Excellent! Thanks for the reply. -J
-- 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: 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" <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 > > > ___________________________________________________________ > > > Please keep all replies on the list by using "reply all" > > > in your mail client. To manage your subscriptions to this > > > and other Galaxy lists, please use the interface at: > > > http://lists.bx.psu.edu/ >
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