2
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1 git --git-dir /home/backdoor/.planemo/gx_repo fetch >/dev/null 2>&1
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2 cd /tmp/tmpBnX6kx; git clone --branch 'master' '/home/backdoor/.planemo/gx_repo' 'galaxy-dev'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/backdoor/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/backdoor/.linuxbrew/bin/virtualenv -p /home/backdoor/.linuxbrew/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; 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}
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3 Cloning into 'galaxy-dev'...
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4 done.
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5 Set COMMON_STARTUP_ARGS to --dev-wheels
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6 Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample
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7 Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample
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8 Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample
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9 Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample
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10 Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample
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11 Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample
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12 Initializing tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample
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13 Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample
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14 Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample
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15 Initializing static/welcome.html from welcome.html.sample
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16 Activating virtualenv at /home/backdoor/.planemo/gx_venv
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17 Requirement already satisfied: pip>=8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages
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18 Requirement already satisfied: bx-python==0.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2))
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19 Requirement already satisfied: MarkupSafe==0.23 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3))
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20 Requirement already satisfied: PyYAML==3.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))
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21 Requirement already satisfied: SQLAlchemy==1.0.15 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))
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22 Requirement already satisfied: mercurial==3.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6))
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23 Requirement already satisfied: numpy==1.9.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7))
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24 Requirement already satisfied: pycrypto==2.6.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))
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25 Requirement already satisfied: Paste==2.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15))
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26 Requirement already satisfied: PasteDeploy==1.5.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16))
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27 Requirement already satisfied: docutils==0.12 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17))
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28 Requirement already satisfied: wchartype==0.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18))
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29 Requirement already satisfied: repoze.lru==0.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19))
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30 Requirement already satisfied: Routes==2.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20))
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31 Requirement already satisfied: WebOb==1.4.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21))
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|
32 Requirement already satisfied: WebHelpers==1.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22))
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33 Requirement already satisfied: Mako==1.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23))
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|
34 Requirement already satisfied: pytz==2015.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24))
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|
35 Requirement already satisfied: Babel==2.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25))
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|
36 Requirement already satisfied: Beaker==1.7.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26))
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|
37 Requirement already satisfied: dictobj==0.3.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27))
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|
38 Requirement already satisfied: nose==1.3.7 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 28))
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|
39 Requirement already satisfied: Parsley==1.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 29))
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|
40 Requirement already satisfied: six==1.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30))
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|
41 Requirement already satisfied: Whoosh==2.7.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31))
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|
42 Requirement already satisfied: testfixtures==4.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32))
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|
43 Requirement already satisfied: galaxy_sequence_utils==1.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 33))
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44 Requirement already satisfied: Cheetah==2.4.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36))
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|
45 Requirement already satisfied: Markdown==2.6.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37))
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|
46 Requirement already satisfied: bioblend==0.7.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40))
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|
47 Requirement already satisfied: boto==2.38.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41))
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|
48 Requirement already satisfied: requests==2.8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42))
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|
49 Requirement already satisfied: requests-toolbelt==0.4.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 43))
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|
50 Requirement already satisfied: kombu==3.0.30 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46))
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|
51 Requirement already satisfied: amqp==1.4.8 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47))
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|
52 Requirement already satisfied: anyjson==0.3.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48))
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|
53 Requirement already satisfied: psutil==4.1.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51))
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|
54 Requirement already satisfied: pulsar-galaxy-lib==0.7.0.dev5 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52))
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|
55 Requirement already satisfied: sqlalchemy-migrate==0.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 55))
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|
56 Requirement already satisfied: decorator==4.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 56))
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|
57 Requirement already satisfied: Tempita==0.5.3dev in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57))
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|
58 Requirement already satisfied: sqlparse==0.1.16 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58))
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|
59 Requirement already satisfied: pbr==1.8.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59))
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|
60 Requirement already satisfied: svgwrite==1.1.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 62))
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|
61 Requirement already satisfied: pyparsing==2.1.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 63))
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|
62 Requirement already satisfied: Fabric==1.10.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66))
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|
63 Requirement already satisfied: paramiko==1.15.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 67))
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|
64 Requirement already satisfied: ecdsa==0.13 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 68))
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|
