Entering edit mode
5.6 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
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 theexport k
andfor k in
EDIT: OK, after your reformat the
;
is not gonna be an issue ;)So I need to run this by bash script? I want to know the execution way
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
.