Question: (Closed) How to parallel task in bash elegantly?
1
gravatar for wang.yiguan
6 months ago by
wang.yiguan10
wang.yiguan10 wrote:

Are there any elegant way to parallel processing in bash? Something like R packages "parallel" or Python module "multiprocessing"! Thanks!

bash parallel • 346 views
ADD COMMENTlink modified 6 months ago by WouterDeCoster32k • written 6 months ago by wang.yiguan10

Hello wang.yiguan!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

PS: many duplicate on biostars.search for gnu parallel, Makefile , snakemake, cwl, xargs ...

ADD REPLYlink modified 6 months ago • written 6 months ago by Pierre Lindenbaum112k
3
gravatar for WouterDeCoster
6 months ago by
Belgium
WouterDeCoster32k wrote:

GNU parallel is a very flexible tool for this, e.g.

ls *.fastq | parallel -j 8 'bwa mem ref.fa {} > {.}.sam'

Use 8 jobs, do alignment for each file in *.fastq, output is input without extension (+ .sam).

ADD COMMENTlink modified 6 months ago • written 6 months ago by WouterDeCoster32k
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