Mercurial > repos > eschen42 > w4mclassfilter

comparison test_log.txt @ 0:bab3a658f74e draft

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planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
author eschen42
date Tue, 09 May 2017 18:34:35 -0400
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-1:000000000000 0:bab3a658f74e
1 git clone --bare 'https://github.com/galaxyproject/galaxy' '/home/backdoor/.planemo/gx_repo'
2 Cloning into bare repository '/home/backdoor/.planemo/gx_repo'...
3 cd /tmp/tmp4Jz5Zv; 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}
4 Cloning into 'galaxy-dev'...
5 done.
6 New python executable in /home/backdoor/.planemo/gx_venv/bin/python2.7
7 Also creating executable in /home/backdoor/.planemo/gx_venv/bin/python
8 Installing setuptools, pip, wheel...done.
9 Running virtualenv with interpreter /home/backdoor/.linuxbrew/bin/python2.7
10 Set COMMON_STARTUP_ARGS to --dev-wheels
11 Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample
12 Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample
13 Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample
14 Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample
15 Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample
16 Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample
17 Initializing tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample
18 Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample
19 Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample
20 Initializing static/welcome.html from welcome.html.sample
21 Activating virtualenv at /home/backdoor/.planemo/gx_venv
22 Collecting pip>=8.1
23 Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB)
24 Installing collected packages: pip
25 Found existing installation: pip 7.1.2
26 Uninstalling pip-7.1.2:
27 Successfully uninstalled pip-7.1.2
28 Successfully installed pip-9.0.1
29 Collecting bx-python==0.7.3 (from -r requirements.txt (line 2))
30 Downloading https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27m-manylinux1_x86_64.whl (2.1MB)
31 Collecting MarkupSafe==0.23 (from -r requirements.txt (line 3))
32 Downloading https://wheels.galaxyproject.org/packages/MarkupSafe-0.23-cp27-cp27m-manylinux1_x86_64.whl
33 Collecting PyYAML==3.11 (from -r requirements.txt (line 4))
34 Downloading https://wheels.galaxyproject.org/packages/PyYAML-3.11-cp27-cp27m-manylinux1_x86_64.whl (367kB)
35 Collecting SQLAlchemy==1.0.15 (from -r requirements.txt (line 5))
36 Downloading https://wheels.galaxyproject.org/packages/SQLAlchemy-1.0.15-cp27-cp27m-manylinux1_x86_64.whl (1.0MB)
37 Collecting mercurial==3.7.3 (from -r requirements.txt (line 6))
38 Downloading https://wheels.galaxyproject.org/packages/mercurial-3.7.3-cp27-cp27m-manylinux1_x86_64.whl (1.5MB)
39 Collecting numpy==1.9.2 (from -r requirements.txt (line 7))
40 Downloading https://wheels.galaxyproject.org/packages/numpy-1.9.2-cp27-cp27m-manylinux1_x86_64.whl (10.2MB)
41 Collecting pycrypto==2.6.1 (from -r requirements.txt (line 8))
42 Downloading https://wheels.galaxyproject.org/packages/pycrypto-2.6.1-cp27-cp27m-manylinux1_x86_64.whl (492kB)
43 Collecting Paste==2.0.2 (from -r requirements.txt (line 15))
44 Downloading https://wheels.galaxyproject.org/packages/Paste-2.0.2-py2-none-any.whl (610kB)
45 Collecting PasteDeploy==1.5.2 (from -r requirements.txt (line 16))
46 Downloading https://wheels.galaxyproject.org/packages/PasteDeploy-1.5.2-py2.py3-none-any.whl
47 Collecting docutils==0.12 (from -r requirements.txt (line 17))
48 Downloading https://wheels.galaxyproject.org/packages/docutils-0.12-py2-none-any.whl (509kB)
49 Collecting wchartype==0.1 (from -r requirements.txt (line 18))
50 Downloading https://wheels.galaxyproject.org/packages/wchartype-0.1-py2-none-any.whl
51 Collecting repoze.lru==0.6 (from -r requirements.txt (line 19))
52 Downloading repoze.lru-0.6.tar.gz
53 Collecting Routes==2.2 (from -r requirements.txt (line 20))
54 Downloading https://wheels.galaxyproject.org/packages/Routes-2.2-py2-none-any.whl (46kB)
55 Collecting WebOb==1.4.1 (from -r requirements.txt (line 21))
56 Downloading https://wheels.galaxyproject.org/packages/WebOb-1.4.1-py2.py3-none-any.whl (73kB)
57 Collecting WebHelpers==1.3 (from -r requirements.txt (line 22))
58 Downloading https://wheels.galaxyproject.org/packages/WebHelpers-1.3-py2-none-any.whl (149kB)
59 Collecting Mako==1.0.2 (from -r requirements.txt (line 23))
60 Downloading https://wheels.galaxyproject.org/packages/Mako-1.0.2-py2-none-any.whl (76kB)
61 Collecting pytz==2015.4 (from -r requirements.txt (line 24))
62 Downloading https://wheels.galaxyproject.org/packages/pytz-2015.4-py2-none-any.whl (475kB)
63 Collecting Babel==2.0 (from -r requirements.txt (line 25))
64 Downloading https://wheels.galaxyproject.org/packages/Babel-2.0-py2-none-any.whl (3.6MB)
