GenomeSTRIP and Slurm

tfarauttfaraut Toulouse, FranceMember

Hi Wusheng,

A few words regarding your question about running genomeSTRIP on a cluster
with a SLURM scheduler (I am using slurm 17.02.7).
Here is what I understood, and I hope someone will correct me if I am wrong.

deletions

SVPreprocess, SVDiscovery and SVGenotyper

with drmaa
Make sure the Drmaa library is in your path

export DRMAA_LIBRARY_PATH=PATH_TO_YOUR_DRMAA_LIB/libdrmaa.so

and simply add the following arguments

  -jobRunner Drmaa
  -gatkJobRunner Drmaa
  -jobNative "--mem-per-cpu=XXXX --time=XXXX ..."
  -jobQueue THE_PARTITION

to the SVPreprocess, SVDiscovery and SVGenotyper scripts, and it will
smoothly interact with slurm using the drmaa API.

without drmaa
This will still work, simply omit the previous 4 lines and it will run as a
single process, hence without prarallelization... Mentionning slurm
here is meaningless because genomestrip doesn't interact with the cluster

mCNV

CNVDiscoveryPipeline

with drmaa
same as above
without drmaa
not possible

I Hope this helps,
Thomas

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