Excellent! Thanks for the reply.
-- Jason Greenbaum, Ph.D.
Manager, Bioinformatics Core | jgb...@liai.org
La Jolla Institute for Allergy and Immunology
----- Original Message -----
> From: "Anthonius deBoer" <thondeb...@me.com>
> To: "J. Greenbaum" <jgb...@liai.org>
> Cc: firstname.lastname@example.org
> 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
> and check the section:
> 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
> On May 23, 2012, at 12:47 PM, "J. Greenbaum" <jgb...@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 | jgb...@liai.org
> > La Jolla Institute for Allergy and Immunology
> > ___________________________________________________________
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