--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie_build_wrapper.pl	Wed Jul 23 10:27:07 2014 -0400
@@ -0,0 +1,33 @@
+#!/usr/bin/perl
+
+use File::Copy qw/ copy /;
+
+$ENV{PATH} .= ":/usr/local/apps/mirdeep2/2.0.0.5:/usr/local/apps/bowtie/0.12.9:/usr/local/apps/viennarna/current/bin:/usr/local/randfold-2.0/bin";
+
+$fastafile = $ARGV[0];
+$file_path = $ARGV[1];
+$output_file = $ARGV[2];
+$fastafile_text = $ARGV[3];
+
+$output_basename = `basename $output_file`;
+chomp $output_basename;
+$filepath_basename = `basename $file_path`;
+chomp $filepath_basename;
+
+$output_dir = $output_file;
+$output_dir =~ s/$output_basename/$filepath_basename/;
+
+system ("mkdir -p $file_path");
+copy ($fastafile, $output_file);
+copy ($output_file, $file_path);
+
+system ("bowtie-build $fastafile $file_path/$output_basename");
+
+open (OUTPUT,">$output_file");
+print OUTPUT "<h1>Bowtie index on $fastafile_text</h1>\n";
+$dirout = `ls $file_path`;
+
+foreach $file (split (/\n/, $dirout)) {
+	print OUTPUT "<a href='$file'>$file</a><br/>\n";
+}
+close (OUTPUT);