Hello

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/12.2.4.142262) 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)

  File "/softs/bioinfo/galaxy-prod/.venv/lib/python2.7/site-packages/drmaa/session.py", line 314, in runJob

    c(drmaa_run_job, jid, sizeof(jid), jobTemplate)

  File "/softs/bioinfo/galaxy-prod/.venv/lib/python2.7/site-packages/drmaa/helpers.py", line 299, in c

    return f(*(args + (error_buffer, sizeof(error_buffer))))

  File "/softs/bioinfo/galaxy-prod/.venv/lib/python2.7/site-packages/drmaa/errors.py", 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 12.2.4.142262, DRMAA 1.0.19 and the latest galaxy (after a git pull command)

Fred

---

Frederic Sapet

Bioinformatics Research Engineer

BIOGEMMA - Upstream Genomics Group

Centre de Recherche de Chappes

CS 90126

63720 CHAPPES

FRANCE

Tel : +33 (0)4 73 67 88 54

Fax : +33 (0)4 73 67 88 99

E-mail : frederic.sapet@biogemma.com