If you need to use PBS Pro with Galaxy 16.01.

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If you need to use PBS Pro with Galaxy 16.01.

SAPET, Frederic

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 : [hidden email]

 


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