Hello All,

We are using a Bio-Linux 8 Galaxy instance and are currently trying to integrate in into a PBS/Torque cluster. Currently we are able to run jobs locally but not via PBS. Can anyone provide us with a step by step guide to configure Galaxy and the PBS.


I have included some of the errors we are receiving below:

galaxy.datatypes.metadata DEBUG 2015-08-19 14:56:42,920 Failed to cleanup MetadataTempFile temp files from /usr/lib/galaxy-server/database/job_working_directory/000/96 /metadata_out_HistoryDatasetAssociation_100_Kk1ajw: No JSON object could be decoded

galaxy.jobs.runners.pbs ERROR 2015-08-19 14:56:42,960 Connection to PBS server for submit failed: 0: no error

We can not figure out what is stopping our jobs from entering the PBS queue. Below is our job_conf.xml.

<?xml version="1.0"?>
<job_conf>
  <plugins workers="2">
<!-- 'workers' is the number of threads for the runner's work queue. -->
<!-- The default from <plugins> is used if not defined for a <plugin> -->
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner"/>
  </plugins>
  <handlers>
    <handler id="main"/>
<!-- Additional job handlers - the id should match the name of a [server:<id>] in universe_wsgi.ini -->
  </handlers>
  <destinations default="defaultq">
<!-- Destinations define details about remote resources and how jobs should be executed on those remote resources -->
    <destination id="defaultq" runner="pbs" tags="cluster">
    <param id="-q">defaultq</param>
        <param id="-l">walltime=24:00:00</param>
    </destination>
  </destinations>
</job_conf>

Thank you very much for all the assistance!

Regards,
Ryan

--
Ryan S. Johnson, PhD
  Applications Scientist
  Center for Advanced Research Computing
  P: (650) 430-6194
  E:rjohn...@carc.unm.edu



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