Running standalone Galaxy stable_2013.06.03 version on RH6.2 with postgresl
db with GPFS filesystem.
Setup via the directions in
to run all jobs through the LSF DRMAA runner.
<plugin id="drmaa" type="runner"
<destination id="lsf" runner="drmaa"/>
Scheduler and Galaxy were started.
Submit a FASTQ groomer job on a FASTQ file under Galaxy.
The groomer job in History will stay in GREY "Job is waiting to run" state
until one physically go onto the node and submits a command line job
through the scheduler.
Once that command line job (e.g. sleep 5) is submitted then the groomer
job will show up in the scheduler's job queue and galaxy's HISTORY will now
show it as running.
I can submit another groomer job after this and it will show up as running.
At times, one will see this type of scenario again where one has to
manually start a job under the scheduler on the command line to trigger the
galaxy's jobs to start running under the scheduler.
Is there some setup I am missing in the job_conf.xml above or a flag not
set in universe_wsgi.ini?
Searching the Galaxy web, I had read that one can set the
track_jobs_in_database=True to trigger it to look in memory or database.
But that didn't work either.
Wonder if anyone seen this type of issue with any runners and have any
suggestions on how to debug and fix this.
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