65 Requirement already satisfied: pysam==0.8.4+gx5 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 71))
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|
66 Requirement already satisfied: PasteScript in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 52))
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|
67 Requirement already satisfied: nose in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1))
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68 Requirement already satisfied: NoseHTML in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2))
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|
69 Requirement already satisfied: twill==0.9.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3))
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|
70 Requirement already satisfied: mock in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
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|
71 Requirement already satisfied: selenium in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5))
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72 Requirement already satisfied: pbr>=0.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
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73 Requirement already satisfied: funcsigs>=1; python_version < "3.3" in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
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74 Requirement already satisfied: six>=1.9 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
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75 Testing using galaxy_root /tmp/tmpBnX6kx/galaxy-dev
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76 Testing tools with command [cd /tmp/tmpBnX6kx/galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/backdoor/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/backdoor/.linuxbrew/bin/virtualenv -p /home/backdoor/.linuxbrew/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /home/backdoor/toolshed_test/w4mclassfilter/tool_test_output.html --xunit_report_file /tmp/tmpBnX6kx/xunit.xml --structured_data_report_file /home/backdoor/toolshed_test/w4mclassfilter/tool_test_output.json functional.test_toolbox]
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77 Activating virtualenv at /home/backdoor/.planemo/gx_venv
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78 Requirement already satisfied: pip>=8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages
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|
79 Requirement already satisfied: bx-python==0.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2))
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80 Requirement already satisfied: MarkupSafe==0.23 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3))
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|
81 Requirement already satisfied: PyYAML==3.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))
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|
82 Requirement already satisfied: SQLAlchemy==1.0.15 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))
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|
83 Requirement already satisfied: mercurial==3.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6))
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|
84 Requirement already satisfied: numpy==1.9.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7))
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|
85 Requirement already satisfied: pycrypto==2.6.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))
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|
86 Requirement already satisfied: Paste==2.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15))
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|
87 Requirement already satisfied: PasteDeploy==1.5.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16))
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|
88 Requirement already satisfied: docutils==0.12 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17))
|
|
89 Requirement already satisfied: wchartype==0.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18))
|
|
90 Requirement already satisfied: repoze.lru==0.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19))
|
|
91 Requirement already satisfied: Routes==2.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20))
|
|
92 Requirement already satisfied: WebOb==1.4.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21))
|
|
93 Requirement already satisfied: WebHelpers==1.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22))
|
|
94 Requirement already satisfied: Mako==1.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23))
|
|
95 Requirement already satisfied: pytz==2015.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24))
|
|
96 Requirement already satisfied: Babel==2.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25))
|
|
97 Requirement already satisfied: Beaker==1.7.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26))
|
|
98 Requirement already satisfied: dictobj==0.3.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27))
|
|
99 Requirement already satisfied: nose==1.3.7 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 28))
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|
100 Requirement already satisfied: Parsley==1.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 29))
|
|
101 Requirement already satisfied: six==1.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30))
|
|
102 Requirement already satisfied: Whoosh==2.7.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31))
|
|
103 Requirement already satisfied: testfixtures==4.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32))
|
|
104 Requirement already satisfied: galaxy_sequence_utils==1.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 33))
|
|
105 Requirement already satisfied: Cheetah==2.4.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36))
|
|
106 Requirement already satisfied: Markdown==2.6.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37))
|
|
107 Requirement already satisfied: bioblend==0.7.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40))
|
|
108 Requirement already satisfied: boto==2.38.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41))
|
|
109 Requirement already satisfied: requests==2.8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42))
|
|
110 Requirement already satisfied: requests-toolbelt==0.4.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 43))
|
|
111 Requirement already satisfied: kombu==3.0.30 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46))
|
|
112 Requirement already satisfied: amqp==1.4.8 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47))
|
|
113 Requirement already satisfied: anyjson==0.3.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48))
|
|
114 Requirement already satisfied: psutil==4.1.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51))
|
|
115 Requirement already satisfied: pulsar-galaxy-lib==0.7.0.dev5 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52))
|
|
116 Requirement already satisfied: sqlalchemy-migrate==0.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 55))
|
|
117 Requirement already satisfied: decorator==4.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 56))
|
|
118 Requirement already satisfied: Tempita==0.5.3dev in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57))
|
|
119 Requirement already satisfied: sqlparse==0.1.16 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58))
|
|
120 Requirement already satisfied: pbr==1.8.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59))
|
|
121 Requirement already satisfied: svgwrite==1.1.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 62))
|
|
122 Requirement already satisfied: pyparsing==2.1.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 63))
|
|
123 Requirement already satisfied: Fabric==1.10.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66))
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|
124 Requirement already satisfied: paramiko==1.15.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 67))
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|
125 Requirement already satisfied: ecdsa==0.13 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 68))
|
|
126 Requirement already satisfied: pysam==0.8.4+gx5 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 71))
|
|
127 Requirement already satisfied: PasteScript in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 52))
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|
128 Requirement already satisfied: nose in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1))
|
|
129 Requirement already satisfied: NoseHTML in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2))
|
|
130 Requirement already satisfied: twill==0.9.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3))
|
|
131 Requirement already satisfied: mock in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
|
|
132 Requirement already satisfied: selenium in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5))
|
|
133 Requirement already satisfied: pbr>=0.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
|
|
134 Requirement already satisfied: funcsigs>=1; python_version < "3.3" in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
|
|
135 Requirement already satisfied: six>=1.9 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
|
|
136 Activating virtualenv at /home/backdoor/.planemo/gx_venv
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137 2017-05-09 17:41:18,784 INFO [galaxy.queue_worker] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite://
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138 2017-05-09 17:41:18,932 INFO [galaxy.model.migrate.check] Migrating 127 -> 128...
