--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamqc_wrapper.pl	Tue Feb 12 04:48:36 2013 -0500
@@ -0,0 +1,142 @@
+#!/usr/bin/perl
+# bamqc_wrapper.pl
+# Joachim Jacob - joachim.jacob@gmail.com - 2013
+
+use strict;
+use File::Temp 'tempdir';
+use File::Basename;
+use Log::Log4perl qw(:easy);
+
+# ---------------------- Prepping Logging -----------------------------#
+########################################################################
+# Log levels: 			$DEBUG	$INFO	$WARN	$ERROR	$FATAL
+# ConversionPattern:	%d %-5p %F{1} [%M] (line %L): %m%n%n
+my $log_conf = q/ 
+    log4perl.category = ERROR, Screen 
+    log4perl.appender.Screen.stderr=1
+    log4perl.appender.Screen.layout=Log::Log4perl::Layout::PatternLayout
+    log4perl.appender.Screen.layout.ConversionPattern = %d %-5p %m%n
+    log4perl.appender.Screen        = Log::Log4perl::Appender::Screen 
+/;
+
+Log::Log4perl::init( \$log_conf );
+my $logger = get_logger();
+
+# ----------------- Getting parameters file ---------------------------#
+########################################################################
+my ($configfile) = @ARGV;
+my (%para);
+open(CONFIG,"<$configfile");
+while (<CONFIG>) {
+	if (/(\S+)==(.+)$/){ $para{ $1 } = $2 ; }
+}
+close(CONFIG);
+
+=Excerpt Config parameters
+
+    ## first we pass some galaxy environment variables
+        galtemp==${__new_file_path__}
+
+        bam==$bam
+        c==$c
+        hm==$hm
+        nr==$nr
+        #if $customgtf.upload=="yes"
+         gff==$customgtf.gff
+         os==$customgtf.os
+         p==$customgtf.p
+        #end if
+
+=cut
+
+for my $para (keys %para){
+	INFO "$para\tset to\t$para{$para}";
+}
+
+
+# ---------------------- Prepping temp dir ----------------------------#
+########################################################################
+# within the temporary directory of Galaxy, we create a temporary dir
+
+my $galtemp = $para{'galtemp'};
+DEBUG "\nReceived Galaxy temporary directory:\n$galtemp";
+
+my $tempdir = File::Temp->tempdir('tmpXXXXX', DIR => $galtemp, CLEANUP => 1); 
+mkdir "$tempdir", 077 unless -d "$tempdir";
+INFO "\nTemporary directory:\n$tempdir";
+
+
+# ---------------------- Output files ---------------------------------#
+########################################################################
+# Two possible scenarios
+# - output is written to the file at the output location in config file
+# - output is moved to the output file location
+
+# open (SAMOUTPUT, ">$para{'output_sam'}") 
+# 	or ( ERROR "Could not open output file for writing! (file:$para{'output_sam'}" and die );
+# print SAMOUTPUT "Here comes sam\n";
+# close (SAMOUTPUT);	
+
+
+# -------------------- Assembling command  ----------------------------#
+########################################################################
+my $outdir="bamqc_output";
+my $qualimap_path="";						# for tool_dependency later on
+my $command = $qualimap_path."qualimap bamqc --outdir $outdir"; # this will ultimately be executed
+
+# based on parameters, which are called by $para{'parametername'}
+# the command is assembled
+$command .= " -bam $para{'bam'} -hm $para{'hm'} -nr $para{'nr'}";
+if($para{'c'}){$command .= " $para{'c'} "; }
+if ( $para{'gff'} ){
+	$command .= " -gff $para{'gff'} -p $para{'p'} ";
+	if($para{'os'}) {
+	    $command .= $para{'os'}; 
+	}
+} 
+	
+$command .= " -nt 4 -outformat HTML";
+
+
+# --------------------- Executing command  ----------------------------#
+########################################################################
+run_process($command, "qualimap bamqc", ".");
+
+
+# ----------------- Postprocessing command  ---------------------------#
+########################################################################
+# Hackish !!
+
+my $librarydir = dirname($para{'bamqc_result'});
+my $jobworkdir = dirname($para{'outputdir'});
+my $files_path_name = basename($para{'outputdir'});
+INFO "\n Librarydir = $librarydir \n jobworkdir = $jobworkdir \n files_path_name = $files_path_name \n";
+system("mv $jobworkdir/bamqc_output $librarydir/$files_path_name") == 0 or die "Could not move output data to $librarydir\n";
+system("rm -rf $para{'bamqc_result'}") == 0 or die "Could not post-process the results...\n";
+system("ln -s $librarydir/$files_path_name/qualimapReport.html $para{'bamqc_result'}") == 0 or die "Could not move output data to $librarydir\n";
+
+
+# --------------------------- Exiting  --------------------------------#
+########################################################################
+exit 0;
+
+
+
+###	      Subroutines 					     ###
+########################################################################
+sub run_process {
+	my ($command, $name, $tempdir)= @_;
+	my $logger = get_logger();
+	INFO "\nProcess to launch:\n $command\nIn directory\n$tempdir\n";
+	system("cd $tempdir; $command 2>/dev/null") == 0 or die "$name failed\nExit status $?\nCommand: $command";
+	if ($? == -1) {
+		print "failed to execute: $!\n";
+	} elsif ($? & 127) {
+		printf "child died with signal %d, %s coredump\n", ($? & 127), ($? & 128) ? 'with' : 'without';
+	} else {
+		printf "$name executed successfully\n", $? >> 8;
+	}	
+}
+
+
+