GenomeSTRIP and Slurm
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.
SVPreprocess, SVDiscovery and SVGenotyper
Make sure the Drmaa library is in your path
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.
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
same as above
I Hope this helps,