.20191225192155) | |
94 Requirement already satisfied: debtcollector==1.22.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) (1.22.0) | |
95 Requirement already satisfied: decorator==4.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) (4.4.1) | |
96 Requirement already satisfied: deprecated==1.2.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) (1.2.7) | |
97 Requirement already satisfied: deprecation==2.0.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) (2.0.7) | |
98 Requirement already satisfied: dictobj==0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) (0.4) | |
99 Requirement already satisfied: docopt==0.6.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) (0.6.2) | |
100 Requirement already satisfied: docutils==0.15.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) (0.15.2) | |
101 Requirement already satisfied: dogpile.cache==0.9.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) (0.9.0) | |
102 Requirement already satisfied: ecdsa==0.14.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) (0.14.1) | |
103 Requirement already satisfied: enum34==1.1.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) (1.1.6) | |
104 Requirement already satisfied: fabric3==1.14.post1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) (1.14.post1) | |
105 Requirement already satisfied: funcsigs==1.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) (1.0.2) | |
106 Requirement already satisfied: functools32==3.2.3.post2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) (3.2.3.post2) | |
107 Requirement already satisfied: future==0.18.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 61)) (0.18.2) | |
108 Requirement already satisfied: futures==3.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 62)) (3.3.0) | |
109 Requirement already satisfied: galaxy-sequence-utils==1.1.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) (1.1.4) | |
110 Requirement already satisfied: google-api-python-client==1.7.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) (1.7.8) | |
111 Requirement already satisfied: google-auth-httplib2==0.0.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) (0.0.3) | |
112 Requirement already satisfied: google-auth==1.7.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) (1.7.1) | |
113 Requirement already satisfied: gxformat2==0.10.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) (0.10.1) | |
114 Requirement already satisfied: h5py==2.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 68)) (2.10.0) | |
115 Requirement already satisfied: httplib2==0.15.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) (0.15.0) | |
116 Requirement already satisfied: humanfriendly==4.18 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) (4.18) | |
117 Requirement already satisfied: idna==2.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) (2.8) | |
118 Requirement already satisfied: importlib-metadata==1.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 72)) (1.2.0) | |
119 Requirement already satisfied: ipaddress==1.0.23 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 73)) (1.0.23) | |
120 Requirement already satisfied: isa-rwval==0.10.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) (0.10.7) | |
121 Requirement already satisfied: iso8601==0.1.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) (0.1.12) | |
122 Requirement already satisfied: isodate==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) (0.6.0) | |
123 Requirement already satisfied: jmespath==0.9.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 77)) (0.9.4) | |
124 Requirement already satisfied: jsonpatch==1.24 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 78)) (1.24) | |
125 Requirement already satisfied: jsonpointer==2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) (2.0) | |
126 Requirement already satisfied: jsonschema==3.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 80)) (3.2.0) | |
127 Requirement already satisfied: keystoneauth1==3.18.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 81)) (3.18.0) | |
128 Requirement already satisfied: kombu==4.6.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) (4.6.6) | |
129 Requirement already satisfied: lockfile==0.12.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 83)) (0.12.2) | |
130 Requirement already satisfied: lxml==4.4.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 84)) (4.4.2) | |
131 Requirement already satisfied: mako==1.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 85)) (1.1.0) | |
132 Requirement already satisfied: markdown==3.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 86)) (3.1.1) | |
133 Requirement already satisfied: markupsafe==1.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 87)) (1.1.1) | |
134 Requirement already satisfied: mercurial==5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 88)) (5.2) | |
135 Requirement already satisfied: mistune==0.8.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 89)) (0.8.4) | |
136 Requirement already satisfied: monotonic==1.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 90)) (1.5) | |
137 Requirement already satisfied: more-itertools==5.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 91)) (5.0.0) | |
138 Requirement already satisfied: msgpack==0.6.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 92)) (0.6.2) | |
139 Requirement already satisfied: msrest==0.5.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 93)) (0.5.5) | |
140 Requirement already satisfied: msrestazure==0.5.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 94)) (0.5.0) | |
141 Requirement already satisfied: munch==2.5.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 95)) (2.5.0) | |
142 Requirement already satisfied: mypy-extensions==0.4.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 96)) (0.4.3) | |
143 Requirement already satisfied: netaddr==0.7.19 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 97)) (0.7.19) | |
144 Requirement already satisfied: netifaces==0.10.9 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 98)) (0.10.9) | |
145 Requirement already satisfied: networkx==1.11 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 99)) (1.11) | |
146 Requirement already satisfied: nodeenv==1.3.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 100)) (1.3.3) | |
147 Requirement already satisfied: nose==1.3.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 101)) (1.3.7) | |
148 Requirement already satisfied: numpy==1.16.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 102)) (1.16.5) | |
149 Requirement already satisfied: oauth2client==4.1.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 103)) (4.1.3) | |
150 Requirement already satisfied: oauthlib==3.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 104)) (3.1.0) | |
151 Requirement already satisfied: openstacksdk==0.17.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 105)) (0.17.0) | |
152 Requirement already satisfied: os-client-config==1.33.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 106)) (1.33.0) | |
153 Requirement already satisfied: os-service-types==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 107)) (1.7.0) | |
154 Requirement already satisfied: osc-lib==1.14.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 108)) (1.14.1) | |
155 Requirement already satisfied: oslo.config==6.12.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 109)) (6.12.0) | |
156 Requirement already satisfied: oslo.context==2.23.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 110)) (2.23.0) | |
157 Requirement already satisfied: oslo.i18n==3.25.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 111)) (3.25.0) | |
158 Requirement already satisfied: oslo.log==3.45.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 112)) (3.45.0) | |
159 Requirement already satisfied: oslo.serialization==2.29.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 113)) (2.29.2) | |
160 Requirement already satisfied: oslo.utils==3.42.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 114)) (3.42.0) | |
161 Requirement already satisfied: packaging==20.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 115)) (20.0) | |
162 Requirement already satisfied: paramiko==2.7.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 116)) (2.7.1) | |
163 Requirement already satisfied: parsley==1.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 117)) (1.3) | |
164 Requirement already satisfied: paste==3.2.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 118)) (3.2.3) | |
165 Requirement already satisfied: pastedeploy==2.0.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 119)) (2.0.1) | |
166 Requirement already satisfied: pastescript==3.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 120)) (3.2.0) | |
167 Requirement already satisfied: pathlib2==2.3.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 121)) (2.3.5) | |
168 Requirement already satisfied: pbr==5.4.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 122)) (5.4.4) | |
169 Requirement already satisfied: prettytable==0.7.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 123)) (0.7.2) | |
170 Requirement already satisfied: prov==1.5.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 124)) (1.5.1) | |
171 Requirement already satisfied: psutil==5.6.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 125)) (5.6.7) | |
172 Requirement already satisfied: pulsar-galaxy-lib==0.14.0.dev1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 126)) (0.14.0.dev1) | |
173 Requirement already satisfied: pyasn1-modules==0.2.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 127)) (0.2.7) | |
174 Requirement already satisfied: pyasn1==0.4.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 128)) (0.4.8) | |
175 Requirement already satisfied: pycparser==2.19 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 129)) (2.19) | |
176 Requirement already satisfied: pycryptodome==3.9.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 130)) (3.9.6) | |
177 Requirement already satisfied: pyeventsystem==0.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 131)) (0.1.0) | |
178 Requirement already satisfied: pyjwt==1.7.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 133)) (1.7.1) | |
179 Requirement already satisfied: pykwalify==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 134)) (1.7.0) | |
180 Requirement already satisfied: pynacl==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 135)) (1.3.0) | |
181 Requirement already satisfied: pyopenssl==19.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 136)) (19.1.0) | |
182 Requirement already satisfied: pyparsing==2.4.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 137)) (2.4.5) | |
183 Requirement already satisfied: pyperclip==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 138)) (1.7.0) | |
184 Requirement already satisfied: pyrsistent==0.15.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 139)) (0.15.6) | |
185 Requirement already satisfied: pysam==0.15.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 140)) (0.15.2) | |
186 Requirement already satisfied: pysftp==0.2.9 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 141)) (0.2.9) | |
187 Requirement already satisfied: python-cinderclient==4.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 142)) (4.0.0) | |
188 Requirement already satisfied: python-dateutil==2.8.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 143)) (2.8.1) | |
189 Requirement already satisfied: python-glanceclient==2.12.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 144)) (2.12.0) | |
190 Requirement already satisfied: python-jose==3.0.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 145)) (3.0.1) | |
191 Requirement already satisfied: python-keystoneclient==3.17.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 146)) (3.17.0) | |
192 Requirement already satisfied: python-neutronclient==6.9.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 147)) (6.9.0) | |
193 Requirement already satisfied: python-novaclient==11.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 148)) (11.0.0) | |
194 Requirement already satisfied: python-openid==2.2.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 149)) (2.2.5) | |
195 Requirement already satisfied: python-swiftclient==3.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 150)) (3.6.0) | |
196 Requirement already satisfied: pytz==2019.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 151)) (2019.3) | |
197 Requirement already satisfied: pyuwsgi==2.0.18.post0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 152)) (2.0.18.post0) | |
198 Requirement already satisfied: pyyaml==5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 153)) (5.2) | |
199 Requirement already satisfied: rdflib-jsonld==0.4.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 154)) (0.4.0) | |
200 Requirement already satisfied: rdflib==4.2.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 155)) (4.2.2) | |
201 Requirement already satisfied: repoze.lru==0.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 156)) (0.7) | |
202 Requirement already satisfied: requests-oauthlib==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 157)) (1.3.0) | |
203 Requirement already satisfied: requests-toolbelt==0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 158)) (0.9.1) | |
204 Requirement already satisfied: requests==2.22.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 159)) (2.22.0) | |
205 Requirement already satisfied: requestsexceptions==1.4.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 160)) (1.4.0) | |
