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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
