diff mapper_wrapper.pl @ 0:1bdefe8a8676 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mapper_wrapper.pl	Fri Jul 18 13:55:59 2014 -0400
@@ -0,0 +1,15 @@
+#!/usr/bin/perl
+
+$ENV{PATH} .= ":/usr/local/apps/mirdeep2/2.0.0.5:/usr/local/apps/bowtie/0.12.9:/usr/local/apps/viennarna/current/bin:/usr/local/randfold-2.0/bin";
+
+$bowtie_index_name = $ARGV[0];
+$output_arf = $ARGV[1];
+$bowtie_files_path = $ARGV[2];
+$options = join (" ", @ARGV[3..$#ARGV]);
+
+$basename = `basename $bowtie_index_name`;
+chomp $basename;
+
+system ("mapper.pl $options -p $bowtie_files_path/$basename -t $output_arf 2> /dev/null");
+
+if (-s $output_arf == 0) {die "No reads aligned to the reference.";}