combine GNU parallel with nested for loops and multiple variables

Question

I have n folders in destdir. Each folder contains two files: *R1.fastq and *R2.fastq. Using this script, it will do the job (bowtie2) one by one and output {name of the sub folder}.sam in the destdir.

#!/bin/bash

mm9_index="/Users/bowtie2-2.2.6/indexes/mm9/mm9"
destdir=/Users/Desktop/test/outdir/

for f in $destdir/*
do
fbase=$(basename "$f")
echo "Sample $fbase"
bowtie2 -p 4 -x $mm9_index -X 2000 \
-1 "$f"/*R1.fastq \
-2 "$f"/*R2.fastq \
-S $destdir/${fbase}.sam
done

I want to use gnu parallel tool to speed this up, can you help? Thanks.

Answer 1

Use a bash function:

#!/bin/bash

my_bowtie() {
  mm9_index="/Users/bowtie2-2.2.6/indexes/mm9/mm9"
  destdir=/Users/Desktop/test/outdir/
  f="$1"
  fbase=$(basename "$f")
  echo "Sample $fbase"
  bowtie2 -p 4 -x $mm9_index -X 2000 \
  -1 "$f"/*R1.fastq \
  -2 "$f"/*R2.fastq \
  -S $destdir/${fbase}.sam
}
export -f my_bowtie
parallel my_bowtie ::: $destdir/*

For more details: man parallel or http://www.gnu.org/software/parallel/man.html#EXAMPLE:-Calling-Bash-functions