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