--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mirdeep2_wrapper.pl	Wed Jul 23 10:27:07 2014 -0400
@@ -0,0 +1,71 @@
+#!/usr/bin/perl
+
+use File::Temp qw/ tempfile tempdir /;
+use File::Copy qw/ copy /;
+use Cwd;
+
+$ENV{PATH} .= ":/usr/local/apps/mirdeep2/2.0.0.5:/usr/local/apps/bowtie/0.12.9:/usr/local/apps/viennarna/current/bin:/usr/local/randfold-2.0/bin";
+
+$collapsed_reads = $ARGV[0];
+$bowtie_index_name = $ARGV[1];
+$bowtie_files_path = $ARGV[2];
+$arf_file = $ARGV[3];
+$mirna_ref = $ARGV[4];
+$mirna_other = $ARGV[5];
+$precursors = $ARGV[6];
+$file_path = $ARGV[7];
+$input_name = $ARGV[8];
+
+$csv_output = $ARGV[9];
+$html_output = $ARGV[10];
+$survey_output = $ARGV[11];
+$mrd_output = $ARGV[12];
+
+# the rest are options
+$options = join (" ", @ARGV[13..$#ARGV]);
+
+#point to correct bowtie index path
+$basename = `basename $bowtie_index_name`;
+chomp $basename;
+
+# create the path used to house the pdfs
+chomp $file_path;
+system ("mkdir -p $file_path");
+
+# do all the dirty work in a temp directory
+$cwd = cwd();
+$tempdir = tempdir(CLEANUP => 1);
+chdir ($tempdir);
+
+if ($mirna_ref eq "None") {$mirna_ref="none";}
+if ($mirna_other eq "None") {$mirna_other="none";}
+if ($precursors eq "None") {$precursors="none";}
+
+$ret_mirdeep2 = `miRDeep2.pl $collapsed_reads $bowtie_files_path/$basename $arf_file $mirna_ref $mirna_other $precursors -v $options 2> /dev/null`;
+system ("cp $tempdir/pdfs*/*.pdf $file_path");
+
+$csv_file = `ls $tempdir/result*.csv`;
+chomp $csv_file;
+if ($csv_file eq "") {die "Error: Cannot find csv result file in dir $tempdir\n";}
+
+$html_file = `ls $tempdir/result*.html`;
+chomp $html_file;
+if ($html_file eq "") {die "Error: Cannot find html result file in dir $tempdir\n";}
+
+$survey_file = `ls $tempdir/mirdeep_runs/run*/survey.csv`;
+chomp $survey_file;
+if ($survey_file eq "") {die "Error: Cannot find survey result file in dir $tempdir\n";}
+
+$mrd_file = `ls $tempdir/mirdeep_runs/run*/output.mrd`;
+chomp $mrd_file;
+if ($mrd_file eq "") {die "Error: Cannot find hairpin result file in dir $tempdir\n";}
+
+# replacing mirdeep created links with relative links in galaxy
+system ("sed -r -i 's/file:\\/\\/.+\\/(.+\\.pdf)/\\1/g' $html_file");
+
+copy ($csv_file, $csv_output);
+copy ($html_file, $html_output);
+copy ($survey_file, $survey_output);
+copy ($mrd_file, $mrd_output);
+
+chdir($cwd);