206 Requirement already satisfied: rfc3986==1.3.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 161)) (1.3.2) | |
207 Requirement already satisfied: routes==2.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 162)) (2.4.1) | |
208 Requirement already satisfied: rsa==4.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 163)) (4.0) | |
209 Requirement already satisfied: ruamel.ordereddict==0.4.14 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 164)) (0.4.14) | |
210 Requirement already satisfied: ruamel.yaml.clib==0.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 165)) (0.2.0) | |
211 Requirement already satisfied: ruamel.yaml==0.16.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 166)) (0.16.0) | |
212 Requirement already satisfied: s3transfer==0.2.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 167)) (0.2.1) | |
213 Requirement already satisfied: scandir==1.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 168)) (1.10.0) | |
214 Requirement already satisfied: schema-salad==4.5.20191229160203 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 169)) (4.5.20191229160203) | |
215 Requirement already satisfied: setuptools-scm==3.3.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 170)) (3.3.3) | |
216 Requirement already satisfied: shellescape==3.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 171)) (3.4.1) | |
217 Requirement already satisfied: simplejson==3.17.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 172)) (3.17.0) | |
218 Requirement already satisfied: six==1.11.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 173)) (1.11.0) | |
219 Requirement already satisfied: social-auth-core[openidconnect]==3.1.0+gx0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 174)) (3.1.0+gx0) | |
220 Requirement already satisfied: sqlalchemy-migrate==0.13.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 175)) (0.13.0) | |
221 Requirement already satisfied: sqlalchemy-utils==0.35.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 176)) (0.35.0) | |
222 Requirement already satisfied: sqlalchemy==1.3.11 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 177)) (1.3.11) | |
223 Requirement already satisfied: sqlparse==0.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 178)) (0.3.0) | |
224 Requirement already satisfied: stevedore==1.31.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 179)) (1.31.0) | |
225 Requirement already satisfied: subprocess32==3.5.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 180)) (3.5.4) | |
226 Requirement already satisfied: svgwrite==1.3.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 181)) (1.3.1) | |
227 Requirement already satisfied: tempita==0.5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 182)) (0.5.2) | |
228 Requirement already satisfied: tenacity==4.12.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 183)) (4.12.0) | |
229 Requirement already satisfied: typing-extensions==3.7.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 184)) (3.7.4.1) | |
230 Requirement already satisfied: typing==3.7.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 185)) (3.7.4.1) | |
231 Requirement already satisfied: tzlocal==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 186)) (2.0.0) | |
232 Requirement already satisfied: unicodecsv==0.14.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 187)) (0.14.1) | |
233 Requirement already satisfied: uritemplate==3.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 188)) (3.0.0) | |
234 Requirement already satisfied: urllib3==1.25.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 189)) (1.25.7) | |
235 Requirement already satisfied: vine==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 190)) (1.3.0) | |
236 Requirement already satisfied: warlock==1.3.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 191)) (1.3.3) | |
237 Requirement already satisfied: wcwidth==0.1.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 192)) (0.1.7) | |
238 Requirement already satisfied: webencodings==0.5.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 193)) (0.5.1) | |
239 Requirement already satisfied: webob==1.8.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 194)) (1.8.5) | |
240 Requirement already satisfied: whoosh==2.7.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 195)) (2.7.4) | |
241 Requirement already satisfied: wrapt==1.11.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 196)) (1.11.2) | |
242 Requirement already satisfied: zipp==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 197)) (0.6.0) | |
243 Requirement already satisfied: alabaster==0.7.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (0.7.12) | |
244 Requirement already satisfied: argh==0.26.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) (0.26.2) | |
245 Requirement already satisfied: atomicwrites==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) (1.3.0) | |
246 Requirement already satisfied: commonmark==0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 10)) (0.9.1) | |
247 Requirement already satisfied: coverage==4.5.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 13)) (4.5.4) | |
248 Requirement already satisfied: gunicorn==19.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 18)) (19.10.0) | |
249 Requirement already satisfied: imagesize==1.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (1.1.0) | |
250 Requirement already satisfied: jinja2==2.10.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 22)) (2.10.3) | |
251 Requirement already satisfied: mirakuru==1.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 26)) (1.1.0) | |
252 Requirement already satisfied: mock==3.0.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (3.0.5) | |
253 Requirement already satisfied: nosehtml==0.4.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 30)) (0.4.5) | |
254 Requirement already satisfied: pathtools==0.1.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 33)) (0.1.2) | |
255 Requirement already satisfied: pluggy==0.13.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 34)) (0.13.1) | |
256 Requirement already satisfied: port-for==0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 35)) (0.4) | |
257 Requirement already satisfied: py==1.8.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 37)) (1.8.0) | |
258 Requirement already satisfied: pygithub==1.45 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 38)) (1.45) | |
259 Requirement already satisfied: pygments==2.5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 39)) (2.5.2) | |
260 Requirement already satisfied: pytest-cov==2.8.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 42)) (2.8.1) | |
261 Requirement already satisfied: pytest-html==1.22.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 43)) (1.22.1) | |
262 Requirement already satisfied: pytest-metadata==1.8.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (1.8.0) | |
263 Requirement already satisfied: pytest-postgresql==1.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 45)) (1.4.1) | |
264 Requirement already satisfied: pytest-pythonpath==0.7.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 46)) (0.7.3) | |
265 Requirement already satisfied: pytest==4.6.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 47)) (4.6.6) | |
266 Requirement already satisfied: recommonmark==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 49)) (0.6.0) | |
267 Requirement already satisfied: selenium==3.141.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 52)) (3.141.0) | |
268 Requirement already satisfied: snowballstemmer==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 54)) (2.0.0) | |
269 Requirement already satisfied: sphinx-markdown-tables==0.0.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55)) (0.0.12) | |
270 Requirement already satisfied: sphinx-rtd-theme==0.4.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 56)) (0.4.3) | |
271 Requirement already satisfied: sphinx==1.8.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 57)) (1.8.5) | |
272 Requirement already satisfied: sphinxcontrib-websupport==1.1.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 58)) (1.1.2) | |
273 Requirement already satisfied: testfixtures==6.10.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 59)) (6.10.3) | |
274 Requirement already satisfied: twill==0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 60)) (0.9.1) | |
275 Requirement already satisfied: watchdog==0.9.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 63)) (0.9.0) | |
276 Requirement already satisfied: setuptools in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 47)) (28.8.0) | |
277 DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support | |
278 DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support | |
279 Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple | |
280 Requirement already satisfied: pykube==0.15.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r /dev/stdin (line 1)) (0.15.0) | |
281 Requirement already satisfied: PyYAML in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (5.2) | |
282 Requirement already satisfied: requests>=2.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (2.22.0) | |
283 Requirement already satisfied: tzlocal in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (2.0.0) | |
284 Requirement already satisfied: six>=1.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (1.11.0) | |
285 Requirement already satisfied: requests-oauthlib in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (1.3.0) | |
286 Requirement already satisfied: oauth2client in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (4.1.3) | |
287 Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (3.0.4) | |
288 Requirement already satisfied: idna<2.9,>=2.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (2.8) | |
289 Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (1.25.7) | |
290 Requirement already satisfied: certifi>=2017.4.17 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (2019.11.28) | |
291 Requirement already satisfied: pytz in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from tzlocal->pykube==0.15.0->-r /dev/stdin (line 1)) (2019.3) | |
292 Requirement already satisfied: oauthlib>=3.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests-oauthlib->pykube==0.15.0->-r /dev/stdin (line 1)) (3.1.0) | |
293 Requirement already satisfied: pyasn1>=0.1.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (0.4.8) | |
294 Requirement already satisfied: pyasn1-modules>=0.0.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (0.2.7) | |
295 Requirement already satisfied: httplib2>=0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (0.15.0) | |
296 Requirement already satisfied: rsa>=3.1.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (4.0) | |
297 The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable. | |
298 Testing using galaxy_root /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev | |
299 Testing tools with command [cd /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev && if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/Users/jj/.planemo/gx_venv; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /Users/jj/.planemo/gx_venv/bin/virtualenv -p /Users/jj/.planemo/gx_venv/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; fi && sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /Users/jj/gx/gh/jj/galaxytools/optitype/tool_test_output.html --xunit_report_file /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/xunit.xml --structured_data_report_file /Users/jj/gx/gh/jj/galaxytools/optitype/tool_test_output.json functional.test_toolbox] | |
300 galaxy.tool_util.deps.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input | |
301 Unsetting $PYTHONPATH | |
302 Activating virtualenv at /Users/jj/.planemo/gx_venv | |
303 Galaxy support for Python 2.7 is deprecated, please consider moving to | |
304 Python >= 3.5 . | |
305 https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions | |
306 on how to force Galaxy to use a different version. | |
307 DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support | |
308 Requirement already satisfied: pip>=8.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (20.0.2) | |
309 DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support | |
310 Ignoring pyinotify: markers 'sys_platform != "win32" and sys_platform != "darwin" and sys_platform != "sunos5"' don't match your environment | |
311 Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple | |
312 Requirement already satisfied: adal==1.2.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) (1.2.2) | |
313 Requirement already satisfied: amqp==2.5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) (2.5.2) | |
314 Requirement already satisfied: appdirs==1.4.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) (1.4.3) | |
315 Requirement already satisfied: attrs==19.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) (19.3.0) | |
316 Requirement already satisfied: azure-common==1.1.14 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) (1.1.14) | |
317 Requirement already satisfied: azure-cosmosdb-nspkg==2.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) (2.0.2) | |
318 Requirement already satisfied: azure-cosmosdb-table==1.0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) (1.0.4) | |
319 Requirement already satisfied: azure-mgmt-compute==4.0.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 10)) (4.0.1) | |
320 Requirement already satisfied: azure-mgmt-devtestlabs==2.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 11)) (2.2.0) | |
