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 : [email protected]<mailto:[email protected]>
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