65 Collecting Beaker==1.7.0 (from -r requirements.txt (line 26))
66 Downloading https://wheels.galaxyproject.org/packages/Beaker-1.7.0-py2-none-any.whl (44kB)
67 Collecting dictobj==0.3.1 (from -r requirements.txt (line 27))
68 Downloading https://wheels.galaxyproject.org/packages/dictobj-0.3.1-py2-none-any.whl
69 Collecting nose==1.3.7 (from -r requirements.txt (line 28))
70 Downloading https://wheels.galaxyproject.org/packages/nose-1.3.7-py2-none-any.whl (154kB)
71 Collecting Parsley==1.3 (from -r requirements.txt (line 29))
72 Downloading https://wheels.galaxyproject.org/packages/Parsley-1.3-py2-none-any.whl (88kB)
73 Collecting six==1.10.0 (from -r requirements.txt (line 30))
74 Downloading https://wheels.galaxyproject.org/packages/six-1.10.0-py2.py3-none-any.whl
75 Collecting Whoosh==2.7.4 (from -r requirements.txt (line 31))
76 Downloading https://wheels.galaxyproject.org/packages/Whoosh-2.7.4-py2.py3-none-any.whl (468kB)
77 Collecting testfixtures==4.10.0 (from -r requirements.txt (line 32))
78 Downloading testfixtures-4.10.0-py2.py3-none-any.whl (73kB)
79 Collecting galaxy_sequence_utils==1.0.2 (from -r requirements.txt (line 33))
80 Downloading https://wheels.galaxyproject.org/packages/galaxy_sequence_utils-1.0.2-py2.py3-none-any.whl
81 Collecting Cheetah==2.4.4 (from -r requirements.txt (line 36))
82 Downloading https://wheels.galaxyproject.org/packages/Cheetah-2.4.4-cp27-cp27m-manylinux1_x86_64.whl (193kB)
83 Collecting Markdown==2.6.3 (from -r requirements.txt (line 37))
84 Downloading https://wheels.galaxyproject.org/packages/Markdown-2.6.3-py2-none-any.whl (158kB)
85 Collecting bioblend==0.7.0 (from -r requirements.txt (line 40))
86 Downloading https://wheels.galaxyproject.org/packages/bioblend-0.7.0-py2.py3-none-any.whl (82kB)
87 Collecting boto==2.38.0 (from -r requirements.txt (line 41))
88 Downloading https://wheels.galaxyproject.org/packages/boto-2.38.0-py2.py3-none-any.whl (1.3MB)
89 Collecting requests==2.8.1 (from -r requirements.txt (line 42))
90 Downloading https://wheels.galaxyproject.org/packages/requests-2.8.1-py2.py3-none-any.whl (497kB)
91 Collecting requests-toolbelt==0.4.0 (from -r requirements.txt (line 43))
92 Downloading https://wheels.galaxyproject.org/packages/requests_toolbelt-0.4.0-py2.py3-none-any.whl
93 Collecting kombu==3.0.30 (from -r requirements.txt (line 46))
94 Downloading https://wheels.galaxyproject.org/packages/kombu-3.0.30-py2.py3-none-any.whl (241kB)
95 Collecting amqp==1.4.8 (from -r requirements.txt (line 47))
96 Downloading https://wheels.galaxyproject.org/packages/amqp-1.4.8-py2.py3-none-any.whl (51kB)
97 Collecting anyjson==0.3.3 (from -r requirements.txt (line 48))
98 Downloading https://wheels.galaxyproject.org/packages/anyjson-0.3.3-py2-none-any.whl
99 Collecting psutil==4.1.0 (from -r requirements.txt (line 51))
100 Downloading https://wheels.galaxyproject.org/packages/psutil-4.1.0-cp27-cp27m-manylinux1_x86_64.whl (168kB)
101 Collecting pulsar-galaxy-lib==0.7.0.dev5 (from -r requirements.txt (line 52))
102 Downloading https://wheels.galaxyproject.org/packages/pulsar_galaxy_lib-0.7.0.dev5-py2-none-any.whl (160kB)
103 Collecting sqlalchemy-migrate==0.10.0 (from -r requirements.txt (line 55))
104 Downloading https://wheels.galaxyproject.org/packages/sqlalchemy_migrate-0.10.0-py2-none-any.whl (108kB)
105 Collecting decorator==4.0.2 (from -r requirements.txt (line 56))
106 Downloading https://wheels.galaxyproject.org/packages/decorator-4.0.2-py2.py3-none-any.whl
107 Collecting Tempita==0.5.3dev (from -r requirements.txt (line 57))
108 Downloading https://wheels.galaxyproject.org/packages/Tempita-0.5.3.dev0-py2-none-any.whl
109 Collecting sqlparse==0.1.16 (from -r requirements.txt (line 58))
110 Downloading https://wheels.galaxyproject.org/packages/sqlparse-0.1.16-py2-none-any.whl
111 Collecting pbr==1.8.0 (from -r requirements.txt (line 59))
112 Downloading https://wheels.galaxyproject.org/packages/pbr-1.8.0-py2.py3-none-any.whl (87kB)
113 Collecting svgwrite==1.1.6 (from -r requirements.txt (line 62))
114 Downloading https://wheels.galaxyproject.org/packages/svgwrite-1.1.6-py2-none-any.whl (62kB)
115 Collecting pyparsing==2.1.1 (from -r requirements.txt (line 63))
116 Downloading https://wheels.galaxyproject.org/packages/pyparsing-2.1.1-py2.py3-none-any.whl
117 Collecting Fabric==1.10.2 (from -r requirements.txt (line 66))
118 Downloading https://wheels.galaxyproject.org/packages/Fabric-1.10.2-py2-none-any.whl (90kB)
119 Collecting paramiko==1.15.2 (from -r requirements.txt (line 67))
120 Downloading https://wheels.galaxyproject.org/packages/paramiko-1.15.2-py2.py3-none-any.whl (165kB)
121 Collecting ecdsa==0.13 (from -r requirements.txt (line 68))
122 Downloading https://wheels.galaxyproject.org/packages/ecdsa-0.13-py2.py3-none-any.whl (44kB)
123 Collecting pysam==0.8.4+gx5 (from -r requirements.txt (line 71))
