diff blat_wrapper.pl @ 1:da4426cac227 draft

Fixed tests

--- a/blat_wrapper.pl	Thu May 30 07:13:55 2013 -0400
+++ b/blat_wrapper.pl	Wed Jul 24 16:23:44 2013 +0200
@@ -28,16 +28,14 @@
 ########################################################################
 my ($configfile) = @ARGV;
 my (%para);
-open(CONFIG,"<$configfile");
+open(CONFIG,"<",$configfile);
 while (<CONFIG>) {
 	if (/(\S+)==(.+)$/){ $para{ $1 } = $2 ; }
 }
 close(CONFIG);
 
 =Excerpt Config parameters
-			## first we pass some galaxy environment variables
-			galtemp==${__new_file_path__}
-			
+
 			## first we pass some galaxy environment variables
 			galtemp==${__new_file_path__}
 			
@@ -76,7 +74,6 @@
 	INFO "$para\tset to\t$para{$para}";
 }
 
-
 # ---------------------- Prepping temp dir ----------------------------#
 ########################################################################
 # within the temporary directory of Galaxy, we create a temporary dir
@@ -90,10 +87,14 @@
 mkdir "$tempdir", 077 unless -d "$tempdir";
 INFO "\nTemporary directory:\n$tempdir";
 
+# --------------------- Checking executable ---------------------------#
+########################################################################
+#~ my $command = "which blat ";
+#~ run_process($command, "Testing path", $tempdir);
 
 # -------------------- Assembling command  ----------------------------#                                                             
 ########################################################################                                                             
-my $command = "blat ";   # this will ultimately be executed
+my $command = "blat ";   			# this will ultimately be executed
 $command .= " $para{'referencepath'}";     
 if ( $para{'range'} ) { 
 	## format checking of the provided range
@@ -118,7 +119,7 @@
 
 if ( $para{'advanced_params.use'} eq "yes" ){
 	delete($para{'advanced_params.use'});
-	$command .= " 	-minScore=$para{'minScore'} -maxGap=$para{'maxGap'} -mask=$para{'mask'} -qMask=$para{'qMask'} -oneOff=$para{'oneOff'}  -minMatch=$para{'minMatch'} -tileSize=$para{'tileSize'} 	-stepSize=$para{'stepSize'} -maxIntron=$para{'maxIntron'} ";
+	$command .= " -minScore=$para{'minScore'} -maxGap=$para{'maxGap'} -mask=$para{'mask'} -qMask=$para{'qMask'} -oneOff=$para{'oneOff'}  -minMatch=$para{'minMatch'} -tileSize=$para{'tileSize'} -stepSize=$para{'stepSize'} -maxIntron=$para{'maxIntron'} ";
 	if($para{'repeats'} eq 'yes' ){
 		$command .= " -repeats=$para{'qMask'}";
 	}