I'm trying to get my instance of Galaxy working with Sun Grid Engine. The
page https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster is not
100% clear on how to do this but I here's what my job_conf.xml looks like:
<?xml version="1.0"?>
<job_conf>
<plugins>
<plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
<plugin id="sge" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
<!-- Override the $DRMAA_LIBRARY_PATH environment
variable -->
<param
id="drmaa_library_path">/apps/sys/sge/ge2011.11/lib/linux-x64/libdrmaa.so</param>
</plugin>
</plugins>
<handlers>
<handler id="sge"/>
</handlers>
<destinations default="sge">
<destination id="local" runner="local" />
<destination id="sge" runner="sge">
</destination>
</destinations>
</job_conf>
I tried to submit a job via Galaxy and at first the log files indicated the
shell script got created in the job_working_dir and I was a job ID, but
when the job completed, Galaxy didn't know about it. Now, I have no jobs
runnings and I can't submit anything via Galaxy. It doesn't appear to
submit them to SGE or even create the directory for the job. Pastor.log
doesn't show anything either. So, I guess I could use a little help with
getting Galaxy running with SGE. I have a simple set up so nothing fancy.
Any ideas where to get started?
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