Has anyone tried to run SNPEff, Bedtools or Prokka with GNU parallel or a similar batch engine?

Question

[bioinformatics_bel]

Has anyone tried to run SNPEff, Bedtools, BEDOPS or Prokka with GNU parallel or a similar batch engine? I need some code samples and patterns/example, pls. Thx.

[Madelaine Gogol]

You may find Pierre Lindenbaum's tutorial on parallel useful.

Answer 1

[5heikki]

#!/bin/bash

function doSomething(){
    program "$1"
}

export -f doSomething
find /place/with/input/files -name "*.txt" \
    | parallel -j 32 doSomething {}

GNU parallel is great for embarrassingly parallel problems..

Answer 2

[WouterDeCoster]

The GNU parallel manual is overwhelming, but you can solve your own question by just doing some reading.

Nevertheless, default gnu-parallel command for my applications:

ls *.vcf | parallel -j 8 'do snpeff stuff on file {}'