124 Downloading https://wheels.galaxyproject.org/packages/pysam-0.8.4+gx5-cp27-cp27m-manylinux1_x86_64.whl (11.8MB)
125 Collecting PasteScript (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 52))
126 Downloading PasteScript-2.0.2-py2.py3-none-any.whl (74kB)
127 Building wheels for collected packages: repoze.lru
128 Running setup.py bdist_wheel for repoze.lru: started
129 Running setup.py bdist_wheel for repoze.lru: finished with status 'done'
130 Stored in directory: /home/backdoor/.cache/pip/wheels/b2/cd/b3/7e24400bff83325a01d492940eff6e9579f553f33348323d79
131 Successfully built repoze.lru
132 Installing collected packages: bx-python, MarkupSafe, PyYAML, SQLAlchemy, mercurial, numpy, pycrypto, six, Paste, PasteDeploy, docutils, wchartype, repoze.lru, Routes, WebOb, WebHelpers, Mako, pytz, Babel, Beaker, dictobj, nose, Parsley, Whoosh, testfixtures, galaxy-sequence-utils, Markdown, Cheetah, boto, requests, requests-toolbelt, bioblend, anyjson, amqp, kombu, psutil, PasteScript, pulsar-galaxy-lib, pbr, Tempita, decorator, sqlparse, sqlalchemy-migrate, pyparsing, svgwrite, ecdsa, paramiko, Fabric, pysam
133 Successfully installed Babel-2.0 Beaker-1.7.0 Cheetah-2.4.4 Fabric-1.10.2 Mako-1.0.2 Markdown-2.6.3 MarkupSafe-0.23 Parsley-1.3 Paste-2.0.2 PasteDeploy-1.5.2 PasteScript-2.0.2 PyYAML-3.11 Routes-2.2 SQLAlchemy-1.0.15 Tempita-0.5.3.dev0 WebHelpers-1.3 WebOb-1.4.1 Whoosh-2.7.4 amqp-1.4.8 anyjson-0.3.3 bioblend-0.7.0 boto-2.38.0 bx-python-0.7.3 decorator-4.0.2 dictobj-0.3.1 docutils-0.12 ecdsa-0.13 galaxy-sequence-utils-1.0.2 kombu-3.0.30 mercurial-3.7.3 nose-1.3.7 numpy-1.9.2 paramiko-1.15.2 pbr-1.8.0 psutil-4.1.0 pulsar-galaxy-lib-0.7.0.dev5 pycrypto-2.6.1 pyparsing-2.1.1 pysam-0.8.4+gx5 pytz-2015.4 repoze.lru-0.6 requests-2.8.1 requests-toolbelt-0.4.0 six-1.10.0 sqlalchemy-migrate-0.10.0 sqlparse-0.1.16 svgwrite-1.1.6 testfixtures-4.10.0 wchartype-0.1
134 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))
135 Collecting NoseHTML (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2))
136 Downloading NoseHTML-0.4.2-py2-none-any.whl
137 Collecting twill==0.9.1 (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3))
138 Downloading https://wheels.galaxyproject.org/packages/twill-0.9.1-py2-none-any.whl (203kB)
139 Collecting mock (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
140 Downloading mock-2.0.0-py2.py3-none-any.whl (56kB)
141 Collecting selenium (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5))
142 Downloading https://wheels.galaxyproject.org/packages/selenium-3.0.1-py2.py3-none-any.whl (913kB)
143 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))
144 Collecting funcsigs>=1; python_version < "3.3" (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
145 Downloading funcsigs-1.0.2-py2.py3-none-any.whl
146 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))
147 Installing collected packages: NoseHTML, twill, funcsigs, mock, selenium
148 Successfully installed NoseHTML-0.4.2 funcsigs-1.0.2 mock-2.0.0 selenium-3.0.1 twill-0.9.1
149 Testing using galaxy_root /tmp/tmp4Jz5Zv/galaxy-dev
150 Testing tools with command [cd /tmp/tmp4Jz5Zv/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/w4mclassfilter_galaxy_wrapper/tool_test_output.html --xunit_report_file /tmp/tmp4Jz5Zv/xunit.xml --structured_data_report_file /home/backdoor/w4mclassfilter_galaxy_wrapper/tool_test_output.json functional.test_toolbox]
151 Activating virtualenv at /home/backdoor/.planemo/gx_venv
152 Requirement already satisfied: pip>=8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages
153 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))
154 Requirement already satisfied: MarkupSafe==0.23 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3))
155 Requirement already satisfied: PyYAML==3.11 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))
156 Requirement already satisfied: SQLAlchemy==1.0.15 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))
157 Requirement already satisfied: mercurial==3.7.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6))
158 Requirement already satisfied: numpy==1.9.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7))
159 Requirement already satisfied: pycrypto==2.6.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))
160 Requirement already satisfied: Paste==2.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15))
161 Requirement already satisfied: PasteDeploy==1.5.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16))
162 Requirement already satisfied: docutils==0.12 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17))
163 Requirement already satisfied: wchartype==0.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18))
164 Requirement already satisfied: repoze.lru==0.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19))
