Hi,

I'm using pbs/torque with galaxy, without any issues. However, I'm not using the drmaa interface, but the pbs-egg. Have you tried that one?


See: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#pbs_python_egg

after scrambling, I just set the following in universe:
start_job_runners = pbs
default_cluster_job_runner = pbs:///

and optionally per tool configurations:
bowtie_wrapper = pbs:///batch/-l nodes=1:ppn=8,mem=2700mb/
bowtie_color_wrapper = pbs:///batch/-l nodes=1:ppn=8,mem=2700mb/
bowtie2 = pbs:///batch/-l nodes=1:ppn=8,mem=2700mb/
tophat = pbs:///batch/-l nodes=1:ppn=8,mem=2700mb/
bwa_wrapper = pbs:///batch/-l nodes=1:ppn=8,mem=3500mb/

I did not set any drmaa-settings !

I also made sure that the galaxy-user was able to submit jobs from the commandline using qsub.

geert


On 06/01/2012 09:52 AM, Marc Bras wrote:
Hi !!

I've got a problem with PBS when I want to submit a job to our cluster with Galaxy. Every time, PBS says me /*"pbs_submit failed, PBS error 15023: Bad user - no password entry".*/

Indeed, Galaxy uses my email address (used in Galaxy) as user by default !
But, before, when I used SGE on my previous lab, Galaxy used the galaxy owner user and not my email...

Is it possible to set the owner user as previous Galaxy version ? (I found the */"drmaa_external_*"/* session in universe but I don't really understand how to configure this part...).

Thanks a lot,

Best Regards


BRAS Marc


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--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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