This pretty much looks like it should work to me. Do you have a single
process Galaxy setup (i.e. is [server:main] the only server:* section
in your galaxy.ini file? Is there anything in the Galaxy log that
indicates a problem (can you send me a portion of log or post it here
related to the job submission)?.

-John

On Wed, Jul 22, 2015 at 7:51 PM, Benjamin Datko <bda...@carc.unm.edu> wrote:
> 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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