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139 2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check]
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140 2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check] Migration script to add session update time (used for timeouts)
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141 2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check]
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142 2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check]
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143 2017-05-09 17:41:19,345 INFO [galaxy.model.migrate.check] Migrating 128 -> 129...
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144 2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check]
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145 2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check] Migration script to allow invalidation of job external output metadata temp files
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146 2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check]
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147 2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check]
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148 2017-05-09 17:41:19,750 INFO [galaxy.model.migrate.check] Migrating 129 -> 130...
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149 2017-05-09 17:41:20,242 INFO [galaxy.model.migrate.check]
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150 2017-05-09 17:41:20,243 INFO [galaxy.model.migrate.check] Migration script to change the value column of user_preference from varchar to text.
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151 2017-05-09 17:41:20,243 INFO [galaxy.model.migrate.check]
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152 2017-05-09 17:41:20,243 INFO [galaxy.model.migrate.check]
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153 2017-05-09 17:41:20,243 INFO [galaxy.model.migrate.check] Migrating 130 -> 131...
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154 2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check]
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155 2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check] Migration script to support subworkflows and workflow request input parameters
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156 2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check]
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157 2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check]
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158 2017-05-09 17:41:20,998 INFO [galaxy.model.migrate.check] Migrating 131 -> 132...
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159 2017-05-09 17:41:21,054 INFO [galaxy.model.migrate.check]
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160 2017-05-09 17:41:21,055 INFO [galaxy.model.migrate.check] Migrating 132 -> 133...
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161 2017-05-09 17:41:21,452 INFO [galaxy.model.migrate.check]
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162 2017-05-09 17:41:21,452 INFO [galaxy.model.migrate.check] Add dependencies column to jobs table
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163 2017-05-09 17:41:21,452 INFO [galaxy.model.migrate.check]
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164 2017-05-09 17:41:21,452 INFO [galaxy.model.migrate.check]
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165 2017-05-09 17:41:21,467 INFO [galaxy.config] Install database targetting Galaxy's database configuration.
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166 2017-05-09 17:41:22,106 ERROR [galaxy.visualization.genomes] Error reading twobit.loc: [Errno 2] No such file or directory: '/tmp/tmpBnX6kx/galaxy-dev/tool-data/twobit.loc'
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167 Traceback (most recent call last):
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168 File "/tmp/tmpBnX6kx/galaxy-dev/lib/galaxy/visualization/genomes.py", line 210, in reload_genomes
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169 for line in open( os.path.join( self.app.config.tool_data_path, "twobit.loc" ) ):
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170 IOError: [Errno 2] No such file or directory: '/tmp/tmpBnX6kx/galaxy-dev/tool-data/twobit.loc'
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171 2017-05-09 17:41:22,117 INFO [galaxy.jobs] Setting <handlers> default to child with id 'main'
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172 2017-05-09 17:41:22,135 INFO [galaxy.tools.toolbox.watcher] Watchdog library unavailable, cannot monitor tools.
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173 2017-05-09 17:41:22,135 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmpBnX6kx/tool_conf.xml
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174 2017-05-09 17:41:22,146 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmpBnX6kx/shed_tools_conf.xml
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175 2017-05-09 17:41:22,146 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmpBnX6kx/empty_tool_conf.xml
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176 No handlers could be found for logger "galaxy.datatypes.display_applications.application"
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177 2017-05-09 17:41:22,482 WARNI [galaxy.webhooks] directory not found: /tmp/tmpBnX6kx/galaxy-dev/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config
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178 2017-05-09 17:41:22,492 INFO [galaxy.jobs] Handler 'main' will load all configured runner plugins
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179 2017-05-09 17:41:22,497 INFO [galaxy.jobs.handler] job handler stop queue started
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180 2017-05-09 17:41:22,505 INFO [galaxy.jobs.handler] job handler queue started
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181 2017-05-09 17:41:23,279 INFO [galaxy.queue_worker] Binding and starting galaxy control worker for main
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182 /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: 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.