321 Requirement already satisfied: azure-mgmt-network==2.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 12)) (2.1.0) | |
322 Requirement already satisfied: azure-mgmt-nspkg==3.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 13)) (3.0.2) | |
323 Requirement already satisfied: azure-mgmt-resource==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 14)) (2.0.0) | |
324 Requirement already satisfied: azure-mgmt-storage==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15)) (2.0.0) | |
325 Requirement already satisfied: azure-nspkg==3.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) (3.0.2) | |
326 Requirement already satisfied: azure-storage-blob==1.3.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) (1.3.1) | |
327 Requirement already satisfied: azure-storage-common==1.4.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) (1.4.2) | |
328 Requirement already satisfied: azure-storage-nspkg==3.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) (3.1.0) | |
329 Requirement already satisfied: babel==2.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) (2.7.0) | |
330 Requirement already satisfied: bagit==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) (1.7.0) | |
331 Requirement already satisfied: bcrypt==3.1.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) (3.1.7) | |
332 Requirement already satisfied: bdbag==1.5.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) (1.5.6) | |
333 Requirement already satisfied: beaker==1.11.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) (1.11.0) | |
334 Requirement already satisfied: bioblend==0.13.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) (0.13.0) | |
335 Requirement already satisfied: bleach==3.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) (3.1.1) | |
336 Requirement already satisfied: boltons==19.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) (19.3.0) | |
337 Requirement already satisfied: boto3==1.9.114 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) (1.9.114) | |
338 Requirement already satisfied: boto==2.49.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) (2.49.0) | |
339 Requirement already satisfied: botocore==1.12.253 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) (1.12.253) | |
340 Requirement already satisfied: bx-python==0.8.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) (0.8.8) | |
341 Requirement already satisfied: bz2file==0.98 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) (0.98) | |
342 Requirement already satisfied: cachecontrol==0.11.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) (0.11.7) | |
343 Requirement already satisfied: cachetools==3.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) (3.1.1) | |
344 Requirement already satisfied: certifi==2019.11.28 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) (2019.11.28) | |
345 Requirement already satisfied: cffi==1.13.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) (1.13.2) | |
346 Requirement already satisfied: chardet==3.0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) (3.0.4) | |
347 Requirement already satisfied: cheetah3==3.2.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 38)) (3.2.4) | |
348 Requirement already satisfied: cliff==2.16.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) (2.16.0) | |
349 Requirement already satisfied: cloudauthz==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) (0.6.0) | |
350 Requirement already satisfied: cloudbridge==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) (2.0.0) | |
351 Requirement already satisfied: cmd2==0.8.9 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) (0.8.9) | |
352 Requirement already satisfied: coloredlogs==10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 43)) (10.0) | |
353 Requirement already satisfied: configparser==4.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) (4.0.2) | |
354 Requirement already satisfied: contextlib2==0.6.0.post1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) (0.6.0.post1) | |
355 Requirement already satisfied: cryptography==2.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) (2.8) | |
356 Requirement already satisfied: cwltool==1.0.20191225192155 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) (1.0.20191225192155) | |
357 Requirement already satisfied: debtcollector==1.22.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) (1.22.0) | |
358 Requirement already satisfied: decorator==4.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) (4.4.1) | |
359 Requirement already satisfied: deprecated==1.2.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) (1.2.7) | |
360 Requirement already satisfied: deprecation==2.0.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) (2.0.7) | |
361 Requirement already satisfied: dictobj==0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) (0.4) | |
362 Requirement already satisfied: docopt==0.6.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) (0.6.2) | |
363 Requirement already satisfied: docutils==0.15.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) (0.15.2) | |
364 Requirement already satisfied: dogpile.cache==0.9.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) (0.9.0) | |
365 Requirement already satisfied: ecdsa==0.14.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) (0.14.1) | |
366 Requirement already satisfied: enum34==1.1.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) (1.1.6) | |
367 Requirement already satisfied: fabric3==1.14.post1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) (1.14.post1) | |
368 Requirement already satisfied: funcsigs==1.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) (1.0.2) | |
369 Requirement already satisfied: functools32==3.2.3.post2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) (3.2.3.post2) | |
370 Requirement already satisfied: future==0.18.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 61)) (0.18.2) | |
371 Requirement already satisfied: futures==3.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 62)) (3.3.0) | |
372 Requirement already satisfied: galaxy-sequence-utils==1.1.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) (1.1.4) | |
373 Requirement already satisfied: google-api-python-client==1.7.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) (1.7.8) | |
374 Requirement already satisfied: google-auth-httplib2==0.0.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) (0.0.3) | |
375 Requirement already satisfied: google-auth==1.7.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) (1.7.1) | |
376 Requirement already satisfied: gxformat2==0.10.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) (0.10.1) | |
377 Requirement already satisfied: h5py==2.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 68)) (2.10.0) | |
378 Requirement already satisfied: httplib2==0.15.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) (0.15.0) | |
379 Requirement already satisfied: humanfriendly==4.18 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) (4.18) | |
380 Requirement already satisfied: idna==2.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) (2.8) | |
381 Requirement already satisfied: importlib-metadata==1.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 72)) (1.2.0) | |
382 Requirement already satisfied: ipaddress==1.0.23 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 73)) (1.0.23) | |
383 Requirement already satisfied: isa-rwval==0.10.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) (0.10.7) | |
384 Requirement already satisfied: iso8601==0.1.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) (0.1.12) | |
385 Requirement already satisfied: isodate==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) (0.6.0) | |
386 Requirement already satisfied: jmespath==0.9.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 77)) (0.9.4) | |
387 Requirement already satisfied: jsonpatch==1.24 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 78)) (1.24) | |
388 Requirement already satisfied: jsonpointer==2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) (2.0) | |
389 Requirement already satisfied: jsonschema==3.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 80)) (3.2.0) | |
390 Requirement already satisfied: keystoneauth1==3.18.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 81)) (3.18.0) | |
391 Requirement already satisfied: kombu==4.6.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) (4.6.6) | |
392 Requirement already satisfied: lockfile==0.12.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 83)) (0.12.2) | |
393 Requirement already satisfied: lxml==4.4.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 84)) (4.4.2) | |
394 Requirement already satisfied: mako==1.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 85)) (1.1.0) | |
395 Requirement already satisfied: markdown==3.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 86)) (3.1.1) | |
396 Requirement already satisfied: markupsafe==1.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 87)) (1.1.1) | |
397 Requirement already satisfied: mercurial==5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 88)) (5.2) | |
398 Requirement already satisfied: mistune==0.8.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 89)) (0.8.4) | |
399 Requirement already satisfied: monotonic==1.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 90)) (1.5) | |
400 Requirement already satisfied: more-itertools==5.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 91)) (5.0.0) | |
401 Requirement already satisfied: msgpack==0.6.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 92)) (0.6.2) | |
402 Requirement already satisfied: msrest==0.5.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 93)) (0.5.5) | |
403 Requirement already satisfied: msrestazure==0.5.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 94)) (0.5.0) | |
404 Requirement already satisfied: munch==2.5.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 95)) (2.5.0) | |
405 Requirement already satisfied: mypy-extensions==0.4.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 96)) (0.4.3) | |
406 Requirement already satisfied: netaddr==0.7.19 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 97)) (0.7.19) | |
407 Requirement already satisfied: netifaces==0.10.9 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 98)) (0.10.9) | |
408 Requirement already satisfied: networkx==1.11 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 99)) (1.11) | |
409 Requirement already satisfied: nodeenv==1.3.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 100)) (1.3.3) | |
410 Requirement already satisfied: nose==1.3.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 101)) (1.3.7) | |
411 Requirement already satisfied: numpy==1.16.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 102)) (1.16.5) | |
412 Requirement already satisfied: oauth2client==4.1.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 103)) (4.1.3) | |
413 Requirement already satisfied: oauthlib==3.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 104)) (3.1.0) | |
414 Requirement already satisfied: openstacksdk==0.17.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 105)) (0.17.0) | |
415 Requirement already satisfied: os-client-config==1.33.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 106)) (1.33.0) | |
416 Requirement already satisfied: os-service-types==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 107)) (1.7.0) | |
417 Requirement already satisfied: osc-lib==1.14.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 108)) (1.14.1) | |
418 Requirement already satisfied: oslo.config==6.12.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 109)) (6.12.0) | |
419 Requirement already satisfied: oslo.context==2.23.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 110)) (2.23.0) | |
420 Requirement already satisfied: oslo.i18n==3.25.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 111)) (3.25.0) | |
421 Requirement already satisfied: oslo.log==3.45.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 112)) (3.45.0) | |
422 Requirement already satisfied: oslo.serialization==2.29.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 113)) (2.29.2) | |
423 Requirement already satisfied: oslo.utils==3.42.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 114)) (3.42.0) | |
424 Requirement already satisfied: packaging==20.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 115)) (20.0) | |
425 Requirement already satisfied: paramiko==2.7.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 116)) (2.7.1) | |
426 Requirement already satisfied: parsley==1.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 117)) (1.3) | |
427 Requirement already satisfied: paste==3.2.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 118)) (3.2.3) | |
428 Requirement already satisfied: pastedeploy==2.0.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 119)) (2.0.1) | |
429 Requirement already satisfied: pastescript==3.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 120)) (3.2.0) | |
430 Requirement already satisfied: pathlib2==2.3.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 121)) (2.3.5) | |
431 Requirement already satisfied: pbr==5.4.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 122)) (5.4.4) | |
432 Requirement already satisfied: prettytable==0.7.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 123)) (0.7.2) | |
433 Requirement already satisfied: prov==1.5.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 124)) (1.5.1) | |
434 Requirement already satisfied: psutil==5.6.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 125)) (5.6.7) | |
