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
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