Hello, I am going to move your question over to the galaxt-dev@bx.psu.edu mailing list to give it better visibility to the development/local install community. http://wiki.galaxyproject.org/MailingLists#The_lists
I didn't find it over here already, but apologies if double posted. Also, since I don't know the best answer, will let others jump in!
Galaxy team

On 11/14/13 6:35 AM, Xian Su wrote:

I'm having a hard time getting job submission to work via torque. Posted below is the relevant part of my universe file and job_conf.xml.

The main cause comes from our torque server requiring a queue to be requested. I can submit jobs just fine via job .sub files via command line using qsub -q M30

Running jobs via webgui results in the following:
galaxy.jobs.runners.pbs WARNING 2013-11-14 13:54:23,722 (28) pbs_submit failed (try 5/5), PBS error 15039: Route rejected by all destinations
galaxy.jobs.runners.pbs ERROR 2013-11-14 13:54:25,724 (28) All attempts to submit job failed

On the torque server's pbs logs, I see the corresponding
11/14/2013 13:54:23;0080;PBS_Server.66159;Req;req_reject;Reject reply code=15039(No default queue specified MSG=requested queue not found), aux=0, type=QueueJob, from xians@podmt1-100-62.novalocal

In my universe_wsgi.ini, I'm currently using the settings:
start_job_runners = pbs
default_cluster_job_runner = pbs:///-q M30 -l nodes=1:ppn=12/
^I mainly have no idea how to find the correct syntax for this pbs:///

But when I comment out default_cluster_job_runner and instead uncomment the line for the following job conf, I get the same error:
<?xml version="1.0"?>
    <plugins workers="4">
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
        <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/>
    <handlers default="handlers">
        <handler id="main" tags="handlers"/>
    <destinations default="pbs">
        <destination id="local" runner="local"/>
        <destination id="pbs" runner="pbs" tags="mycluster">
            <param id="Resource_List">walltime=72:00:00,nodes=1:ppn=12</param>
            <param id="-q">M30</param>
        <tool id="main" handler="main" destination="pbs"/>

Thank you in advance for any help.


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Jennifer Hillman-Jackson