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.be...@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

________________________________
From: 
galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu> 
[galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Chorny, Ilya 
[icho...@illumina.com]
Sent: Tuesday, September 13, 2011 7:58 PM
To: galaxy-dev@lists.bx.psu.edu<mailto: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: icho...@illumina.com<mailto:icho...@illumina.com>
Website: www.illumina.com<http://www.illumina.com>


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