Question

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

1

Entering edit mode

6.5 years ago

bioinformatics_bel ▴ 20

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.

gnu parallel snpeff bedtools prokka • 1.5k views

ADD COMMENT • link updated 6.5 years ago by WouterDeCoster 47k • written 6.5 years ago by bioinformatics_bel ▴ 20

0

Entering edit mode

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

ADD REPLY • link 6.5 years ago by Madelaine Gogol 5.3k

score 2 · Answer 1 · 2017-11-01

2

Entering edit mode

6.5 years ago

5heikki 11k

#!/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..

ADD COMMENT • link 6.5 years ago by 5heikki 11k

score 1 · Answer 2 · 2017-11-02

1

Entering edit mode

6.5 years ago

WouterDeCoster 47k

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 {}'

ADD COMMENT • link 6.5 years ago by WouterDeCoster 47k