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