165 Requirement already satisfied: Routes==2.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20))
166 Requirement already satisfied: WebOb==1.4.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21))
167 Requirement already satisfied: WebHelpers==1.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22))
168 Requirement already satisfied: Mako==1.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23))
169 Requirement already satisfied: pytz==2015.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24))
170 Requirement already satisfied: Babel==2.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25))
171 Requirement already satisfied: Beaker==1.7.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26))
172 Requirement already satisfied: dictobj==0.3.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27))
173 Requirement already satisfied: nose==1.3.7 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 28))
174 Requirement already satisfied: Parsley==1.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 29))
175 Requirement already satisfied: six==1.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30))
176 Requirement already satisfied: Whoosh==2.7.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31))
177 Requirement already satisfied: testfixtures==4.10.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32))
178 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))
179 Requirement already satisfied: Cheetah==2.4.4 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36))
180 Requirement already satisfied: Markdown==2.6.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37))
181 Requirement already satisfied: bioblend==0.7.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40))
182 Requirement already satisfied: boto==2.38.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41))
183 Requirement already satisfied: requests==2.8.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42))
184 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))
185 Requirement already satisfied: kombu==3.0.30 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46))
186 Requirement already satisfied: amqp==1.4.8 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47))
187 Requirement already satisfied: anyjson==0.3.3 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48))
188 Requirement already satisfied: psutil==4.1.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51))
189 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))
190 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))
191 Requirement already satisfied: decorator==4.0.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 56))
192 Requirement already satisfied: Tempita==0.5.3dev in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57))
193 Requirement already satisfied: sqlparse==0.1.16 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58))
194 Requirement already satisfied: pbr==1.8.0 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59))
195 Requirement already satisfied: svgwrite==1.1.6 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 62))
196 Requirement already satisfied: pyparsing==2.1.1 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 63))
197 Requirement already satisfied: Fabric==1.10.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66))
198 Requirement already satisfied: paramiko==1.15.2 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 67))
199 Requirement already satisfied: ecdsa==0.13 in /home/backdoor/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 68))
200 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))
201 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))
202 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))
203 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))
204 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))
205 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))
206 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))
207 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))
208 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))
209 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))
210 Activating virtualenv at /home/backdoor/.planemo/gx_venv
211 2017-05-09 15:52:58,568 INFO [galaxy.queue_worker] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite://
212 2017-05-09 15:52:58,717 INFO [galaxy.model.migrate.check] Migrating 127 -> 128...
213 2017-05-09 15:52:59,159 INFO [galaxy.model.migrate.check]
214 2017-05-09 15:52:59,159 INFO [galaxy.model.migrate.check] Migration script to add session update time (used for timeouts)
215 2017-05-09 15:52:59,159 INFO [galaxy.model.migrate.check]
216 2017-05-09 15:52:59,159 INFO [galaxy.model.migrate.check]
217 2017-05-09 15:52:59,160 INFO [galaxy.model.migrate.check] Migrating 128 -> 129...
