Question: Best way to define rule ressources, and interactions with cluster submission or local submission
gravatar for maria.bernard
19 months ago by
INRA France
maria.bernard0 wrote:


I was looking for a way to access cluster_config dictionnary to define specific ressources in some particular rules (like -Xmx memory for java programs).

I understood that it's not ideally, because the Snakefile became dependant of the execution mode on a cluster.

I tried to understand the resources options and rule's tag. But it's not clear for me how it works and how it interact with --drmaa syntaxe or with --cluster

For me, ideally, I would like to define a resources.yaml that can be accessible in the Snakefile and in the submit command sheme (something like : " qsub -pe parallel_smp {resources.cpu} -l mem={resources.mem}" )

Is that possible ? If not, what is the solution : - define resources in rule AND in cluster-config if executing Snakefile on a cluster ?

I don't see any other solutions for now ....but I believe that we can do better, no ?

Any help would be much appreciate.

Best regards


snakemake • 310 views
ADD COMMENTlink written 19 months ago by maria.bernard0
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