435 Requirement already satisfied: pulsar-galaxy-lib==0.14.0.dev1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 126)) (0.14.0.dev1) | |
436 Requirement already satisfied: pyasn1-modules==0.2.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 127)) (0.2.7) | |
437 Requirement already satisfied: pyasn1==0.4.8 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 128)) (0.4.8) | |
438 Requirement already satisfied: pycparser==2.19 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 129)) (2.19) | |
439 Requirement already satisfied: pycryptodome==3.9.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 130)) (3.9.6) | |
440 Requirement already satisfied: pyeventsystem==0.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 131)) (0.1.0) | |
441 Requirement already satisfied: pyjwt==1.7.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 133)) (1.7.1) | |
442 Requirement already satisfied: pykwalify==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 134)) (1.7.0) | |
443 Requirement already satisfied: pynacl==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 135)) (1.3.0) | |
444 Requirement already satisfied: pyopenssl==19.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 136)) (19.1.0) | |
445 Requirement already satisfied: pyparsing==2.4.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 137)) (2.4.5) | |
446 Requirement already satisfied: pyperclip==1.7.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 138)) (1.7.0) | |
447 Requirement already satisfied: pyrsistent==0.15.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 139)) (0.15.6) | |
448 Requirement already satisfied: pysam==0.15.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 140)) (0.15.2) | |
449 Requirement already satisfied: pysftp==0.2.9 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 141)) (0.2.9) | |
450 Requirement already satisfied: python-cinderclient==4.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 142)) (4.0.0) | |
451 Requirement already satisfied: python-dateutil==2.8.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 143)) (2.8.1) | |
452 Requirement already satisfied: python-glanceclient==2.12.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 144)) (2.12.0) | |
453 Requirement already satisfied: python-jose==3.0.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 145)) (3.0.1) | |
454 Requirement already satisfied: python-keystoneclient==3.17.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 146)) (3.17.0) | |
455 Requirement already satisfied: python-neutronclient==6.9.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 147)) (6.9.0) | |
456 Requirement already satisfied: python-novaclient==11.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 148)) (11.0.0) | |
457 Requirement already satisfied: python-openid==2.2.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 149)) (2.2.5) | |
458 Requirement already satisfied: python-swiftclient==3.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 150)) (3.6.0) | |
459 Requirement already satisfied: pytz==2019.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 151)) (2019.3) | |
460 Requirement already satisfied: pyuwsgi==2.0.18.post0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 152)) (2.0.18.post0) | |
461 Requirement already satisfied: pyyaml==5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 153)) (5.2) | |
462 Requirement already satisfied: rdflib-jsonld==0.4.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 154)) (0.4.0) | |
463 Requirement already satisfied: rdflib==4.2.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 155)) (4.2.2) | |
464 Requirement already satisfied: repoze.lru==0.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 156)) (0.7) | |
465 Requirement already satisfied: requests-oauthlib==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 157)) (1.3.0) | |
466 Requirement already satisfied: requests-toolbelt==0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 158)) (0.9.1) | |
467 Requirement already satisfied: requests==2.22.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 159)) (2.22.0) | |
468 Requirement already satisfied: requestsexceptions==1.4.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 160)) (1.4.0) | |
469 Requirement already satisfied: rfc3986==1.3.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 161)) (1.3.2) | |
470 Requirement already satisfied: routes==2.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 162)) (2.4.1) | |
471 Requirement already satisfied: rsa==4.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 163)) (4.0) | |
472 Requirement already satisfied: ruamel.ordereddict==0.4.14 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 164)) (0.4.14) | |
473 Requirement already satisfied: ruamel.yaml.clib==0.2.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 165)) (0.2.0) | |
474 Requirement already satisfied: ruamel.yaml==0.16.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 166)) (0.16.0) | |
475 Requirement already satisfied: s3transfer==0.2.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 167)) (0.2.1) | |
476 Requirement already satisfied: scandir==1.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 168)) (1.10.0) | |
477 Requirement already satisfied: schema-salad==4.5.20191229160203 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 169)) (4.5.20191229160203) | |
478 Requirement already satisfied: setuptools-scm==3.3.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 170)) (3.3.3) | |
479 Requirement already satisfied: shellescape==3.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 171)) (3.4.1) | |
480 Requirement already satisfied: simplejson==3.17.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 172)) (3.17.0) | |
481 Requirement already satisfied: six==1.11.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 173)) (1.11.0) | |
482 Requirement already satisfied: social-auth-core[openidconnect]==3.1.0+gx0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 174)) (3.1.0+gx0) | |
483 Requirement already satisfied: sqlalchemy-migrate==0.13.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 175)) (0.13.0) | |
484 Requirement already satisfied: sqlalchemy-utils==0.35.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 176)) (0.35.0) | |
485 Requirement already satisfied: sqlalchemy==1.3.11 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 177)) (1.3.11) | |
486 Requirement already satisfied: sqlparse==0.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 178)) (0.3.0) | |
487 Requirement already satisfied: stevedore==1.31.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 179)) (1.31.0) | |
488 Requirement already satisfied: subprocess32==3.5.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 180)) (3.5.4) | |
489 Requirement already satisfied: svgwrite==1.3.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 181)) (1.3.1) | |
490 Requirement already satisfied: tempita==0.5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 182)) (0.5.2) | |
491 Requirement already satisfied: tenacity==4.12.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 183)) (4.12.0) | |
492 Requirement already satisfied: typing-extensions==3.7.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 184)) (3.7.4.1) | |
493 Requirement already satisfied: typing==3.7.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 185)) (3.7.4.1) | |
494 Requirement already satisfied: tzlocal==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 186)) (2.0.0) | |
495 Requirement already satisfied: unicodecsv==0.14.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 187)) (0.14.1) | |
496 Requirement already satisfied: uritemplate==3.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 188)) (3.0.0) | |
497 Requirement already satisfied: urllib3==1.25.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 189)) (1.25.7) | |
498 Requirement already satisfied: vine==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 190)) (1.3.0) | |
499 Requirement already satisfied: warlock==1.3.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 191)) (1.3.3) | |
500 Requirement already satisfied: wcwidth==0.1.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 192)) (0.1.7) | |
501 Requirement already satisfied: webencodings==0.5.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 193)) (0.5.1) | |
502 Requirement already satisfied: webob==1.8.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 194)) (1.8.5) | |
503 Requirement already satisfied: whoosh==2.7.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 195)) (2.7.4) | |
504 Requirement already satisfied: wrapt==1.11.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 196)) (1.11.2) | |
505 Requirement already satisfied: zipp==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 197)) (0.6.0) | |
506 Requirement already satisfied: alabaster==0.7.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (0.7.12) | |
507 Requirement already satisfied: argh==0.26.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) (0.26.2) | |
508 Requirement already satisfied: atomicwrites==1.3.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) (1.3.0) | |
509 Requirement already satisfied: commonmark==0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 10)) (0.9.1) | |
510 Requirement already satisfied: coverage==4.5.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 13)) (4.5.4) | |
511 Requirement already satisfied: gunicorn==19.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 18)) (19.10.0) | |
512 Requirement already satisfied: imagesize==1.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (1.1.0) | |
513 Requirement already satisfied: jinja2==2.10.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 22)) (2.10.3) | |
514 Requirement already satisfied: mirakuru==1.1.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 26)) (1.1.0) | |
515 Requirement already satisfied: mock==3.0.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (3.0.5) | |
516 Requirement already satisfied: nosehtml==0.4.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 30)) (0.4.5) | |
517 Requirement already satisfied: pathtools==0.1.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 33)) (0.1.2) | |
518 Requirement already satisfied: pluggy==0.13.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 34)) (0.13.1) | |
519 Requirement already satisfied: port-for==0.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 35)) (0.4) | |
520 Requirement already satisfied: py==1.8.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 37)) (1.8.0) | |
521 Requirement already satisfied: pygithub==1.45 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 38)) (1.45) | |
522 Requirement already satisfied: pygments==2.5.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 39)) (2.5.2) | |
523 Requirement already satisfied: pytest-cov==2.8.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 42)) (2.8.1) | |
524 Requirement already satisfied: pytest-html==1.22.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 43)) (1.22.1) | |
525 Requirement already satisfied: pytest-metadata==1.8.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (1.8.0) | |
526 Requirement already satisfied: pytest-postgresql==1.4.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 45)) (1.4.1) | |
527 Requirement already satisfied: pytest-pythonpath==0.7.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 46)) (0.7.3) | |
528 Requirement already satisfied: pytest==4.6.6 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 47)) (4.6.6) | |
529 Requirement already satisfied: recommonmark==0.6.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 49)) (0.6.0) | |
530 Requirement already satisfied: selenium==3.141.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 52)) (3.141.0) | |
531 Requirement already satisfied: snowballstemmer==2.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 54)) (2.0.0) | |
532 Requirement already satisfied: sphinx-markdown-tables==0.0.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55)) (0.0.12) | |
533 Requirement already satisfied: sphinx-rtd-theme==0.4.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 56)) (0.4.3) | |
534 Requirement already satisfied: sphinx==1.8.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 57)) (1.8.5) | |
535 Requirement already satisfied: sphinxcontrib-websupport==1.1.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 58)) (1.1.2) | |
536 Requirement already satisfied: testfixtures==6.10.3 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 59)) (6.10.3) | |
537 Requirement already satisfied: twill==0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 60)) (0.9.1) | |
538 Requirement already satisfied: watchdog==0.9.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 63)) (0.9.0) | |
539 Requirement already satisfied: setuptools in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 47)) (28.8.0) | |
540 DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support | |
541 DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support | |
542 Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple | |
543 Requirement already satisfied: pykube==0.15.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r /dev/stdin (line 1)) (0.15.0) | |
544 Requirement already satisfied: watchdog in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from -r /dev/stdin (line 2)) (0.9.0) | |
545 Requirement already satisfied: PyYAML in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (5.2) | |
546 Requirement already satisfied: requests>=2.12 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (2.22.0) | |
547 Requirement already satisfied: tzlocal in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (2.0.0) | |
