genome music bmr calc-covg [Run in parallel]

Question

[Chirag Nepal]

I used genome music to calculate significant pathways, which works great.

In the first, where coverage is calculated,

genome music bmr calc-covg --gene-covg-dir geneCov_combined --bam-list $bamList --output-dir $outDir --reference-sequence $assembly --roi-file $roi

This step is very time consuming when you have 100s of samples.

Is there any way if this can be run in parallel?

I think, dividing sample into subgroups also does not work here.

Any suggestions?

Answer 1

[Chris Miller]

I believe there is a --cmd-list-file argument to that tool which outputs a list of commands for each bam into a file. Those can then be run in parallel or submitted to a cluster.

[Cyriac Kandoth]

Also note the --cmd-prefix which allows you to specify the job submission command. Read The Fancy Manual for more information.