Has anyone tried to run SNPEff, Bedtools or Prokka with GNU parallel or a similar batch engine?
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.
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2 answers
#!/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..
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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 {}'
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You may find Pierre Lindenbaum's tutorial on parallel useful.