218 2017-05-09 15:52:59,576 INFO [galaxy.model.migrate.check]
219 2017-05-09 15:52:59,576 INFO [galaxy.model.migrate.check] Migration script to allow invalidation of job external output metadata temp files
220 2017-05-09 15:52:59,576 INFO [galaxy.model.migrate.check]
221 2017-05-09 15:52:59,576 INFO [galaxy.model.migrate.check]
222 2017-05-09 15:52:59,576 INFO [galaxy.model.migrate.check] Migrating 129 -> 130...
223 2017-05-09 15:53:00,112 INFO [galaxy.model.migrate.check]
224 2017-05-09 15:53:00,112 INFO [galaxy.model.migrate.check] Migration script to change the value column of user_preference from varchar to text.
225 2017-05-09 15:53:00,112 INFO [galaxy.model.migrate.check]
226 2017-05-09 15:53:00,112 INFO [galaxy.model.migrate.check]
227 2017-05-09 15:53:00,112 INFO [galaxy.model.migrate.check] Migrating 130 -> 131...
228 2017-05-09 15:53:00,885 INFO [galaxy.model.migrate.check]
229 2017-05-09 15:53:00,885 INFO [galaxy.model.migrate.check] Migration script to support subworkflows and workflow request input parameters
230 2017-05-09 15:53:00,885 INFO [galaxy.model.migrate.check]
231 2017-05-09 15:53:00,885 INFO [galaxy.model.migrate.check]
232 2017-05-09 15:53:00,885 INFO [galaxy.model.migrate.check] Migrating 131 -> 132...
233 2017-05-09 15:53:00,932 INFO [galaxy.model.migrate.check]
234 2017-05-09 15:53:00,932 INFO [galaxy.model.migrate.check] Migrating 132 -> 133...
235 2017-05-09 15:53:01,340 INFO [galaxy.model.migrate.check]
236 2017-05-09 15:53:01,340 INFO [galaxy.model.migrate.check] Add dependencies column to jobs table
237 2017-05-09 15:53:01,340 INFO [galaxy.model.migrate.check]
238 2017-05-09 15:53:01,340 INFO [galaxy.model.migrate.check]
239 2017-05-09 15:53:01,357 INFO [galaxy.config] Install database targetting Galaxy's database configuration.
240 2017-05-09 15:53:02,016 ERROR [galaxy.visualization.genomes] Error reading twobit.loc: [Errno 2] No such file or directory: '/tmp/tmp4Jz5Zv/galaxy-dev/tool-data/twobit.loc'
241 Traceback (most recent call last):
242 File "/tmp/tmp4Jz5Zv/galaxy-dev/lib/galaxy/visualization/genomes.py", line 210, in reload_genomes
243 for line in open( os.path.join( self.app.config.tool_data_path, "twobit.loc" ) ):
244 IOError: [Errno 2] No such file or directory: '/tmp/tmp4Jz5Zv/galaxy-dev/tool-data/twobit.loc'
245 2017-05-09 15:53:02,027 INFO [galaxy.jobs] Setting <handlers> default to child with id 'main'
246 2017-05-09 15:53:02,045 INFO [galaxy.tools.toolbox.watcher] Watchdog library unavailable, cannot monitor tools.
247 2017-05-09 15:53:02,045 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp4Jz5Zv/tool_conf.xml
248 2017-05-09 15:53:02,056 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp4Jz5Zv/shed_tools_conf.xml
249 2017-05-09 15:53:02,057 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp4Jz5Zv/empty_tool_conf.xml
250 No handlers could be found for logger "galaxy.datatypes.display_applications.application"
251 2017-05-09 15:53:02,392 WARNI [galaxy.webhooks] directory not found: /tmp/tmp4Jz5Zv/galaxy-dev/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config
252 2017-05-09 15:53:02,402 INFO [galaxy.jobs] Handler 'main' will load all configured runner plugins
253 2017-05-09 15:53:02,408 INFO [galaxy.jobs.handler] job handler stop queue started
254 2017-05-09 15:53:02,419 INFO [galaxy.jobs.handler] job handler queue started
255 2017-05-09 15:53:03,184 INFO [galaxy.queue_worker] Binding and starting galaxy control worker for main
256 /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.
257 'storage.' % (dialect.name, dialect.driver))
258 /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.
