I am having trouble getting a toolshed tool to be dispatched to the destination I list in the job_conf.xml file.
My job_conf.xml file looks like this:
<?xml version="1.0"?> <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="20"/> <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="condor"> <destination id="local" runner="local"/> <destination id="condor" runner="condor"> <!-- With no params, jobs are submitted to the 'vanilla' universe with: notification = NEVER getenv = true Additional/override query ClassAd params can be specified with <param> tags, e.g <param id="request_cpus">8</param> --> </destination> </destinations> <tools> <tool id="upload1" destination="local"/> <!-- Upload File --> <tool id="ucsc_table_direct1" destination="local"/> <!-- UCSC Main -->
... stuff omitted ...
<tool id="toolshed-dev.agresearch.co.nz/toolshed/repos/guestsi/emboss_5_native/EMBOSS: infoseq46/5.0.0" destination="local"/> </tools> </job_conf>
So, you can see I have a default destination of condor, but I'm trying to run my toolshed EMBOSS infoseq tool on local. However, it is stubbornly running on condor.
In lib/galaxy/tools/__init__.py:1132, I see this comment which got me wondering: # In the toolshed context, there is no job config.
Is it possible to define tool destinations for toolshed tools? Are there some gotchas that I should know about? Any other ideas why my job is ignoring the config in job_conf.xml? (By the way, I can change say the upload1 tool to run on Condor by setting its destination in that file, so it is doing something.) The other thing I saw in the source code is stuff about old_id and toolshed guids. Do I need to understand this stuff?
The paster.log contains the following when I submit the infoseq job:
147.158.130.216 - - [11/Sep/2013:13:53:34 +1300] "GET /tool_runner?tool_id=toolshed-dev.agresearch.co.nz/toolshed/repos/guestsi/emboss_5_native/EMBOSS%3A%20infoseq46/5.0.0 HTTP/1.1" 200 - "http://galaxy-dev.agresearch.co.nz/" "Mozilla/5.0 (X11; Linux x86_64; rv:23.0) Gecko/20100101 Firefox/23.0" 147.158.130.216 - - [11/Sep/2013:13:53:40 +1300] "POST /tool_runner/index HTTP/1.1" 200 - "http://galaxy-dev.agresearch.co.nz/tool_runner?tool_id=toolshed-dev.agresear..." "Mozilla/5.0 (X11; Linux x86_64; rv:23.0) Gecko/20100101 Firefox/23.0" galaxy.jobs DEBUG 2013-09-11 13:53:40,886 (92) Working directory for job is: /home/galaxy-dev/galaxy/database/job_working_directory/000/92 galaxy.tools DEBUG 2013-09-11 13:53:40,886 Tool::get_job_destination: {'runner': 'condor', 'legacy': False, 'params': {}, 'tags': None, 'url': None, 'converted': False, 'id': 'condor'}. galaxy.jobs.handler DEBUG 2013-09-11 13:53:40,894 (92) Dispatching to condor runner
(I added the debug output for Tool::get_job_destination to see what was going on.)
Any ideas?
cheers, Simon
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