CODEWITHSUNDEEP
bashshellxargs
Shicheng Guo
Shicheng Guo

Reputation: 1293

how to pass two parameter in bash single line?

Suppose I have a command which require two parameter, such as

bismark -1 R1_1.fastq -2 R1_2.fastq

And actually, R1_1.fastq and R1_2.fastq can be obtain with 

ls *fastq | paste - -

or can be obtain with 

echo samplelist.txt

my question is how to merge these two command into one line? 

ls *fastq | paste - - | xargs -n 2 | bismark -1 {} -2 {}

Thanks.

Upvotes: 2

Views: 89

Answers (3)

Ole Tange
Ole Tange

Reputation: 33685

With GNU Parallel you would do:

ls *fastq | parallel -N2 bismark -1 {1} -2 {2}

Upvotes: 1

Zombo
Zombo

Reputation: 1

while read f g
do
  bismark -1 "$f" -2 "$g"
done < samplelist.txt

Or:

xargs -n2 sh -c 'bismark -1 "$1" -2 "$2"' . < samplelist.txt

Upvotes: 2

user8017719
user8017719

Reputation:

With an array, it would be simple:

a=(*fastq) ;  bismark -1 "${a[0]}" -2 "${a[1]}"

Upvotes: 1

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