pvanheus
/ planemo.log
Created
July 5, 2018 11:57
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| git --git-dir /home/pvh/.planemo/gx_repo fetch >/dev/null 2>&1 | |
| cd /tmp/tmp7eiSQ_; git clone --branch 'master' '/home/pvh/.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/pvh/.planemo/gx_venv_None; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/pvh/.virtualenvs/planemo/bin/virtualenv -p /home/pvh/.virtualenvs/planemo/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 ${COMMON_STARTUP_ARGS} | |
| Cloning into 'galaxy-dev'... | |
| done. | |
| Set COMMON_STARTUP_ARGS to --dev-wheels | |
| Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample | |
| Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample | |
| Initializing |
pvanheus
/ jbrowse.xml
Created
July 5, 2018 11:50
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| <tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.3"> | |
| <description>genome browser</description> | |
| <macros> | |
| <import>macros.xml</import> | |
| </macros> | |
| <expand macro="requirements"/> | |
| <expand macro="stdio"/> | |
| <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command> | |
| <command><![CDATA[ |
pvanheus
/ gist:08bec42ddd97c3796bc3fb21097ebf25
Created
June 22, 2018 14:33
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| galaxy.jobs.runners ERROR 2018-06-22 16:22:17,547 [p:25782,w:1,m:0] [LocalRunner.work_thread-0] (1) Failure preparing job | |
| Traceback (most recent call last): | |
| File "lib/galaxy/jobs/runners/__init__.py", line 192, in prepare_job | |
| job_wrapper.prepare() | |
| File "lib/galaxy/jobs/__init__.py", line 857, in prepare | |
| tool_evaluator.set_compute_environment(compute_environment, get_special=get_special) | |
| File "lib/galaxy/tools/evaluation.py", line 73, in set_compute_environment | |
| visit_input_values(self.tool.inputs, incoming, validate_inputs) | |
| File "lib/galaxy/tools/parameters/__init__.py", line 168, in visit_input_values | |
| callback_helper(input, input_values, name_prefix, label_prefix, parent_prefix=parent_prefix, context=context) |
pvanheus
/ gist:c4b9ed6c7227a2e4241c842eba91a588
Created
June 19, 2018 14:37
failed planemo test with TEMP with a space in it
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| $ export TEMP='/tmp/foo bar' | |
| $ mkdir /tmp/foo\ bar | |
| $ planemo test picard_FastqToSam.xml | |
| git --git-dir /home/pvh/.planemo/gx_repo fetch >/dev/null 2>&1 | |
| cd /tmp/foo bar/tmpWFLz4i; git clone --branch 'master' '/home/pvh/.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/pvh/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/pvh/.virtualenvs/planemo/bin/virtualenv -p /home/pvh/.virtualenvs/planemo/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} | |
| /bin/sh: 1: cd: can't cd to /tmp/foo | |
| Cloning into 'galaxy-dev'... | |
| done. | |
| Set COMMON_STARTUP_ARGS to --dev-wheels | |
| Initializing config/migrated_tool |
pvanheus
/ gist:94f5cb00844907ad1fe97f40ee606937
Created
May 25, 2018 10:12
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| $ singularity --debug exec --contain --pid --ipc --userns --bind /tmp/tmpv6cVzR:/var/spool/cwl:rw --bind /tmp/tmpvRfDmI:/tmp:rw --bind /home/pvh/cwltutorial/data/dna.txt:/var/lib/cwl/stgff5e1981-06d7-4a4c-a7c6-e958a8889599/dna.txt:ro --pwd /var/spool/cwl /home/pvh/cwltutorial/pvanheus-reverse-latest.img reverse.py /var/lib/cwl/stgff5e1981-06d7-4a4c-a7c6-e958a8889599/dna.txt > /tmp/tmpv6cVzR/dna_reversed.txt | |
| Enabling debugging | |
| Ending argument loop | |
| Singularity version: 2.4.5-dist | |
| Exec'ing: /usr/local/libexec/singularity/cli/exec.exec | |
