Nate,

Any thoughts on how to do this? Can I add an xml tag that gets parsed and set’s “ –PE mpi $NSLOTS” in the job template. Can you point me to where the xml get’s parsed?

Thanks,

Ilya

From: Glen Beane [mailto:Glen.Beane@jax.org]
Sent: Tuesday, September 13, 2011 5:00 PM
To: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Passing the number of mpi processors to SGE from xml file

I think with the current state of Galaxy this would need to be fixed.  You would need to hard code the number of processors in the xml wrapper and in the corresponding job runner for that tool

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From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Chorny, Ilya [ichorny@illumina.com]
Sent: Tuesday, September 13, 2011 7:58 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Passing the number of mpi processors to SGE from xml file

Any thoughts on how to pass the number of processor I want to use from my xml wrapper to the job template. I am trying to wrap pBWA and use mpi.

Thanks,

Ilya

Ilya Chorny Ph.D.

Bioinformatics Scientist I

Illumina, Inc.

9885 Towne Centre Drive

San Diego, CA 92121

Work: 858.202.4582

Email: ichorny@illumina.com

Website: www.illumina.com