259 'strategies for improved performance.' % expr)
260 W4MClassFilter ( W4MClassFilter ) > Test-1 ... 2017-05-09 15:53:04,374 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 1
261 2017-05-09 15:53:04,877 INFO [galaxy.jobs.handler] (1) Job dispatched
262 2017-05-09 15:53:05,148 DEBUG [galaxy.tools.deps.conda_util] Executing command: /home/backdoor/miniconda2/bin/conda create -y --name __samtools@1.3.1 samtools=1.3.1
263 2017-05-09 15:53:11,359 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
264 2017-05-09 15:53:11,361 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
265 2017-05-09 15:53:11,415 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/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/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpJkw_yw 1:/tmp/tmp4Jz5Zv/job_working_directory/000/1/dataset_1_files:/tmp/tmp4Jz5Zv/files/000/dataset_1.dat]
266 2017-05-09 15:53:11,591 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
267 2017-05-09 15:53:11,591 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
268 2017-05-09 15:53:15,598 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 2
269 2017-05-09 15:53:16,226 INFO [galaxy.jobs.handler] (2) Job dispatched
270 2017-05-09 15:53:16,481 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
271 2017-05-09 15:53:16,483 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
272 2017-05-09 15:53:16,521 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/2/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpytFdxz 2:/tmp/tmp4Jz5Zv/job_working_directory/000/2/dataset_2_files:/tmp/tmp4Jz5Zv/files/000/dataset_2.dat]
273 2017-05-09 15:53:16,678 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
274 2017-05-09 15:53:16,678 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
275 2017-05-09 15:53:20,584 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 3
276 2017-05-09 15:53:21,476 INFO [galaxy.jobs.handler] (3) Job dispatched
277 2017-05-09 15:53:21,731 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
278 2017-05-09 15:53:21,732 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
279 2017-05-09 15:53:21,815 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/3/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpnOpUXZ 3:/tmp/tmp4Jz5Zv/job_working_directory/000/3/dataset_3_files:/tmp/tmp4Jz5Zv/files/000/dataset_3.dat]
280 2017-05-09 15:53:22,056 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
281 2017-05-09 15:53:22,057 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
282 2017-05-09 15:53:25,797 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (34.243 ms)
283 2017-05-09 15:53:25,853 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (55.183 ms)
284 2017-05-09 15:53:25,891 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (38.127 ms)
285 2017-05-09 15:53:25,924 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (32.700 ms)
286 2017-05-09 15:53:25,944 INFO [galaxy.tools.actions] Added output datasets to history (20.286 ms)
287 2017-05-09 15:53:25,996 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (32.287 ms)
288 2017-05-09 15:53:25,996 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (52.038 ms)
289 2017-05-09 15:53:26,036 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=4,tool_id=W4MClassFilter] (39.310 ms)
290 2017-05-09 15:53:26,653 INFO [galaxy.jobs.handler] (4) Job dispatched
291 2017-05-09 15:53:26,888 DEBUG [galaxy.tools.deps.conda_util] Executing command: /home/backdoor/miniconda2/bin/conda create -y --name mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4 r-base=3.3.1 r-batch=1.1_4 w4mclassfilter=0.98.1
292 2017-05-09 15:53:32,394 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda
293 2017-05-09 15:53:32,394 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda
294 2017-05-09 15:53:32,394 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda
295 2017-05-09 15:53:32,394 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda
296 2017-05-09 15:53:32,394 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda
297 2017-05-09 15:53:32,394 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda
298 2017-05-09 15:53:32,483 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/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 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; Rscript /home/backdoor/w4mclassfilter_galaxy_wrapper/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmp4Jz5Zv/files/000/dataset_1.dat" sampleMetadata_in "/tmp/tmp4Jz5Zv/files/000/dataset_2.dat" variableMetadata_in "/tmp/tmp4Jz5Zv/files/000/dataset_3.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmp4Jz5Zv/files/000/dataset_4.dat" sampleMetadata_out "/tmp/tmp4Jz5Zv/files/000/dataset_5.dat" variableMetadata_out "/tmp/tmp4Jz5Zv/files/000/dataset_6.dat" information "/tmp/tmp4Jz5Zv/files/000/dataset_7.dat"]
299 2017-05-09 15:53:33,012 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
300 2017-05-09 15:53:33,013 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
301 ok
302 W4MClassFilter ( W4MClassFilter ) > Test-2 ... 2017-05-09 15:53:40,192 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 5
303 2017-05-09 15:53:41,186 INFO [galaxy.jobs.handler] (5) Job dispatched
304 2017-05-09 15:53:41,438 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
305 2017-05-09 15:53:41,439 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
306 2017-05-09 15:53:41,474 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/5/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpzHo4ws 8:/tmp/tmp4Jz5Zv/job_working_directory/000/5/dataset_8_files:/tmp/tmp4Jz5Zv/files/000/dataset_8.dat]