548 Requirement already satisfied: six>=1.10.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (1.11.0) | |
549 Requirement already satisfied: requests-oauthlib in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (1.3.0) | |
550 Requirement already satisfied: oauth2client in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from pykube==0.15.0->-r /dev/stdin (line 1)) (4.1.3) | |
551 Requirement already satisfied: pathtools>=0.1.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from watchdog->-r /dev/stdin (line 2)) (0.1.2) | |
552 Requirement already satisfied: argh>=0.24.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from watchdog->-r /dev/stdin (line 2)) (0.26.2) | |
553 Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (3.0.4) | |
554 Requirement already satisfied: idna<2.9,>=2.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (2.8) | |
555 Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (1.25.7) | |
556 Requirement already satisfied: certifi>=2017.4.17 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests>=2.12->pykube==0.15.0->-r /dev/stdin (line 1)) (2019.11.28) | |
557 Requirement already satisfied: pytz in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from tzlocal->pykube==0.15.0->-r /dev/stdin (line 1)) (2019.3) | |
558 Requirement already satisfied: oauthlib>=3.0.0 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from requests-oauthlib->pykube==0.15.0->-r /dev/stdin (line 1)) (3.1.0) | |
559 Requirement already satisfied: pyasn1>=0.1.7 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (0.4.8) | |
560 Requirement already satisfied: pyasn1-modules>=0.0.5 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (0.2.7) | |
561 Requirement already satisfied: httplib2>=0.9.1 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (0.15.0) | |
562 Requirement already satisfied: rsa>=3.1.4 in /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages (from oauth2client->pykube==0.15.0->-r /dev/stdin (line 1)) (4.0) | |
563 The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable. | |
564 Unsetting $PYTHONPATH | |
565 Activating virtualenv at /Users/jj/.planemo/gx_venv | |
566 Galaxy support for Python 2.7 is deprecated, please consider moving to | |
567 Python >= 3.5 . | |
568 https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions | |
569 on how to force Galaxy to use a different version. | |
570 2020-03-19 13:08:41,856 INFO [galaxy.queue_worker] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmprRkKGz/tmpaHgrap/tmpqqL2uw/database/control.sqlite?isolation_level=IMMEDIATE | |
571 2020-03-19 13:08:41,894 INFO [galaxy.model.migrate.check] Creating database for URI [sqlite:////private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy.sqlite?isolation_level=IMMEDIATE] | |
572 2020-03-19 13:08:41,900 INFO [galaxy.model.migrate.check] Creating new database from scratch, skipping migrations | |
573 2020-03-19 13:08:42,531 INFO [galaxy.config] Install database targetting Galaxy's database configuration. | |
574 2020-03-19 13:08:42,829 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/all_fasta.loc, reading sample | |
575 2020-03-19 13:08:42,830 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/bfast_indexes.loc, reading sample | |
576 2020-03-19 13:08:42,831 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/blastdb.loc, reading sample | |
577 2020-03-19 13:08:42,832 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/blastdb_p.loc, reading sample | |
578 2020-03-19 13:08:42,832 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/blastdb_d.loc, reading sample | |
579 2020-03-19 13:08:42,833 WARNI [galaxy.tools.data] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes' | |
580 2020-03-19 13:08:42,833 WARNI [galaxy.tools.data] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color' | |
581 2020-03-19 13:08:42,833 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/maf_index.loc, reading sample | |
582 2020-03-19 13:08:42,835 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/ngs_sim_fasta.loc, reading sample | |
583 2020-03-19 13:08:42,835 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/perm_base_index.loc, reading sample | |
584 2020-03-19 13:08:42,836 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/perm_color_index.loc, reading sample | |
585 2020-03-19 13:08:42,836 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/picard_index.loc, reading sample | |
586 2020-03-19 13:08:42,837 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/picard_index.loc, reading sample | |
587 2020-03-19 13:08:42,838 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/mosaik_index.loc, reading sample | |
588 2020-03-19 13:08:42,838 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/twobit.loc, reading sample | |
589 2020-03-19 13:08:43,014 WARNI [galaxy.tools.data] Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields): | |
590 <Server-Side Genome List> | |
591 2020-03-19 13:08:43,017 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/liftOver.loc, reading sample | |
592 2020-03-19 13:08:43,018 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/bam_iobio.loc, reading sample | |
593 2020-03-19 13:08:43,019 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/vcf_iobio.loc, reading sample | |
594 2020-03-19 13:08:43,019 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/biom_simple_display.loc, reading sample | |
595 2020-03-19 13:08:43,020 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/intermine_simple_display.loc, reading sample | |
596 2020-03-19 13:08:43,021 INFO [galaxy.tools.data] Could not find tool data /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tool-data/icn3d_simple_display.loc, reading sample | |
597 2020-03-19 13:08:43,093 INFO [galaxy.web_stack.handlers] JobConfiguration: No job handler assignment method is set, defaulting to 'db-preassign', set the `assign_with` attribute on <handlers> to override the default | |
598 2020-03-19 13:08:43,094 INFO [galaxy.jobs] Job handler assignment methods set to: db-preassign | |
599 2020-03-19 13:08:43,094 INFO [galaxy.jobs] Tag [_default_] handlers: main | |
600 2020-03-19 13:08:43,342 WARNI [galaxy.tools] The default shed tool config file (/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/lib/galaxy/config/sample/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
601 2020-03-19 13:08:43,342 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/tool_conf.xml | |
602 2020-03-19 13:08:43,457 WARNI [galaxy.tools] The default shed tool config file (/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/lib/galaxy/config/sample/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
603 2020-03-19 13:08:43,457 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/shed_tools_conf.xml | |
604 2020-03-19 13:08:43,457 WARNI [galaxy.tools] The default shed tool config file (/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/lib/galaxy/config/sample/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
605 2020-03-19 13:08:43,457 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/empty_tool_conf.xml | |
606 2020-03-19 13:08:44,009 INFO [galaxy.jobs] Handler 'main' will load all configured runner plugins | |
607 2020-03-19 13:08:44,062 INFO [galaxy.jobs.handler] job handler stop queue started | |
608 2020-03-19 13:08:44,076 INFO [galaxy.jobs.handler] job handler queue started | |
609 2020-03-19 13:08:44,079 INFO [galaxy.jobs.handler] job handler stop queue started | |
610 2020-03-19 13:08:44,101 INFO [galaxy.workflow.scheduling_manager] No workflow schedulers plugin config file defined, using default scheduler. | |
611 2020-03-19 13:08:44,125 INFO [galaxy.app] Galaxy app startup finished (3415.358 ms) | |
612 2020-03-19 13:08:45,281 INFO [galaxy.queue_worker] Binding and starting galaxy control worker for main | |
613 2020-03-19 13:08:45,284 INFO [galaxy.web_stack] Galaxy server instance 'main' is running | |
614 /Users/jj/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:666: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. | |
615 "storage." % (dialect.name, dialect.driver) | |
616 ( optitype ) > Test-1 ... 2020-03-19 13:08:46,121 INFO [galaxy.tools] Validated and populated state for tool request (22.694 ms) | |
617 2020-03-19 13:08:46,334 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 1 | |
618 2020-03-19 13:08:46,394 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=1,tool_id=upload1] (18.226 ms) | |
619 2020-03-19 13:08:46,394 INFO [galaxy.web_stack.handlers] (Job[id=1,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method | |
620 2020-03-19 13:08:47,463 INFO [galaxy.jobs.handler] (1) Job dispatched | |
621 2020-03-19 13:08:47,711 INFO [galaxy.jobs.command_factory] Built script [/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/1/tool_script.sh] for tool command [python '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tools/data_source/upload.py' /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/1/registry.xml /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/1/upload_params.json 1:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/1/working/dataset_eff120a9-00d7-49cb-b499-a1aa4d89b675_files:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/e/f/f/dataset_eff120a9-00d7-49cb-b499-a1aa4d89b675.dat] | |
622 2020-03-19 13:08:59,952 INFO [galaxy.tools] Validated and populated state for tool request (16.296 ms) | |
623 2020-03-19 13:09:00,105 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 2 | |
624 2020-03-19 13:09:00,157 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=2,tool_id=upload1] (23.682 ms) | |
625 2020-03-19 13:09:00,157 INFO [galaxy.web_stack.handlers] (Job[id=2,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method | |
626 2020-03-19 13:09:01,142 INFO [galaxy.jobs.handler] (2) Job dispatched | |
627 2020-03-19 13:09:01,352 INFO [galaxy.jobs.command_factory] Built script [/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/2/tool_script.sh] for tool command [python '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tools/data_source/upload.py' /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/2/registry.xml /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/2/upload_params.json 2:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/2/working/dataset_022eddc9-7baf-417f-bf3d-c0ac83dec823_files:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/0/2/2/dataset_022eddc9-7baf-417f-bf3d-c0ac83dec823.dat] | |
628 2020-03-19 13:09:06,983 INFO [galaxy.tools] Validated and populated state for tool request (23.608 ms) | |
629 2020-03-19 13:09:07,003 INFO [galaxy.tools.actions] Handled output named coverage_plot for tool optitype (2.875 ms) | |
630 2020-03-19 13:09:07,005 INFO [galaxy.tools.actions] Handled output named result for tool optitype (2.115 ms) | |
631 2020-03-19 13:09:07,036 INFO [galaxy.tools.actions] Added output datasets to history (30.977 ms) | |
632 2020-03-19 13:09:07,038 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=optitype] complete, ready to be enqueued (2.073 ms) | |
633 2020-03-19 13:09:07,106 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=3,tool_id=optitype] (67.169 ms) | |
634 2020-03-19 13:09:07,106 INFO [galaxy.web_stack.handlers] (Job[id=3,tool_id=optitype]) Handler 'main' assigned using 'db-preassign' assignment method | |
635 2020-03-19 13:09:07,511 INFO [galaxy.jobs.handler] (3) Job dispatched | |
636 | |
637 PackagesNotFoundError: The following packages are not available from current channels: | |
638 | |
639 - optitype=1.3.2 | |
640 | |
641 Current channels: | |
642 | |
643 - https://conda.anaconda.org/iuc/osx-64 | |
644 - https://conda.anaconda.org/iuc/noarch | |
645 - https://conda.anaconda.org/conda-forge/osx-64 | |
646 - https://conda.anaconda.org/conda-forge/noarch | |
647 - https://conda.anaconda.org/bioconda/osx-64 | |
648 - https://conda.anaconda.org/bioconda/noarch | |
649 - https://repo.anaconda.com/pkgs/main/osx-64 | |
650 - https://repo.anaconda.com/pkgs/main/noarch | |
651 - https://repo.anaconda.com/pkgs/free/osx-64 | |
652 - https://repo.anaconda.com/pkgs/free/noarch | |
653 - https://repo.anaconda.com/pkgs/r/osx-64 | |
654 - https://repo.anaconda.com/pkgs/r/noarch | |
655 | |
656 To search for alternate channels that may provide the conda package you're | |
657 looking for, navigate to | |
658 | |
659 https://anaconda.org | |
660 | |
661 and use the search bar at the top of the page. | |
662 | |
663 | |
664 | |
665 PackagesNotFoundError: The following packages are not available from current channels: | |
666 | |
667 - optitype=1.3.2 | |
668 | |
669 Current channels: | |
670 | |
671 - https://conda.anaconda.org/iuc/osx-64 | |
672 - https://conda.anaconda.org/iuc/noarch | |
673 - https://conda.anaconda.org/conda-forge/osx-64 | |
674 - https://conda.anaconda.org/conda-forge/noarch | |
675 - https://conda.anaconda.org/bioconda/osx-64 | |
676 - https://conda.anaconda.org/bioconda/noarch | |
677 - https://repo.anaconda.com/pkgs/main/osx-64 | |
678 - https://repo.anaconda.com/pkgs/main/noarch | |
679 - https://repo.anaconda.com/pkgs/free/osx-64 | |
680 - https://repo.anaconda.com/pkgs/free/noarch | |
681 - https://repo.anaconda.com/pkgs/r/osx-64 | |
682 - https://repo.anaconda.com/pkgs/r/noarch | |
683 | |
684 To search for alternate channels that may provide the conda package you're | |
685 looking for, navigate to | |
686 | |
687 https://anaconda.org | |
688 | |
689 and use the search bar at the top of the page. | |
690 | |
691 | |
692 | |
693 PackagesNotFoundError: The following packages are not available from current channels: | |
694 | |
695 - optitype | |
696 | |
697 Current channels: | |
698 | |
