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> > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/