307 2017-05-09 15:53:41,652 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
308 2017-05-09 15:53:41,652 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
309 2017-05-09 15:53:45,610 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 6
310 2017-05-09 15:53:46,393 INFO [galaxy.jobs.handler] (6) Job dispatched
311 2017-05-09 15:53:46,638 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
312 2017-05-09 15:53:46,645 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
313 2017-05-09 15:53:46,690 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/6/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpWL9Sp3 9:/tmp/tmp4Jz5Zv/job_working_directory/000/6/dataset_9_files:/tmp/tmp4Jz5Zv/files/000/dataset_9.dat]
314 2017-05-09 15:53:46,917 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
315 2017-05-09 15:53:46,918 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
316 2017-05-09 15:53:50,908 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 7
317 2017-05-09 15:53:51,594 INFO [galaxy.jobs.handler] (7) Job dispatched
318 2017-05-09 15:53:51,849 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
319 2017-05-09 15:53:51,849 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
320 2017-05-09 15:53:51,902 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/7/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpmj2ueZ 10:/tmp/tmp4Jz5Zv/job_working_directory/000/7/dataset_10_files:/tmp/tmp4Jz5Zv/files/000/dataset_10.dat]
321 2017-05-09 15:53:52,065 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
322 2017-05-09 15:53:52,066 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
323 2017-05-09 15:53:55,798 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (36.686 ms)
324 2017-05-09 15:53:55,828 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (30.091 ms)
325 2017-05-09 15:53:55,860 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (31.485 ms)
326 2017-05-09 15:53:55,895 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (35.815 ms)
327 2017-05-09 15:53:55,918 INFO [galaxy.tools.actions] Added output datasets to history (22.862 ms)
328 2017-05-09 15:53:55,962 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (24.036 ms)
329 2017-05-09 15:53:55,963 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (44.286 ms)
330 2017-05-09 15:53:56,001 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=8,tool_id=W4MClassFilter] (37.669 ms)
331 2017-05-09 15:53:56,817 INFO [galaxy.jobs.handler] (8) Job dispatched
332 2017-05-09 15:53:57,142 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda
333 2017-05-09 15:53:57,142 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda
334 2017-05-09 15:53:57,142 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda
335 2017-05-09 15:53:57,142 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda
336 2017-05-09 15:53:57,142 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda
337 2017-05-09 15:53:57,142 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda
338 2017-05-09 15:53:57,179 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/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 ; [ "$CONDA_DEFAULT_ENV" = "/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4" ] || . /home/backdoor/miniconda2/bin/activate '/home/backdoor/miniconda2/envs/mulled-v1-e6b0d2ef4e5cf48144629c11c5bc66b43fc076b336419c5c00247560d01a3bc4' > conda_activate.log 2>&1 ; Rscript /home/backdoor/w4mclassfilter_galaxy_wrapper/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmp4Jz5Zv/files/000/dataset_8.dat" sampleMetadata_in "/tmp/tmp4Jz5Zv/files/000/dataset_9.dat" variableMetadata_in "/tmp/tmp4Jz5Zv/files/000/dataset_10.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmp4Jz5Zv/files/000/dataset_11.dat" sampleMetadata_out "/tmp/tmp4Jz5Zv/files/000/dataset_12.dat" variableMetadata_out "/tmp/tmp4Jz5Zv/files/000/dataset_13.dat" information "/tmp/tmp4Jz5Zv/files/000/dataset_14.dat"]
339 2017-05-09 15:53:57,599 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
340 2017-05-09 15:53:57,599 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
341 ok
342 W4MClassFilter ( W4MClassFilter ) > Test-3 ... 2017-05-09 15:54:03,918 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 9
343 2017-05-09 15:54:05,128 INFO [galaxy.jobs.handler] (9) Job dispatched
344 2017-05-09 15:54:05,380 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
345 2017-05-09 15:54:05,381 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
346 2017-05-09 15:54:05,422 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/9/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmp4WoSDp 15:/tmp/tmp4Jz5Zv/job_working_directory/000/9/dataset_15_files:/tmp/tmp4Jz5Zv/files/000/dataset_15.dat]
347 2017-05-09 15:54:05,591 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
348 2017-05-09 15:54:05,592 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
349 2017-05-09 15:54:09,490 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 10
350 2017-05-09 15:54:10,366 INFO [galaxy.jobs.handler] (10) Job dispatched
351 2017-05-09 15:54:10,613 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
352 2017-05-09 15:54:10,615 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
353 2017-05-09 15:54:10,658 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/10/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpGDoAhy 16:/tmp/tmp4Jz5Zv/job_working_directory/000/10/dataset_16_files:/tmp/tmp4Jz5Zv/files/000/dataset_16.dat]