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183 'storage.' % (dialect.name, dialect.driver))
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184 /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance.
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185 'strategies for improved performance.' % expr)
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186 W4MClassFilter ( W4MClassFilter ) > Test-1 ... 2017-05-09 17:41:24,463 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 1
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187 2017-05-09 17:41:24,891 INFO [galaxy.jobs.handler] (1) Job dispatched
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188 2017-05-09 17:41:25,164 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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189 2017-05-09 17:41:25,165 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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190 2017-05-09 17:41:25,198 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/1/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpFEU_uZ 1:/tmp/tmpBnX6kx/job_working_directory/000/1/dataset_1_files:/tmp/tmpBnX6kx/files/000/dataset_1.dat]
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191 2017-05-09 17:41:25,365 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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192 2017-05-09 17:41:25,366 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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193 2017-05-09 17:41:29,174 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 2
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194 2017-05-09 17:41:30,112 INFO [galaxy.jobs.handler] (2) Job dispatched
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195 2017-05-09 17:41:30,372 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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196 2017-05-09 17:41:30,377 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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197 2017-05-09 17:41:30,415 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/2/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmp819dTL 2:/tmp/tmpBnX6kx/job_working_directory/000/2/dataset_2_files:/tmp/tmpBnX6kx/files/000/dataset_2.dat]
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198 2017-05-09 17:41:30,642 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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199 2017-05-09 17:41:30,642 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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200 2017-05-09 17:41:34,617 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 3
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201 2017-05-09 17:41:35,397 INFO [galaxy.jobs.handler] (3) Job dispatched
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202 2017-05-09 17:41:35,661 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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203 2017-05-09 17:41:35,661 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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204 2017-05-09 17:41:35,707 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/3/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpOXdXDH 3:/tmp/tmpBnX6kx/job_working_directory/000/3/dataset_3_files:/tmp/tmpBnX6kx/files/000/dataset_3.dat]
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205 2017-05-09 17:41:35,889 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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206 2017-05-09 17:41:35,890 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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207 2017-05-09 17:41:39,590 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (102.610 ms)
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208 2017-05-09 17:41:39,630 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (39.109 ms)
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209 2017-05-09 17:41:39,662 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (32.632 ms)
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210 2017-05-09 17:41:39,694 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (31.837 ms)
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211 2017-05-09 17:41:39,716 INFO [galaxy.tools.actions] Added output datasets to history (21.785 ms)
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212 2017-05-09 17:41:39,760 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (23.849 ms)
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213 2017-05-09 17:41:39,761 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (44.332 ms)
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214 2017-05-09 17:41:39,795 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=4,tool_id=W4MClassFilter] (34.570 ms)
|
|
215 2017-05-09 17:41:40,615 INFO [galaxy.jobs.handler] (4) Job dispatched
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216 2017-05-09 17:41:40,918 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda
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217 2017-05-09 17:41:40,918 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda
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218 2017-05-09 17:41:40,918 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda
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219 2017-05-09 17:41:40,919 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda
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220 2017-05-09 17:41:40,919 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda
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221 2017-05-09 17:41:40,919 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda
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222 2017-05-09 17:41:40,951 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/4/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; Rscript /home/backdoor/toolshed_test/w4mclassfilter/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmpBnX6kx/files/000/dataset_1.dat" sampleMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_2.dat" variableMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_3.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmpBnX6kx/files/000/dataset_4.dat" sampleMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_5.dat" variableMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_6.dat" information "/tmp/tmpBnX6kx/files/000/dataset_7.dat"]
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223 2017-05-09 17:41:41,340 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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224 2017-05-09 17:41:41,341 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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|
225 ok
|
|
226 W4MClassFilter ( W4MClassFilter ) > Test-2 ... 2017-05-09 17:41:47,453 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 5
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227 2017-05-09 17:41:47,929 INFO [galaxy.jobs.handler] (5) Job dispatched
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228 2017-05-09 17:41:48,185 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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229 2017-05-09 17:41:48,185 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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230 2017-05-09 17:41:48,246 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/5/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpCJ6i2V 8:/tmp/tmpBnX6kx/job_working_directory/000/5/dataset_8_files:/tmp/tmpBnX6kx/files/000/dataset_8.dat]
