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"?>
  <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"/>
    <handler id="main"/>
<!-- Additional job handlers - the id should match the name of a [server:<id>] in universe_wsgi.ini -->
  <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>

Thank you very much for all the assistance!


Ryan S. Johnson, PhD
  Applications Scientist
  Center for Advanced Research Computing
  P: (650) 430-6194

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:

To search Galaxy mailing lists use the unified search at:

Reply via email to