Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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.


SVPreprocess, SVDiscovery and SVGenotyper

with drmaa
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 ..."

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



with drmaa
same as above
without drmaa
not possible

I Hope this helps,


Sign In or Register to comment.