From: "Anthonius deBoer" <thondeboer@me.com>
To: "J. Greenbaum" <jgbaum@liai.org>
Cc: galaxy-dev@lists.bx.psu.edu
Sent: Wednesday, May 23, 2012 2:03:18 PM
Subject: Re: [galaxy-dev] specifying nodes/processors with PBS

Yes, you can set these things for each tool independently.

Check the file

"universe_wsgi.ini"

and check the section:

[galaxy:tool_runners]

There you can set the -pe options for GSUB in the same way you can do on the command line...

Here's an example of my setup:

gatk_variant_select  = drmaa://-V -pe smp 1

gatk_validate_variants  = drmaa://-V -pe smp 1

far = drmaa://-V -pe smp 1

velveth = drmaa://-V -pe mpi 4

velvetg = drmaa://-V -pe mpi 8

I set the -pe mpi option to 8 for VELVETH/G and to 1 for GATK for instance

Thon

On May 23, 2012, at 12:47 PM, "J. Greenbaum" <jgbaum@liai.org> wrote:

Hi,

I've successfully configured a local galaxy instance to submit jobs to our local cluster, but have a question regarding setting PBS options such as the number of nodes and processors to use.  I've followed the guide here:

http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster?highlight=%28pbs%29 

Is there any way to do this in a tool-specific manner.  For example, for running tophat to do a mapping run, I would want it to use 24 CPUs, but for simply converting a file type I would want only 1 CPU requested.  Is there a way to specify this somewhere?

Thanks,

Jason

--

Jason Greenbaum, Ph.D.
Manager, Bioinformatics Core | jgbaum@liai.org
La Jolla Institute for Allergy and Immunology

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