| Evaluating args: '--contain --pid --ipc --userns --bind /tmp/tmpv6cVzR:/var/spool/cwl:rw --bind /tmp/tmpvRfDmI:/tmp:rw --bind /home/pvh/cwltutorial/data/dna.txt:/var/lib/cwl/stgff5e1981-06d7-4a4c-a7c6-e958a8889599/dna.txt:ro --pwd /var/spool/cwl /home/pvh/cwltutorial/pvanheus-reverse-latest.img reverse.py /var/lib/cwl/stgff5e1981-06d7-4a4c-a7c6-e958a8889599/dna.txt' | |
| VERBOSE [U=1024,P=6583] message_init() Set messagelevel to: 5 | |
| DEBUG [U=1024,P=6583] |
pvanheus
/ gist:7d7effb91229d1b51df11b59b46c6dfe
Created
May 23, 2018 18:44
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| <?xml version="1.0"?> | |
| <job_conf> | |
| <plugins> | |
| <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/> | |
| <plugin id="cluster" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="2"/> | |
| </plugins> | |
| <destinations default="cluster_default"> | |
| <destination id="local" runner="local"/> | |
| <destination id="cluster_default" runner="cluster"> | |
| <env id="VIRTUAL_ENV">/galaxy/galaxysrv/galaxy/.venv</env> |
pvanheus
/ gist:5cfdc8782a976cc9b09e1e7e5487567e
Created
May 23, 2018 18:29
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| 169.0.182.52 - - [23/May/2018:18:20:49 +0000] "GET /?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fblastxml_to_tabular%2F0.2.01&version=0.2.01&__identifer=r0ab3v9ctvb HTTP/1.0" 200 - "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/66.0.3359.181 Safari/537.36" | |
| [pid: 6574|app: 0|req: 2313/3015] 192.168.2.20 () {52 vars in 1574 bytes} [Wed May 23 18:20:49 2018] GET /?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fblastxml_to_tabular%2F0.2.01&version=0.2.01&__identifer=r0ab3v9ctvb => generated 246948 bytes in 86 msecs (HTTP/1.0 200) 2 headers in 73 bytes (2 switches on core 1) | |
| 169.0.182.52 - - [23/May/2018:18:20:50 +0000] "GET /api/webhooks HTTP/1.0" 200 - "https://galaxy.sanbi.ac.za/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fblastxml_to_tabular%2F0.2.01&version=0.2.01&__identifer=r0ab3v9ctvb" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/66.0.3359.181 Safari/537.36" | |
| [pid: 65 |
pvanheus
/ gist:e52313212f23a06876dc36ce79d51ea5
Created
May 15, 2018 12:04
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| $ cwltool --debug test.cwl | |
| /home/pvh/.virtualenvs/cwltool/bin/cwltool 1.0.20180403145700 | |
| Resolved 'test.cwl' to 'file:///home/pvh/Documents/code/cwl/testtool/test.cwl' | |
| I'm sorry, I couldn't load this CWL file. The error was: | |
| Traceback (most recent call last): | |
| File "/home/pvh/.virtualenvs/cwltool/local/lib/python2.7/site-packages/cwltool/main.py", line 483, in main | |
| do_validate=args.do_validate) | |
| File "/home/pvh/.virtualenvs/cwltool/local/lib/python2.7/site-packages/cwltool/load_tool.py", line 276, in validate_document | |
| _convert_stdstreams_to_files(workflowobj) | |
| File "/home/pvh/.virtualenvs/cwltool/local/lib/python2.7/site-packages/cwltool/load_tool.py", line 151, in _convert_stdstreams_to_files |
pvanheus
/ gist:d82ca626f500cff053ea89760257dfc5
Created
May 15, 2018 08:57
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| #!/usr/bin/env cwl-runner | |
| $namespaces: | |
| dct: http://purl.org/dc/terms/ | |
| foaf: http://xmlns.com/foaf/0.1/ | |
| $schemas: | |
| - http://dublincore.org/2012/06/14/dcterms.rdf | |
| - http://xmlns.com/foaf/spec/20140114.rdf |
pvanheus
/ gist:1d685ce0667229f771b5a43952766e95
Created
May 15, 2018 08:41
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| #!/usr/bin/env cwl-runner | |
| $namespaces: | |
| dct: http://purl.org/dc/terms/ | |
| foaf: http://xmlns.com/foaf/0.1/ | |
| $schemas: | |
| - http://dublincore.org/2012/06/14/dcterms.rdf | |
| - http://xmlns.com/foaf/spec/20140114.rdf |