Xian and I were able to resolve this on IRC, the problem is is that no default 
queue is specified in the PBS client (intentionally) and the `-q` param was 
improperly handled in the pbs job runner (it expected <param id=“destination”> 
instead).  This has been fixed in the stable branch in changeset 51b4282dce3a.

--nate

On Nov 14, 2013, at 4:50 PM, Jennifer Jackson <j...@bx.psu.edu> wrote:

> Hello, I am going to move your question over to the galaxt-...@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!
> Best,
> Jen
> Galaxy team
> 
> 
> On 11/14/13 6:35 AM, Xian Su wrote:
>> Greetings
>> 
>> 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"?>
>> <job_conf>
>>     <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"/>
>>     </plugins>
>>     <handlers default="handlers">
>>         <handler id="main" tags="handlers"/>
>>     </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>
>>         </destination>
>>     </destinations>
>>     <tools>
>>         <tool id="main" handler="main" destination="pbs"/>
>>     </tools>
>>     <limits>
>>     </limits>
>> </job_conf>
>> 
>> Thank you in advance for any help.
>> 
>> Regards,
>> Xian
>> 
>> 
>> ___________________________________________________________
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> 
> -- 
> Jennifer Hillman-Jackson
> 
> http://galaxyproject.org
> ___________________________________________________________
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