354 2017-05-09 15:54:10,844 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
355 2017-05-09 15:54:10,844 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
356 2017-05-09 15:54:14,773 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 11
357 2017-05-09 15:54:15,569 INFO [galaxy.jobs.handler] (11) Job dispatched
358 2017-05-09 15:54:15,834 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
359 2017-05-09 15:54:15,834 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
360 2017-05-09 15:54:15,923 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/job_working_directory/000/11/tool_script.sh] for tool command [export PATH=$PATH:'/home/backdoor/miniconda2/envs/__samtools@1.3.1/bin' ; python /tmp/tmp4Jz5Zv/galaxy-dev/tools/data_source/upload.py /tmp/tmp4Jz5Zv/galaxy-dev /tmp/tmp0vYrxn /tmp/tmpmnqkmg 17:/tmp/tmp4Jz5Zv/job_working_directory/000/11/dataset_17_files:/tmp/tmp4Jz5Zv/files/000/dataset_17.dat]
361 2017-05-09 15:54:16,158 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
362 2017-05-09 15:54:16,158 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
363 2017-05-09 15:54:19,917 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool W4MClassFilter (55.485 ms)
364 2017-05-09 15:54:19,960 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool W4MClassFilter (43.180 ms)
365 2017-05-09 15:54:19,995 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool W4MClassFilter (34.516 ms)
366 2017-05-09 15:54:20,036 INFO [galaxy.tools.actions] Handled output named information for tool W4MClassFilter (40.337 ms)
367 2017-05-09 15:54:20,062 INFO [galaxy.tools.actions] Added output datasets to history (26.650 ms)
368 2017-05-09 15:54:20,115 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=W4MClassFilter] (28.845 ms)
369 2017-05-09 15:54:20,116 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=W4MClassFilter] complete, ready to flush (52.996 ms)
370 2017-05-09 15:54:20,153 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=12,tool_id=W4MClassFilter] (37.779 ms)
371 2017-05-09 15:54:20,742 INFO [galaxy.jobs.handler] (12) Job dispatched
372 2017-05-09 15:54:20,961 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda
373 2017-05-09 15:54:20,961 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda
374 2017-05-09 15:54:20,961 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda
375 2017-05-09 15:54:20,961 DEBUG [galaxy.tools.deps] Using dependency r-base version 3.3.1 of type conda
376 2017-05-09 15:54:20,961 DEBUG [galaxy.tools.deps] Using dependency r-batch version 1.1_4 of type conda
377 2017-05-09 15:54:20,961 DEBUG [galaxy.tools.deps] Using dependency w4mclassfilter version 0.98.1 of type conda
378 2017-05-09 15:54:21,013 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp4Jz5Zv/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/w4mclassfilter_galaxy_wrapper/w4mclassfilter_wrapper.R dataMatrix_in "/tmp/tmp4Jz5Zv/files/000/dataset_15.dat" sampleMetadata_in "/tmp/tmp4Jz5Zv/files/000/dataset_16.dat" variableMetadata_in "/tmp/tmp4Jz5Zv/files/000/dataset_17.dat" sampleclassNames "M" inclusive "TRUE" classnameColumn "gender" samplenameColumn "sampleMetadata" dataMatrix_out "/tmp/tmp4Jz5Zv/files/000/dataset_18.dat" sampleMetadata_out "/tmp/tmp4Jz5Zv/files/000/dataset_19.dat" variableMetadata_out "/tmp/tmp4Jz5Zv/files/000/dataset_20.dat" information "/tmp/tmp4Jz5Zv/files/000/dataset_21.dat"]
379 2017-05-09 15:54:21,503 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
380 2017-05-09 15:54:21,503 DEBUG [galaxy.tools.deps] Using dependency samtools version None of type conda
381 ok
382
383 ----------------------------------------------------------------------
384 XML: /tmp/tmp4Jz5Zv/xunit.xml
385 ----------------------------------------------------------------------
386 Ran 3 tests in 83.693s
387
388 OK
389 2017-05-09 15:54:27,359 INFO [test_driver] Shutting down
390 2017-05-09 15:54:27,359 INFO [test_driver] Shutting down embedded galaxy web server
391 2017-05-09 15:54:27,361 INFO [test_driver] Embedded web server galaxy stopped
392 2017-05-09 15:54:27,361 INFO [test_driver] Stopping application galaxy
393 2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] sending stop signal to worker thread
394 2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] job handler queue stopped
395 2017-05-09 15:54:27,361 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads
396 2017-05-09 15:54:27,361 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads
397 2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] sending stop signal to worker thread
398 2017-05-09 15:54:27,361 INFO [galaxy.jobs.handler] job handler stop queue stopped
399 2017-05-09 15:54:27,362 INFO [test_driver] Application galaxy stopped.
400 2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] sending stop signal to worker thread
401 2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] job handler queue stopped
402 2017-05-09 15:54:28,335 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 worker threads
403 2017-05-09 15:54:28,335 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 worker threads
404 2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] sending stop signal to worker thread
405 2017-05-09 15:54:28,335 INFO [galaxy.jobs.handler] job handler stop queue stopped
406 Testing complete. HTML report is in "/home/backdoor/w4mclassfilter_galaxy_wrapper/tool_test_output.html".
407 All 3 test(s) executed passed.
408 W4MClassFilter[0]: passed
409 W4MClassFilter[1]: passed
410 W4MClassFilter[2]: passed