Abyss (Optimizing the parameter k)

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5.5 years ago

Mbillah ▴ 140

How can i run this script on linux? what is "export k" mean?

export k

for k in {20..40}; do

mkdir k$k

abyss-pe -C k$k name=ecoli in=../reads.fa

done

abyss-fac k*/ecoli-contigs.fa

TIA

abyss Assembly kmer • 1.4k views

ADD COMMENT • link updated 5.4 years ago by Biostar 20 • written 5.5 years ago by Mbillah ▴ 140

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what exactly is not working?

the export k is bash syntax to declare a global variable but nothing to worry about that in your case. Not sure if this might cause the issue but there need to be at least a ; in between the export k and for k in

EDIT: OK, after your reformat the ; is not gonna be an issue ;)

ADD REPLY • link 5.5 years ago by lieven.sterck 15k

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So I need to run this by bash script? I want to know the execution way

ADD REPLY • link 5.5 years ago by Mbillah ▴ 140

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yes indeed, this is all linux cmdline.

What you need to do is to put all those commands (exactly how they are mentioned here) in a file (eg. runABySS.sh) and then run it on your machine with eg bash runABySS.sh .

ADD REPLY • link 5.5 years ago by lieven.sterck 15k

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