Using the previous version of Galaxy (before the 16.01) we were able to use PBS 
Pro as job management system.

It was ok using  PBS (/opt/pbs/ and DRMAA (pbs-drmaa-1.0.17).
This only thing to do was to truncate the job name that Galaxy send to PBS.
Indeed, in the file lib/galaxy/jobs/runners/__init__.py you need to add :
self.job_name = self.job_name[:15]
in the AsynchronousJobState class otherwise PBS will reject the job.

Using the current version of Galaxy, this is not enough.
You will need to change another file : lib/galaxy/jobs/runners/drmaa.py

And change jt.jobName = ajs.job_name to jt.jobName = ajs.job_name[:15] in the 
DRMAAJobRunner class (around line 140)

You will then avoid this error :

galaxy.jobs.runners.drmaa ERROR 2016-03-24 15:23:23,880 (18) 
drmaa.Session.runJob() failed unconditionally
Traceback (most recent call last):
  File "/softs/bioinfo/galaxy-prod/lib/galaxy/jobs/runners/drmaa.py", line 181, 
in queue_job
    external_job_id = self.ds.runJob(jt)
 line 314, in runJob
    c(drmaa_run_job, jid, sizeof(jid), jobTemplate)
 line 299, in c
    return f(*(args + (error_buffer, sizeof(error_buffer))))
line 151, in error_check
    raise _ERRORS[code - 1](error_string)
InvalidAttributeValueException: code 14: Illegal attribute or resource value: 
Illegal attribute or resource value
galaxy.jobs.runners.drmaa ERROR 2016-03-24 15:23:23,883 (18) All attempts to 
submit job failed

I hope this will help if you plan to use Galaxy over PBS Pro. We currently used 
PBS, DRMAA 1.0.19 and the latest galaxy (after a git pull command)


Frederic Sapet
Bioinformatics Research Engineer
BIOGEMMA - Upstream Genomics Group
Centre de Recherche de Chappes
CS 90126
Tel : +33 (0)4 73 67 88 54
Fax : +33 (0)4 73 67 88 99
E-mail : frederic.sa...@biogemma.com<mailto:frederic.sa...@biogemma.com>

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