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231 2017-05-09 17:41:48,468 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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232 2017-05-09 17:41:48,469 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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233 2017-05-09 17:41:52,575 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 6
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234 2017-05-09 17:41:53,192 INFO [galaxy.jobs.handler] (6) Job dispatched
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235 2017-05-09 17:41:53,442 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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236 2017-05-09 17:41:53,444 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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237 2017-05-09 17:41:53,484 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/6/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpTkRIU7 9:/tmp/tmpBnX6kx/job_working_directory/000/6/dataset_9_files:/tmp/tmpBnX6kx/files/000/dataset_9.dat]
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238 2017-05-09 17:41:53,711 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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239 2017-05-09 17:41:53,712 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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240 2017-05-09 17:41:57,685 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 7
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241 2017-05-09 17:41:58,415 INFO [galaxy.jobs.handler] (7) Job dispatched
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242 2017-05-09 17:41:58,668 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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243 2017-05-09 17:41:58,669 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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|
244 2017-05-09 17:41:58,718 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/7/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmppTa3ww 10:/tmp/tmpBnX6kx/job_working_directory/000/7/dataset_10_files:/tmp/tmpBnX6kx/files/000/dataset_10.dat]
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245 2017-05-09 17:41:58,874 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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246 2017-05-09 17:41:58,874 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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|
247 2017-05-09 17:42:02,544 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (54.150 ms)
|
|
248 2017-05-09 17:42:02,576 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (32.411 ms)
|
|
249 2017-05-09 17:42:02,613 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (36.563 ms)
|
|
250 2017-05-09 17:42:02,660 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (46.442 ms)
|
|
251 2017-05-09 17:42:02,682 INFO [galaxy.tools.actions] Added output datasets to history (21.663 ms)
|
|
252 2017-05-09 17:42:02,732 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (25.405 ms)
|
|
253 2017-05-09 17:42:02,732 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (50.729 ms)
|
|
254 2017-05-09 17:42:02,766 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=8,tool_id=W4MClassFilter] (33.131 ms)
|
|
255 2017-05-09 17:42:03,604 INFO [galaxy.jobs.handler] (8) Job dispatched
|
|
256 2017-05-09 17:42:03,920 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda
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|
257 2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda
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258 2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda
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|
259 2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda
|
|
260 2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda
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|
261 2017-05-09 17:42:03,921 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda
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|
262 2017-05-09 17:42:03,960 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/8/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; Rscript /home/backdoor/toolshed_test/w4mclassfilter/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmpBnX6kx/files/000/dataset_8.dat" sampleMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_9.dat" variableMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_10.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmpBnX6kx/files/000/dataset_11.dat" sampleMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_12.dat" variableMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_13.dat" information "/tmp/tmpBnX6kx/files/000/dataset_14.dat"]
|
|
263 2017-05-09 17:42:04,366 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
|
|
264 2017-05-09 17:42:04,366 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
|
|
265 ok
|
|
266 W4MClassFilter ( W4MClassFilter ) > Test-3 ... 2017-05-09 17:42:10,658 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 9
|
|
267 2017-05-09 17:42:10,906 INFO [galaxy.jobs.handler] (9) Job dispatched
|
|
268 2017-05-09 17:42:11,150 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
|
|
269 2017-05-09 17:42:11,151 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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270 2017-05-09 17:42:11,233 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/9/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmp0F7oAs 15:/tmp/tmpBnX6kx/job_working_directory/000/9/dataset_15_files:/tmp/tmpBnX6kx/files/000/dataset_15.dat]
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271 2017-05-09 17:42:11,471 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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272 2017-05-09 17:42:11,472 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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273 2017-05-09 17:42:15,491 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 10
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274 2017-05-09 17:42:16,194 INFO [galaxy.jobs.handler] (10) Job dispatched
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275 2017-05-09 17:42:16,447 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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276 2017-05-09 17:42:16,448 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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277 2017-05-09 17:42:16,485 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/10/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpmkABaW 16:/tmp/tmpBnX6kx/job_working_directory/000/10/dataset_16_files:/tmp/tmpBnX6kx/files/000/dataset_16.dat]
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278 2017-05-09 17:42:16,649 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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279 2017-05-09 17:42:16,650 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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280 2017-05-09 17:42:20,509 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 11
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281 2017-05-09 17:42:21,426 INFO [galaxy.jobs.handler] (11) Job dispatched