699 - https://conda.anaconda.org/iuc/osx-64 | |
700 - https://conda.anaconda.org/iuc/noarch | |
701 - https://conda.anaconda.org/conda-forge/osx-64 | |
702 - https://conda.anaconda.org/conda-forge/noarch | |
703 - https://conda.anaconda.org/bioconda/osx-64 | |
704 - https://conda.anaconda.org/bioconda/noarch | |
705 - https://repo.anaconda.com/pkgs/main/osx-64 | |
706 - https://repo.anaconda.com/pkgs/main/noarch | |
707 - https://repo.anaconda.com/pkgs/free/osx-64 | |
708 - https://repo.anaconda.com/pkgs/free/noarch | |
709 - https://repo.anaconda.com/pkgs/r/osx-64 | |
710 - https://repo.anaconda.com/pkgs/r/noarch | |
711 | |
712 To search for alternate channels that may provide the conda package you're | |
713 looking for, navigate to | |
714 | |
715 https://anaconda.org | |
716 | |
717 and use the search bar at the top of the page. | |
718 | |
719 | |
720 | |
721 PackagesNotFoundError: The following packages are not available from current channels: | |
722 | |
723 - optitype | |
724 | |
725 Current channels: | |
726 | |
727 - https://conda.anaconda.org/iuc/osx-64 | |
728 - https://conda.anaconda.org/iuc/noarch | |
729 - https://conda.anaconda.org/conda-forge/osx-64 | |
730 - https://conda.anaconda.org/conda-forge/noarch | |
731 - https://conda.anaconda.org/bioconda/osx-64 | |
732 - https://conda.anaconda.org/bioconda/noarch | |
733 - https://repo.anaconda.com/pkgs/main/osx-64 | |
734 - https://repo.anaconda.com/pkgs/main/noarch | |
735 - https://repo.anaconda.com/pkgs/free/osx-64 | |
736 - https://repo.anaconda.com/pkgs/free/noarch | |
737 - https://repo.anaconda.com/pkgs/r/osx-64 | |
738 - https://repo.anaconda.com/pkgs/r/noarch | |
739 | |
740 To search for alternate channels that may provide the conda package you're | |
741 looking for, navigate to | |
742 | |
743 https://anaconda.org | |
744 | |
745 and use the search bar at the top of the page. | |
746 | |
747 | |
748 | |
749 PackagesNotFoundError: The following packages are not available from current channels: | |
750 | |
751 - optitype=1.3.2 | |
752 | |
753 Current channels: | |
754 | |
755 - https://conda.anaconda.org/iuc/osx-64 | |
756 - https://conda.anaconda.org/iuc/noarch | |
757 - https://conda.anaconda.org/conda-forge/osx-64 | |
758 - https://conda.anaconda.org/conda-forge/noarch | |
759 - https://conda.anaconda.org/bioconda/osx-64 | |
760 - https://conda.anaconda.org/bioconda/noarch | |
761 - https://repo.anaconda.com/pkgs/main/osx-64 | |
762 - https://repo.anaconda.com/pkgs/main/noarch | |
763 - https://repo.anaconda.com/pkgs/free/osx-64 | |
764 - https://repo.anaconda.com/pkgs/free/noarch | |
765 - https://repo.anaconda.com/pkgs/r/osx-64 | |
766 - https://repo.anaconda.com/pkgs/r/noarch | |
767 | |
768 To search for alternate channels that may provide the conda package you're | |
769 looking for, navigate to | |
770 | |
771 https://anaconda.org | |
772 | |
773 and use the search bar at the top of the page. | |
774 | |
775 | |
776 | |
777 PackagesNotFoundError: The following packages are not available from current channels: | |
778 | |
779 - optitype=1.3.2 | |
780 | |
781 Current channels: | |
782 | |
783 - https://conda.anaconda.org/iuc/osx-64 | |
784 - https://conda.anaconda.org/iuc/noarch | |
785 - https://conda.anaconda.org/conda-forge/osx-64 | |
786 - https://conda.anaconda.org/conda-forge/noarch | |
787 - https://conda.anaconda.org/bioconda/osx-64 | |
788 - https://conda.anaconda.org/bioconda/noarch | |
789 - https://repo.anaconda.com/pkgs/main/osx-64 | |
790 - https://repo.anaconda.com/pkgs/main/noarch | |
791 - https://repo.anaconda.com/pkgs/free/osx-64 | |
792 - https://repo.anaconda.com/pkgs/free/noarch | |
793 - https://repo.anaconda.com/pkgs/r/osx-64 | |
794 - https://repo.anaconda.com/pkgs/r/noarch | |
795 | |
796 To search for alternate channels that may provide the conda package you're | |
797 looking for, navigate to | |
798 | |
799 https://anaconda.org | |
800 | |
801 and use the search bar at the top of the page. | |
802 | |
803 | |
804 | |
805 PackagesNotFoundError: The following packages are not available from current channels: | |
806 | |
807 - optitype | |
808 | |
809 Current channels: | |
810 | |
811 - https://conda.anaconda.org/iuc/osx-64 | |
812 - https://conda.anaconda.org/iuc/noarch | |
813 - https://conda.anaconda.org/conda-forge/osx-64 | |
814 - https://conda.anaconda.org/conda-forge/noarch | |
815 - https://conda.anaconda.org/bioconda/osx-64 | |
816 - https://conda.anaconda.org/bioconda/noarch | |
817 - https://repo.anaconda.com/pkgs/main/osx-64 | |
818 - https://repo.anaconda.com/pkgs/main/noarch | |
819 - https://repo.anaconda.com/pkgs/free/osx-64 | |
820 - https://repo.anaconda.com/pkgs/free/noarch | |
821 - https://repo.anaconda.com/pkgs/r/osx-64 | |
822 - https://repo.anaconda.com/pkgs/r/noarch | |
823 | |
824 To search for alternate channels that may provide the conda package you're | |
825 looking for, navigate to | |
826 | |
827 https://anaconda.org | |
828 | |
829 and use the search bar at the top of the page. | |
830 | |
831 | |
832 | |
833 PackagesNotFoundError: The following packages are not available from current channels: | |
834 | |
835 - optitype | |
836 | |
837 Current channels: | |
838 | |
839 - https://conda.anaconda.org/iuc/osx-64 | |
840 - https://conda.anaconda.org/iuc/noarch | |
841 - https://conda.anaconda.org/conda-forge/osx-64 | |
842 - https://conda.anaconda.org/conda-forge/noarch | |
843 - https://conda.anaconda.org/bioconda/osx-64 | |
844 - https://conda.anaconda.org/bioconda/noarch | |
845 - https://repo.anaconda.com/pkgs/main/osx-64 | |
846 - https://repo.anaconda.com/pkgs/main/noarch | |
847 - https://repo.anaconda.com/pkgs/free/osx-64 | |
848 - https://repo.anaconda.com/pkgs/free/noarch | |
849 - https://repo.anaconda.com/pkgs/r/osx-64 | |
850 - https://repo.anaconda.com/pkgs/r/noarch | |
851 | |
852 To search for alternate channels that may provide the conda package you're | |
853 looking for, navigate to | |
854 | |
855 https://anaconda.org | |
856 | |
857 and use the search bar at the top of the page. | |
858 | |
859 | |
860 2020-03-19 13:10:02,015 INFO [galaxy.jobs.command_factory] Built script [/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/3/tool_script.sh] for tool command [ln -s '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/e/f/f/dataset_eff120a9-00d7-49cb-b499-a1aa4d89b675.dat' reads_1.fastq && ln -s '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/0/2/2/dataset_022eddc9-7baf-417f-bf3d-c0ac83dec823.dat' reads_2.fastq && RAZERS3=`which razers3` && sed "s#path_to_razers3#$RAZERS3#" '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/3/configs/tmpTaGSuA' | sed "s/threads=16/threads=$GALAXY_SLOTS/" > config.ini && OptiTypePipeline.py --rna --input reads_1.fastq reads_2.fastq --config "`pwd`/config.ini" --outdir output_dir && cp output_dir/*/*_coverage_plot.pdf /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/d/5/f/dataset_d5ff36fd-e6ca-4e61-89ee-dc626fb865fe.dat && cp output_dir/*/*_result.tsv /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/1/0/7/dataset_10776cbe-d39b-419d-9014-c8b440e96190.dat] | |
861 2020-03-19 13:10:05,636 INFO [galaxy.tool_util.output_checker] Job 3: {'code_desc': '', 'error_level': 3, 'type': 'exit_code', 'exit_code': 1, 'desc': 'Fatal error: Exit code 1 ()'} | |
862 FAIL | |
863 ( optitype ) > Test-2 ... 2020-03-19 13:10:51,885 INFO [galaxy.tools] Validated and populated state for tool request (22.757 ms) | |
864 2020-03-19 13:10:52,059 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 4 | |
865 2020-03-19 13:10:52,103 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=4,tool_id=upload1] (16.285 ms) | |
866 2020-03-19 13:10:52,104 INFO [galaxy.web_stack.handlers] (Job[id=4,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method | |
867 2020-03-19 13:10:52,739 INFO [galaxy.jobs.handler] (4) Job dispatched | |
868 2020-03-19 13:10:52,939 INFO [galaxy.jobs.command_factory] Built script [/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/4/tool_script.sh] for tool command [python '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tools/data_source/upload.py' /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/4/registry.xml /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/4/upload_params.json 5:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/4/working/dataset_e0780a69-3eba-44ba-a023-0167344a63fd_files:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/e/0/7/dataset_e0780a69-3eba-44ba-a023-0167344a63fd.dat] | |
869 2020-03-19 13:10:58,904 INFO [galaxy.tools] Validated and populated state for tool request (19.855 ms) | |
870 2020-03-19 13:10:59,090 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 5 | |
871 2020-03-19 13:10:59,135 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=5,tool_id=upload1] (15.200 ms) | |
872 2020-03-19 13:10:59,135 INFO [galaxy.web_stack.handlers] (Job[id=5,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method | |
873 2020-03-19 13:11:00,120 INFO [galaxy.jobs.handler] (5) Job dispatched | |
874 2020-03-19 13:11:00,313 INFO [galaxy.jobs.command_factory] Built script [/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/5/tool_script.sh] for tool command [python '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/tools/data_source/upload.py' /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/5/registry.xml /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/5/upload_params.json 6:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/5/working/dataset_5d34cb9a-478f-46a2-8a64-3534234ee2d3_files:/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/5/d/3/dataset_5d34cb9a-478f-46a2-8a64-3534234ee2d3.dat] | |
875 2020-03-19 13:11:05,958 INFO [galaxy.tools] Validated and populated state for tool request (21.036 ms) | |
876 2020-03-19 13:11:05,975 INFO [galaxy.tools.actions] Handled output named coverage_plot for tool optitype (0.857 ms) | |
877 2020-03-19 13:11:05,976 INFO [galaxy.tools.actions] Handled output named result for tool optitype (0.626 ms) | |
878 2020-03-19 13:11:06,008 INFO [galaxy.tools.actions] Added output datasets to history (31.926 ms) | |
879 2020-03-19 13:11:06,010 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=optitype] complete, ready to be enqueued (1.959 ms) | |
880 2020-03-19 13:11:06,082 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=6,tool_id=optitype] (71.447 ms) | |
881 2020-03-19 13:11:06,082 INFO [galaxy.web_stack.handlers] (Job[id=6,tool_id=optitype]) Handler 'main' assigned using 'db-preassign' assignment method | |
882 2020-03-19 13:11:06,400 INFO [galaxy.jobs.handler] (6) Job dispatched | |
883 | |
884 PackagesNotFoundError: The following packages are not available from current channels: | |
885 | |
886 - optitype=1.3.2 | |
887 | |
888 Current channels: | |
889 | |
890 - https://conda.anaconda.org/iuc/osx-64 | |
891 - https://conda.anaconda.org/iuc/noarch | |
892 - https://conda.anaconda.org/conda-forge/osx-64 | |
893 - https://conda.anaconda.org/conda-forge/noarch | |
894 - https://conda.anaconda.org/bioconda/osx-64 | |
895 - https://conda.anaconda.org/bioconda/noarch | |
896 - https://repo.anaconda.com/pkgs/main/osx-64 | |
897 - https://repo.anaconda.com/pkgs/main/noarch | |
898 - https://repo.anaconda.com/pkgs/free/osx-64 | |
899 - https://repo.anaconda.com/pkgs/free/noarch | |
900 - https://repo.anaconda.com/pkgs/r/osx-64 | |
901 - https://repo.anaconda.com/pkgs/r/noarch | |
902 | |
903 To search for alternate channels that may provide the conda package you're | |
904 looking for, navigate to | |
905 | |
906 https://anaconda.org | |
907 | |
908 and use the search bar at the top of the page. | |
909 | |
910 | |
911 | |
912 PackagesNotFoundError: The following packages are not available from current channels: | |
913 | |
914 - optitype=1.3.2 | |
915 | |
916 Current channels: | |
917 | |
918 - https://conda.anaconda.org/iuc/osx-64 | |
919 - https://conda.anaconda.org/iuc/noarch | |
920 - https://conda.anaconda.org/conda-forge/osx-64 | |
921 - https://conda.anaconda.org/conda-forge/noarch | |
922 - https://conda.anaconda.org/bioconda/osx-64 | |
923 - https://conda.anaconda.org/bioconda/noarch | |
924 - https://repo.anaconda.com/pkgs/main/osx-64 | |
925 - https://repo.anaconda.com/pkgs/main/noarch | |
926 - https://repo.anaconda.com/pkgs/free/osx-64 | |
927 - https://repo.anaconda.com/pkgs/free/noarch | |
928 - https://repo.anaconda.com/pkgs/r/osx-64 | |
929 - https://repo.anaconda.com/pkgs/r/noarch | |
930 | |
931 To search for alternate channels that may provide the conda package you're | |
932 looking for, navigate to | |
933 | |
934 https://anaconda.org | |
935 | |
936 and use the search bar at the top of the page. | |
937 | |
938 | |
939 | |
940 PackagesNotFoundError: The following packages are not available from current channels: | |
941 | |
942 - optitype | |
943 | |
944 Current channels: | |
945 | |
946 - https://conda.anaconda.org/iuc/osx-64 | |
947 - https://conda.anaconda.org/iuc/noarch | |
948 - https://conda.anaconda.org/conda-forge/osx-64 | |
949 - https://conda.anaconda.org/conda-forge/noarch | |
950 - https://conda.anaconda.org/bioconda/osx-64 | |
951 - https://conda.anaconda.org/bioconda/noarch | |
952 - https://repo.anaconda.com/pkgs/main/osx-64 | |
953 - https://repo.anaconda.com/pkgs/main/noarch | |
954 - https://repo.anaconda.com/pkgs/free/osx-64 | |
955 - https://repo.anaconda.com/pkgs/free/noarch | |
956 - https://repo.anaconda.com/pkgs/r/osx-64 | |
957 - https://repo.anaconda.com/pkgs/r/noarch | |
958 | |
959 To search for alternate channels that may provide the conda package you're | |
960 looking for, navigate to | |
961 | |
962 https://anaconda.org | |
963 | |
964 and use the search bar at the top of the page. | |
