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,JasonJason Greenbaum, Ph.D.--
Manager, Bioinformatics Core | jgb...@liai.org
La Jolla Institute for Allergy and Immunology___________________________________________________________
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