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.agresearch.co.nz/toolshed/repos/guestsi/emboss_5_native/EMBOSS%3A%20infoseq46/5.0.0";
"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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