This is my code for running samtools pileup:

open INP,"< $ARGV[0]"
 or die "Cannot open file! $!";
open INP2, "< $ARGV[1]"
 or die "Cannot open file! $!";

open OUT,"> $ARGV[2]"
 or die "Cannot open file! $!";
open SCRIPT,"samtools pileup -cv -f $ARGV[0] $ARGV[1] 2>/dev/null | ";
while(<SCRIPT>) {
 print OUT $_;
close INP;
close INP2;
close OUT;
close SCRIPT;
In the console, it works perfectly. But when run in Galaxy, it gives me an
empty file. I don't think it has something to do with the files that I am
using as input, for I just uploaded the ones that I used in the console
test-run. Any idea why this might be happening?


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