965 | |
966 | |
967 | |
968 PackagesNotFoundError: The following packages are not available from current channels: | |
969 | |
970 - optitype | |
971 | |
972 Current channels: | |
973 | |
974 - https://conda.anaconda.org/iuc/osx-64 | |
975 - https://conda.anaconda.org/iuc/noarch | |
976 - https://conda.anaconda.org/conda-forge/osx-64 | |
977 - https://conda.anaconda.org/conda-forge/noarch | |
978 - https://conda.anaconda.org/bioconda/osx-64 | |
979 - https://conda.anaconda.org/bioconda/noarch | |
980 - https://repo.anaconda.com/pkgs/main/osx-64 | |
981 - https://repo.anaconda.com/pkgs/main/noarch | |
982 - https://repo.anaconda.com/pkgs/free/osx-64 | |
983 - https://repo.anaconda.com/pkgs/free/noarch | |
984 - https://repo.anaconda.com/pkgs/r/osx-64 | |
985 - https://repo.anaconda.com/pkgs/r/noarch | |
986 | |
987 To search for alternate channels that may provide the conda package you're | |
988 looking for, navigate to | |
989 | |
990 https://anaconda.org | |
991 | |
992 and use the search bar at the top of the page. | |
993 | |
994 | |
995 | |
996 PackagesNotFoundError: The following packages are not available from current channels: | |
997 | |
998 - optitype=1.3.2 | |
999 | |
1000 Current channels: | |
1001 | |
1002 - https://conda.anaconda.org/iuc/osx-64 | |
1003 - https://conda.anaconda.org/iuc/noarch | |
1004 - https://conda.anaconda.org/conda-forge/osx-64 | |
1005 - https://conda.anaconda.org/conda-forge/noarch | |
1006 - https://conda.anaconda.org/bioconda/osx-64 | |
1007 - https://conda.anaconda.org/bioconda/noarch | |
1008 - https://repo.anaconda.com/pkgs/main/osx-64 | |
1009 - https://repo.anaconda.com/pkgs/main/noarch | |
1010 - https://repo.anaconda.com/pkgs/free/osx-64 | |
1011 - https://repo.anaconda.com/pkgs/free/noarch | |
1012 - https://repo.anaconda.com/pkgs/r/osx-64 | |
1013 - https://repo.anaconda.com/pkgs/r/noarch | |
1014 | |
1015 To search for alternate channels that may provide the conda package you're | |
1016 looking for, navigate to | |
1017 | |
1018 https://anaconda.org | |
1019 | |
1020 and use the search bar at the top of the page. | |
1021 | |
1022 | |
1023 | |
1024 PackagesNotFoundError: The following packages are not available from current channels: | |
1025 | |
1026 - optitype=1.3.2 | |
1027 | |
1028 Current channels: | |
1029 | |
1030 - https://conda.anaconda.org/iuc/osx-64 | |
1031 - https://conda.anaconda.org/iuc/noarch | |
1032 - https://conda.anaconda.org/conda-forge/osx-64 | |
1033 - https://conda.anaconda.org/conda-forge/noarch | |
1034 - https://conda.anaconda.org/bioconda/osx-64 | |
1035 - https://conda.anaconda.org/bioconda/noarch | |
1036 - https://repo.anaconda.com/pkgs/main/osx-64 | |
1037 - https://repo.anaconda.com/pkgs/main/noarch | |
1038 - https://repo.anaconda.com/pkgs/free/osx-64 | |
1039 - https://repo.anaconda.com/pkgs/free/noarch | |
1040 - https://repo.anaconda.com/pkgs/r/osx-64 | |
1041 - https://repo.anaconda.com/pkgs/r/noarch | |
1042 | |
1043 To search for alternate channels that may provide the conda package you're | |
1044 looking for, navigate to | |
1045 | |
1046 https://anaconda.org | |
1047 | |
1048 and use the search bar at the top of the page. | |
1049 | |
1050 | |
1051 | |
1052 PackagesNotFoundError: The following packages are not available from current channels: | |
1053 | |
1054 - optitype | |
1055 | |
1056 Current channels: | |
1057 | |
1058 - https://conda.anaconda.org/iuc/osx-64 | |
1059 - https://conda.anaconda.org/iuc/noarch | |
1060 - https://conda.anaconda.org/conda-forge/osx-64 | |
1061 - https://conda.anaconda.org/conda-forge/noarch | |
1062 - https://conda.anaconda.org/bioconda/osx-64 | |
1063 - https://conda.anaconda.org/bioconda/noarch | |
1064 - https://repo.anaconda.com/pkgs/main/osx-64 | |
1065 - https://repo.anaconda.com/pkgs/main/noarch | |
1066 - https://repo.anaconda.com/pkgs/free/osx-64 | |
1067 - https://repo.anaconda.com/pkgs/free/noarch | |
1068 - https://repo.anaconda.com/pkgs/r/osx-64 | |
1069 - https://repo.anaconda.com/pkgs/r/noarch | |
1070 | |
1071 To search for alternate channels that may provide the conda package you're | |
1072 looking for, navigate to | |
1073 | |
1074 https://anaconda.org | |
1075 | |
1076 and use the search bar at the top of the page. | |
1077 | |
1078 | |
1079 | |
1080 PackagesNotFoundError: The following packages are not available from current channels: | |
1081 | |
1082 - optitype | |
1083 | |
1084 Current channels: | |
1085 | |
1086 - https://conda.anaconda.org/iuc/osx-64 | |
1087 - https://conda.anaconda.org/iuc/noarch | |
1088 - https://conda.anaconda.org/conda-forge/osx-64 | |
1089 - https://conda.anaconda.org/conda-forge/noarch | |
1090 - https://conda.anaconda.org/bioconda/osx-64 | |
1091 - https://conda.anaconda.org/bioconda/noarch | |
1092 - https://repo.anaconda.com/pkgs/main/osx-64 | |
1093 - https://repo.anaconda.com/pkgs/main/noarch | |
1094 - https://repo.anaconda.com/pkgs/free/osx-64 | |
1095 - https://repo.anaconda.com/pkgs/free/noarch | |
1096 - https://repo.anaconda.com/pkgs/r/osx-64 | |
1097 - https://repo.anaconda.com/pkgs/r/noarch | |
1098 | |
1099 To search for alternate channels that may provide the conda package you're | |
1100 looking for, navigate to | |
1101 | |
1102 https://anaconda.org | |
1103 | |
1104 and use the search bar at the top of the page. | |
1105 | |
1106 | |
1107 2020-03-19 13:11:40,443 INFO [galaxy.jobs.command_factory] Built script [/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/6/tool_script.sh] for tool command [ln -s '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/e/0/7/dataset_e0780a69-3eba-44ba-a023-0167344a63fd.dat' reads_1.fastq && ln -s '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/5/d/3/dataset_5d34cb9a-478f-46a2-8a64-3534234ee2d3.dat' reads_2.fastq && RAZERS3=`which razers3` && sed "s#path_to_razers3#$RAZERS3#" '/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/job_working_directory/000/6/configs/tmpn4N9W7' | sed "s/threads=16/threads=$GALAXY_SLOTS/" > config.ini && OptiTypePipeline.py --dna --input reads_1.fastq reads_2.fastq --config "`pwd`/config.ini" --outdir output_dir && cp output_dir/*/*_coverage_plot.pdf /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/2/5/b/dataset_25b6ea5d-79fd-4cee-947a-fefbcba3f2e4.dat && cp output_dir/*/*_result.tsv /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/files/0/1/b/dataset_01b4e0c5-2563-4dc1-8557-411da38239fe.dat] | |
1108 2020-03-19 13:11:43,559 INFO [galaxy.tool_util.output_checker] Job 6: {'code_desc': '', 'error_level': 3, 'type': 'exit_code', 'exit_code': 1, 'desc': 'Fatal error: Exit code 1 ()'} | |
1109 FAIL | |
1110 | |
1111 ====================================================================== | |
1112 FAIL: ( optitype ) > Test-1 | |
1113 ---------------------------------------------------------------------- | |
1114 Traceback (most recent call last): | |
1115 File "/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/test/functional/test_toolbox.py", line 99, in test_tool | |
1116 self.do_it(tool_version=tool_version, test_index=test_index) | |
1117 File "/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/test/functional/test_toolbox.py", line 36, in do_it | |
1118 verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data) | |
1119 File "/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 789, in verify_tool | |
1120 raise e | |
1121 JobOutputsError: Job in error state. | |
1122 Job in error state. | |
1123 -------------------- >> begin captured stdout << --------------------- | |
1124 Collecting package metadata: ...working... done | |
1125 Solving environment: ...working... failed | |
1126 Collecting package metadata: ...working... done | |
1127 Solving environment: ...working... failed | |
1128 Collecting package metadata: ...working... done | |
1129 Solving environment: ...working... failed | |
1130 Collecting package metadata: ...working... done | |
1131 Solving environment: ...working... failed | |
1132 Collecting package metadata: ...working... done | |
1133 Solving environment: ...working... failed | |
1134 Collecting package metadata: ...working... done | |
1135 Solving environment: ...working... failed | |
1136 Collecting package metadata: ...working... done | |
1137 Solving environment: ...working... failed | |
1138 Collecting package metadata: ...working... done | |
1139 Solving environment: ...working... failed | |
1140 Problem in history with id 2891970512fa2d5a - summary of history's datasets and jobs below. | |
1141 -------------------------------------- | |
1142 | 1 - CRC_81_N_1_fished.fastq (HID - NAME) | |
1143 | Dataset State: | |
1144 | ok | |
1145 | Dataset Blurb: | |
1146 | 1,569 sequences | |
1147 | Dataset Info: | |
1148 | uploaded fastqsanger file | |
1149 | Peek: | |
1150 | <table cellspacing="0" cellpadding="3"><tr><td>@SRR397217.2404</td></tr><tr><td>TCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGAGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACAT</td></tr><tr><td>+SRR397217.2404</td></tr><tr><td>9FEEBF?DDEE?F?ECFHDHHHHHHHEAFFF@FFHHFHHFFFHDHFHFHHFHHHHFHFHFHFHHHHHHHHHHHHHHHEHHHHHHHHHHHHHHGGHHHHHHH</td></tr><tr><td>@SRR397217.3931</td></tr></table> | |
1151 | Dataset Job Standard Output: | |
1152 | *Standard output was empty.* | |
1153 | Dataset Job Standard Error: | |
1154 | *Standard error was empty.* | |
1155 | | |
1156 -------------------------------------- | |
1157 | 2 - CRC_81_N_2_fished.fastq (HID - NAME) | |
1158 | Dataset State: | |
1159 | ok | |
1160 | Dataset Blurb: | |
1161 | 1,515 sequences | |
1162 | Dataset Info: | |
1163 | uploaded fastqsanger file | |
1164 | Peek: | |
1165 | <table cellspacing="0" cellpadding="3"><tr><td>@SRR397217.1805</td></tr><tr><td>GGAAACAGTTCCTCGGAGTGGAGAGGTTTACACCTGCCAAGTGGAGCACCCAAGCCTGACGAGCCCTCTCACAGTGGAATGGAGAGCACGGTCTGAATCTG</td></tr><tr><td>+SRR397217.1805</td></tr><tr><td>HHHHHHHHHHHHHHHHFHEHHHHFHHFHFEHHHHHFFHHFHHHHEFHFHCIGCGIHHHFHHHHFFHFHHHFHAHEHHFFHH@HEED.@EEFBGFE@EFDEA</td></tr><tr><td>@SRR397217.2316</td></tr></table> | |
1166 | Dataset Job Standard Output: | |
1167 | *Standard output was empty.* | |
1168 | Dataset Job Standard Error: | |
1169 | *Standard error was empty.* | |
1170 | | |
1171 -------------------------------------- | |
1172 | 3 - OptiType on data 2 and data 1 coverage_plot.pdf (HID - NAME) | |
1173 | Dataset State: | |
1174 | error | |
1175 | Dataset Blurb: | |
1176 | error | |
1177 | Dataset Info: | |
1178 | *Dataset info is empty.* | |
1179 | Peek: | |
1180 | None | |
1181 | Dataset Job Standard Output: | |
1182 | *Standard output was empty.* | |
1183 | Dataset Job Standard Error: | |
1184 | *Standard error was empty.* | |
1185 | | |
1186 -------------------------------------- | |
1187 | 4 - OptiType on data 2 and data 1 result.tsv (HID - NAME) | |
1188 | Dataset State: | |
1189 | error | |
1190 | Dataset Blurb: | |
1191 | error | |
1192 | Dataset Info: | |
1193 | *Dataset info is empty.* | |
1194 | Peek: | |
1195 | None | |
1196 | Dataset Job Standard Output: | |
1197 | *Standard output was empty.* | |
1198 | Dataset Job Standard Error: | |
1199 | *Standard error was empty.* | |
1200 | | |
1201 -------------------------------------- | |
1202 | Job 54f2a3a23292eb07 | |
1203 | State: | |
1204 | error | |
1205 | Update Time: | |
1206 | 2020-03-19T18:10:05.914678 | |
1207 | Create Time: | |
1208 | 2020-03-19T18:09:07.093093 | |
1209 | | |
1210 -------------------------------------- | |
1211 | Job 5729865256bc2525 | |
1212 | State: | |
1213 | ok | |
1214 | Update Time: | |
1215 | 2020-03-19T18:09:06.049350 | |
1216 | Create Time: | |
1217 | 2020-03-19T18:09:00.092142 | |
1218 | | |
1219 -------------------------------------- | |
1220 | Job 2891970512fa2d5a | |
1221 | State: | |
1222 | ok | |
1223 | Update Time: | |
1224 | 2020-03-19T18:08:53.411645 | |
1225 | Create Time: | |
1226 | 2020-03-19T18:08:46.307862 | |
1227 | | |
1228 -------------------------------------- | |
1229 Problem in history with id 2891970512fa2d5a - summary of history's datasets and jobs below. | |
1230 -------------------------------------- | |
1231 | 1 - CRC_81_N_1_fished.fastq (HID - NAME) | |
1232 | Dataset State: | |
1233 | ok | |
1234 | Dataset Blurb: | |
1235 | 1,569 sequences | |
1236 | Dataset Info: | |
1237 | uploaded fastqsanger file | |
1238 | Peek: | |
1239 | <table cellspacing="0" cellpadding="3"><tr><td>@SRR397217.2404</td></tr><tr><td>TCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGAGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACAT</td></tr><tr><td>+SRR397217.2404</td></tr><tr><td>9FEEBF?DDEE?F?ECFHDHHHHHHHEAFFF@FFHHFHHFFFHDHFHFHHFHHHHFHFHFHFHHHHHHHHHHHHHHHEHHHHHHHHHHHHHHGGHHHHHHH</td></tr><tr><td>@SRR397217.3931</td></tr></table> | |
1240 | Dataset Job Standard Output: | |
1241 | *Standard output was empty.* | |
1242 | Dataset Job Standard Error: | |
1243 | *Standard error was empty.* | |
1244 | | |
1245 -------------------------------------- | |
1246 | 2 - CRC_81_N_2_fished.fastq (HID - NAME) | |
1247 | Dataset State: | |
1248 | ok | |
1249 | Dataset Blurb: | |
1250 | 1,515 sequences | |
1251 | Dataset Info: | |
1252 | uploaded fastqsanger file | |
1253 | Peek: | |
1254 | <table cellspacing="0" cellpadding="3"><tr><td>@SRR397217.1805</td></tr><tr><td>GGAAACAGTTCCTCGGAGTGGAGAGGTTTACACCTGCCAAGTGGAGCACCCAAGCCTGACGAGCCCTCTCACAGTGGAATGGAGAGCACGGTCTGAATCTG</td></tr><tr><td>+SRR397217.1805</td></tr><tr><td>HHHHHHHHHHHHHHHHFHEHHHHFHHFHFEHHHHHFFHHFHHHHEFHFHCIGCGIHHHFHHHHFFHFHHHFHAHEHHFFHH@HEED.@EEFBGFE@EFDEA</td></tr><tr><td>@SRR397217.2316</td></tr></table> | |
1255 | Dataset Job Standard Output: | |
1256 | *Standard output was empty.* | |
1257 | Dataset Job Standard Error: | |
1258 | *Standard error was empty.* | |