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282 2017-05-09 17:42:21,680 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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283 2017-05-09 17:42:21,681 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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284 2017-05-09 17:42:21,764 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/11/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmpBnX6kx/galaxy-dev/tools/data_source/upload.py /tmp/tmpBnX6kx/galaxy-dev /tmp/tmpafqPoR /tmp/tmpfEj6tV 17:/tmp/tmpBnX6kx/job_working_directory/000/11/dataset_17_files:/tmp/tmpBnX6kx/files/000/dataset_17.dat]
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285 2017-05-09 17:42:21,991 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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286 2017-05-09 17:42:21,991 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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287 2017-05-09 17:42:25,709 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (34.677 ms)
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288 2017-05-09 17:42:25,751 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (41.778 ms)
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289 2017-05-09 17:42:25,784 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (32.888 ms)
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290 2017-05-09 17:42:25,815 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (30.527 ms)
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291 2017-05-09 17:42:25,838 INFO [galaxy.tools.actions] Added output datasets to history (22.886 ms)
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292 2017-05-09 17:42:25,886 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (26.826 ms)
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293 2017-05-09 17:42:25,887 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (48.981 ms)
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294 2017-05-09 17:42:25,936 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=12,tool_id=W4MClassFilter] (48.570 ms)
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295 2017-05-09 17:42:26,617 INFO [galaxy.jobs.handler] (12) Job dispatched
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296 2017-05-09 17:42:26,893 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda
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297 2017-05-09 17:42:26,900 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda
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298 2017-05-09 17:42:26,902 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda
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299 2017-05-09 17:42:26,903 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda
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300 2017-05-09 17:42:26,903 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda
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301 2017-05-09 17:42:26,903 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda
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302 2017-05-09 17:42:26,955 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmpBnX6kx/job_working_directory/000/12/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; Rscript /home/backdoor/toolshed_test/w4mclassfilter/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmpBnX6kx/files/000/dataset_15.dat" sampleMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_16.dat" variableMetadata_in "/tmp/tmpBnX6kx/files/000/dataset_17.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmpBnX6kx/files/000/dataset_18.dat" sampleMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_19.dat" variableMetadata_out "/tmp/tmpBnX6kx/files/000/dataset_20.dat" information "/tmp/tmpBnX6kx/files/000/dataset_21.dat"]
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303 2017-05-09 17:42:27,374 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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304 2017-05-09 17:42:27,375 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
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305 ok
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306
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307 ----------------------------------------------------------------------
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308 XML: /tmp/tmpBnX6kx/xunit.xml
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309 ----------------------------------------------------------------------
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310 Ran 3 tests in 69.356s
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311
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312 OK
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313 2017-05-09 17:42:33,110 INFO [test_driver] Shutting down
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314 2017-05-09 17:42:33,110 INFO [test_driver] Shutting down embedded galaxy web server
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315 2017-05-09 17:42:33,112 INFO [test_driver] Embedded web server galaxy stopped
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316 2017-05-09 17:42:33,112 INFO [test_driver] Stopping application galaxy
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317 2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] sending stop signal to worker thread
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318 2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] job handler queue stopped
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319 2017-05-09 17:42:33,112 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads
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320 2017-05-09 17:42:33,112 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads
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321 2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] sending stop signal to worker thread
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322 2017-05-09 17:42:33,112 INFO [galaxy.jobs.handler] job handler stop queue stopped
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323 2017-05-09 17:42:33,113 INFO [test_driver] Application galaxy stopped.
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324 2017-05-09 17:42:34,087 INFO [galaxy.jobs.handler] sending stop signal to worker thread
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325 2017-05-09 17:42:34,088 INFO [galaxy.jobs.handler] job handler queue stopped
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326 2017-05-09 17:42:34,088 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads
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327 2017-05-09 17:42:34,089 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads
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328 2017-05-09 17:42:34,089 INFO [galaxy.jobs.handler] sending stop signal to worker thread
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329 2017-05-09 17:42:34,089 INFO [galaxy.jobs.handler] job handler stop queue stopped
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330 Testing complete. HTML report is in "/home/backdoor/toolshed_test/w4mclassfilter/tool_test_output.html".
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331 All 3 test(s) executed passed.
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332 W4MClassFilter[0]: passed
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333 W4MClassFilter[1]: passed
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334 W4MClassFilter[2]: passed
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