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
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,