[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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