1259 | | |
1260 -------------------------------------- | |
1261 | 3 - OptiType on data 2 and data 1 coverage_plot.pdf (HID - NAME) | |
1262 | Dataset State: | |
1263 | error | |
1264 | Dataset Blurb: | |
1265 | error | |
1266 | Dataset Info: | |
1267 | *Dataset info is empty.* | |
1268 | Peek: | |
1269 | None | |
1270 | Dataset Job Standard Output: | |
1271 | *Standard output was empty.* | |
1272 | Dataset Job Standard Error: | |
1273 | *Standard error was empty.* | |
1274 | | |
1275 -------------------------------------- | |
1276 | 4 - OptiType on data 2 and data 1 result.tsv (HID - NAME) | |
1277 | Dataset State: | |
1278 | error | |
1279 | Dataset Blurb: | |
1280 | error | |
1281 | Dataset Info: | |
1282 | *Dataset info is empty.* | |
1283 | Peek: | |
1284 | None | |
1285 | Dataset Job Standard Output: | |
1286 | *Standard output was empty.* | |
1287 | Dataset Job Standard Error: | |
1288 | *Standard error was empty.* | |
1289 | | |
1290 -------------------------------------- | |
1291 | Job 54f2a3a23292eb07 | |
1292 | State: | |
1293 | error | |
1294 | Update Time: | |
1295 | 2020-03-19T18:10:05.914678 | |
1296 | Create Time: | |
1297 | 2020-03-19T18:09:07.093093 | |
1298 | | |
1299 -------------------------------------- | |
1300 | Job 5729865256bc2525 | |
1301 | State: | |
1302 | ok | |
1303 | Update Time: | |
1304 | 2020-03-19T18:09:06.049350 | |
1305 | Create Time: | |
1306 | 2020-03-19T18:09:00.092142 | |
1307 | | |
1308 -------------------------------------- | |
1309 | Job 2891970512fa2d5a | |
1310 | State: | |
1311 | ok | |
1312 | Update Time: | |
1313 | 2020-03-19T18:08:53.411645 | |
1314 | Create Time: | |
1315 | 2020-03-19T18:08:46.307862 | |
1316 | | |
1317 -------------------------------------- | |
1318 | |
1319 --------------------- >> end captured stdout << ---------------------- | |
1320 | |
1321 ====================================================================== | |
1322 FAIL: ( optitype ) > Test-2 | |
1323 ---------------------------------------------------------------------- | |
1324 Traceback (most recent call last): | |
1325 File "/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/test/functional/test_toolbox.py", line 99, in test_tool | |
1326 self.do_it(tool_version=tool_version, test_index=test_index) | |
1327 File "/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/test/functional/test_toolbox.py", line 36, in do_it | |
1328 verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data) | |
1329 File "/private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 789, in verify_tool | |
1330 raise e | |
1331 JobOutputsError: Job in error state. | |
1332 Job in error state. | |
1333 -------------------- >> begin captured stdout << --------------------- | |
1334 Collecting package metadata: ...working... done | |
1335 Solving environment: ...working... failed | |
1336 Collecting package metadata: ...working... done | |
1337 Solving environment: ...working... failed | |
1338 Collecting package metadata: ...working... done | |
1339 Solving environment: ...working... failed | |
1340 Collecting package metadata: ...working... done | |
1341 Solving environment: ...working... failed | |
1342 Collecting package metadata: ...working... done | |
1343 Solving environment: ...working... failed | |
1344 Collecting package metadata: ...working... done | |
1345 Solving environment: ...working... failed | |
1346 Collecting package metadata: ...working... done | |
1347 Solving environment: ...working... failed | |
1348 Collecting package metadata: ...working... done | |
1349 Solving environment: ...working... failed | |
1350 Problem in history with id 5729865256bc2525 - summary of history's datasets and jobs below. | |
1351 -------------------------------------- | |
1352 | 1 - NA11995_SRR766010_1_fished.fastq (HID - NAME) | |
1353 | Dataset State: | |
1354 | ok | |
1355 | Dataset Blurb: | |
1356 | 1,000 sequences | |
1357 | Dataset Info: | |
1358 | uploaded fastqsanger file | |
1359 | Peek: | |
1360 | <table cellspacing="0" cellpadding="3"><tr><td>@SRR766010.692</td></tr><tr><td>TACAAAAAAATTAGCTGGGCGTGGTGGCACATGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATTGCTTGAATCTGGGAGGCAGAGCTTGCA</td></tr><tr><td>+SRR766010.692</td></tr><tr><td>3BBBCCC>>::CABB@?====66.)B@C?ECCIGEA=ECF=IHGGGHDDHDFDDGHHHBGGGF<GEIG?4HGEGGEIGIIHDGEHFEFFHHHHDDA+D<@@</td></tr><tr><td>@SRR766010.944</td></tr></table> | |
1361 | Dataset Job Standard Output: | |
1362 | *Standard output was empty.* | |
1363 | Dataset Job Standard Error: | |
1364 | *Standard error was empty.* | |
1365 | | |
1366 -------------------------------------- | |
1367 | 2 - NA11995_SRR766010_2_fished.fastq (HID - NAME) | |
1368 | Dataset State: | |
1369 | ok | |
1370 | Dataset Blurb: | |
1371 | 1,000 sequences | |
1372 | Dataset Info: | |
1373 | uploaded fastqsanger file | |
1374 | Peek: | |
1375 | <table cellspacing="0" cellpadding="3"><tr><td>@SRR766010.600</td></tr><tr><td>TCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGTTGCGACTACAGGCGCCCACCACCACGCCCAGCTAATTTTTTTTTTTTTTTTT</td></tr><tr><td>+SRR766010.600</td></tr><tr><td>CCCFFFFFHHHHHIIJJJJJJGJJIJJJJJJJJJJJFIJJJJGAHFGGFFFIIGGFFFFEDDDDDBBDDBDDDDDDDDBBDD@CDEDDDDDDDDDBDBDB5</td></tr><tr><td>@SRR766010.666</td></tr></table> | |
1376 | Dataset Job Standard Output: | |
1377 | *Standard output was empty.* | |
1378 | Dataset Job Standard Error: | |
1379 | *Standard error was empty.* | |
1380 | | |
1381 -------------------------------------- | |
1382 | 3 - OptiType on data 2 and data 1 coverage_plot.pdf (HID - NAME) | |
1383 | Dataset State: | |
1384 | error | |
1385 | Dataset Blurb: | |
1386 | error | |
1387 | Dataset Info: | |
1388 | *Dataset info is empty.* | |
1389 | Peek: | |
1390 | None | |
1391 | Dataset Job Standard Output: | |
1392 | *Standard output was empty.* | |
1393 | Dataset Job Standard Error: | |
1394 | *Standard error was empty.* | |
1395 | | |
1396 -------------------------------------- | |
1397 | 4 - OptiType on data 2 and data 1 result.tsv (HID - NAME) | |
1398 | Dataset State: | |
1399 | error | |
1400 | Dataset Blurb: | |
1401 | error | |
1402 | Dataset Info: | |
1403 | *Dataset info is empty.* | |
1404 | Peek: | |
1405 | None | |
1406 | Dataset Job Standard Output: | |
1407 | *Standard output was empty.* | |
1408 | Dataset Job Standard Error: | |
1409 | *Standard error was empty.* | |
1410 | | |
1411 -------------------------------------- | |
1412 | Job fa6d20d0fb68383f | |
1413 | State: | |
1414 | error | |
1415 | Update Time: | |
1416 | 2020-03-19T18:11:43.802965 | |
1417 | Create Time: | |
1418 | 2020-03-19T18:11:06.066886 | |
1419 | | |
1420 -------------------------------------- | |
1421 | Job 7b55dbb89df8f4e5 | |
1422 | State: | |
1423 | ok | |
1424 | Update Time: | |
1425 | 2020-03-19T18:11:05.241405 | |
1426 | Create Time: | |
1427 | 2020-03-19T18:10:59.076071 | |
1428 | | |
1429 -------------------------------------- | |
1430 | Job 8155e4b4bf1581ff | |
1431 | State: | |
1432 | ok | |
1433 | Update Time: | |
1434 | 2020-03-19T18:10:58.105973 | |
1435 | Create Time: | |
1436 | 2020-03-19T18:10:52.045196 | |
1437 | | |
1438 -------------------------------------- | |
1439 Problem in history with id 5729865256bc2525 - summary of history's datasets and jobs below. | |
1440 -------------------------------------- | |
1441 | 1 - NA11995_SRR766010_1_fished.fastq (HID - NAME) | |
1442 | Dataset State: | |
1443 | ok | |
1444 | Dataset Blurb: | |
1445 | 1,000 sequences | |
1446 | Dataset Info: | |
1447 | uploaded fastqsanger file | |
1448 | Peek: | |
1449 | <table cellspacing="0" cellpadding="3"><tr><td>@SRR766010.692</td></tr><tr><td>TACAAAAAAATTAGCTGGGCGTGGTGGCACATGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATTGCTTGAATCTGGGAGGCAGAGCTTGCA</td></tr><tr><td>+SRR766010.692</td></tr><tr><td>3BBBCCC>>::CABB@?====66.)B@C?ECCIGEA=ECF=IHGGGHDDHDFDDGHHHBGGGF<GEIG?4HGEGGEIGIIHDGEHFEFFHHHHDDA+D<@@</td></tr><tr><td>@SRR766010.944</td></tr></table> | |
1450 | Dataset Job Standard Output: | |
1451 | *Standard output was empty.* | |
1452 | Dataset Job Standard Error: | |
1453 | *Standard error was empty.* | |
1454 | | |
1455 -------------------------------------- | |
1456 | 2 - NA11995_SRR766010_2_fished.fastq (HID - NAME) | |
1457 | Dataset State: | |
1458 | ok | |
1459 | Dataset Blurb: | |
1460 | 1,000 sequences | |
1461 | Dataset Info: | |
1462 | uploaded fastqsanger file | |
1463 | Peek: | |
1464 | <table cellspacing="0" cellpadding="3"><tr><td>@SRR766010.600</td></tr><tr><td>TCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGTTGCGACTACAGGCGCCCACCACCACGCCCAGCTAATTTTTTTTTTTTTTTTT</td></tr><tr><td>+SRR766010.600</td></tr><tr><td>CCCFFFFFHHHHHIIJJJJJJGJJIJJJJJJJJJJJFIJJJJGAHFGGFFFIIGGFFFFEDDDDDBBDDBDDDDDDDDBBDD@CDEDDDDDDDDDBDBDB5</td></tr><tr><td>@SRR766010.666</td></tr></table> | |
1465 | Dataset Job Standard Output: | |
1466 | *Standard output was empty.* | |
1467 | Dataset Job Standard Error: | |
1468 | *Standard error was empty.* | |
1469 | | |
1470 -------------------------------------- | |
1471 | 3 - OptiType on data 2 and data 1 coverage_plot.pdf (HID - NAME) | |
1472 | Dataset State: | |
1473 | error | |
1474 | Dataset Blurb: | |
1475 | error | |
1476 | Dataset Info: | |
1477 | *Dataset info is empty.* | |
1478 | Peek: | |
1479 | None | |
1480 | Dataset Job Standard Output: | |
1481 | *Standard output was empty.* | |
1482 | Dataset Job Standard Error: | |
1483 | *Standard error was empty.* | |
1484 | | |
1485 -------------------------------------- | |
1486 | 4 - OptiType on data 2 and data 1 result.tsv (HID - NAME) | |
1487 | Dataset State: | |
1488 | error | |
1489 | Dataset Blurb: | |
1490 | error | |
1491 | Dataset Info: | |
1492 | *Dataset info is empty.* | |
1493 | Peek: | |
1494 | None | |
1495 | Dataset Job Standard Output: | |
1496 | *Standard output was empty.* | |
1497 | Dataset Job Standard Error: | |
1498 | *Standard error was empty.* | |
1499 | | |
1500 -------------------------------------- | |
1501 | Job fa6d20d0fb68383f | |
1502 | State: | |
1503 | error | |
1504 | Update Time: | |
1505 | 2020-03-19T18:11:43.802965 | |
1506 | Create Time: | |
1507 | 2020-03-19T18:11:06.066886 | |
1508 | | |
1509 -------------------------------------- | |
1510 | Job 7b55dbb89df8f4e5 | |
1511 | State: | |
1512 | ok | |
1513 | Update Time: | |
1514 | 2020-03-19T18:11:05.241405 | |
1515 | Create Time: | |
1516 | 2020-03-19T18:10:59.076071 | |
1517 | | |
1518 -------------------------------------- | |
1519 | Job 8155e4b4bf1581ff | |
1520 | State: | |
1521 | ok | |
1522 | Update Time: | |
1523 | 2020-03-19T18:10:58.105973 | |
1524 | Create Time: | |
1525 | 2020-03-19T18:10:52.045196 | |
1526 | | |
1527 -------------------------------------- | |
1528 | |
1529 --------------------- >> end captured stdout << ---------------------- | |
1530 | |
1531 ---------------------------------------------------------------------- | |
1532 XML: /private/var/folders/b0/_sch3jrj0ndbt8tgqq6fn14m0000gn/T/tmphCb9V4/xunit.xml | |
1533 ---------------------------------------------------------------------- | |
1534 Ran 2 tests in 193.479s | |
1535 | |
1536 FAILED (failures=2) | |
1537 2020-03-19 13:11:59,384 INFO [test_driver] Shutting down | |
1538 2020-03-19 13:11:59,384 INFO [test_driver] Shutting down embedded galaxy web server | |
1539 2020-03-19 13:11:59,387 INFO [test_driver] Embedded web server galaxy stopped | |
1540 2020-03-19 13:11:59,387 INFO [test_driver] Stopping application galaxy | |
1541 Exception in thread Thread-6: | |
1542 Traceback (most recent call last): | |
1543 File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 801, in __bootstrap_inner | |
1544 self.run() | |
1545 File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 754, in run | |
1546 self.__target(*self.__args, **self.__kwargs) | |
1547 File "/Users/jj/.planemo/gx_venv/lib/python2.7/site-packages/paste/httpserver.py", line 1107, in serve_forever | |
1548 self.handle_request() | |
1549 File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 274, in handle_request | |
1550 fd_sets = _eintr_retry(select.select, [self], [], [], timeout) | |
1551 File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 150, in _eintr_retry | |
1552 return func(*args) | |
1553 error: (9, 'Bad file descriptor') | |
1554 | |
1555 2020-03-19 13:11:59,957 INFO [galaxy.queue_worker] Sending reconfigure_watcher control task. | |
1556 2020-03-19 13:12:00,046 INFO [galaxy.jobs.handler] sending stop signal to worker thread | |
1557 2020-03-19 13:12:00,047 INFO [galaxy.jobs.handler] job handler queue stopped | |
1558 2020-03-19 13:12:00,048 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 job worker threads | |
1559 2020-03-19 13:12:00,048 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown... | |
1560 2020-03-19 13:12:00,050 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly | |
1561 2020-03-19 13:12:00,050 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 job worker threads | |
1562 2020-03-19 13:12:00,050 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown... | |
1563 2020-03-19 13:12:00,052 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly | |
1564 2020-03-19 13:12:00,052 INFO [galaxy.jobs.handler] sending stop signal to worker thread | |
1565 2020-03-19 13:12:00,122 INFO [galaxy.jobs.handler] job handler stop queue stopped | |
1566 2020-03-19 13:12:00,123 INFO [test_driver] Application galaxy stopped. | |
1567 Testing complete. HTML report is in "/Users/jj/gx/gh/jj/galaxytools/optitype/tool_test_output.html". | |
1568 There were problems with 2 test(s) - out of 2 test(s) executed. See /Users/jj/gx/gh/jj/galaxytools/optitype/tool_test_output.html for detailed breakdown. | |
1569 optitype[0]: failed | |
1570 optitype[1]: failed |