Hello all,
I am trying to config a cluster galaxy server using PBS torque. I have
gone through the documentation but it is not clear to me how the
job_conf.xml should be set up. Are there detailed documents on how
galaxy works with the resource manger and how galaxy submits jobs?
My current problem jobs can be created and submitted but within the
history tab I have "this job is waiting to run". The job never gets
submitted to PBS torque queue and cannot be seen using qstat. My
job_conf.xml is shown below. If anyone can give a sample to a working
configuration file for job_conf.xml using PBS torque that will be most
appreciated.
Ben
<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way
it is configured by default (if there is no explicit config). -->
<job_conf>
<plugins>
<plugin id="pbs" type="runner"
load="galaxy.jobs.runners.pbs:PBSJobRunner"/>
</plugins>
<handlers>
<handler id="main"/>
</handlers>
<destinations default="Core2">
<destination id="Core2" runner="pbs">
<param id="Resource_List">-l
walltime=24:00:00,nodes=1:ppn=2</param>
</destination>
</destinations>
</job_conf>
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