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
/metadata_out_HistoryDatasetAssociation_100_Kk1ajw: No JSON object could
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.
<!-- '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"
<plugin id="pbs" type="runner"
<!-- Additional job handlers - the id should match the name of a
[server:<id>] in universe_wsgi.ini -->
<!-- Destinations define details about remote resources and how jobs
should be executed on those remote resources -->
<destination id="defaultq" runner="pbs" tags="cluster">
Thank you very much for all the assistance!
Ryan S. Johnson, PhD
Center for Advanced Research Computing
P: (650) 430-6194
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