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?

 

Cheers,

 

CL