debian/patches/cgview_path.patch

+--- a/conf/global_settings.conf
++++ b/conf/global_settings.conf
+@@ -44,7 +44,7 @@ myva_file = $cogs_files/myva
+ 
+ cgview_xml_builder = $comparison_tool/lib/scripts/cgview_xml_builder/cgview_xml_builder.pl
+ 
+-cgview = $comparison_tool/bin/cgview.jar
++cgview = /usr/share/java/cgview.jar
+ 
+ project_settings = $comparison_tool/conf/project_settings.conf
+ 

debian/patches/debug.patch

+--- a/lib/scripts/local_blast_client/local_blast_client.pl
++++ b/lib/scripts/local_blast_client/local_blast_client.pl
+@@ -258,8 +258,11 @@ while ( my $sequenceEntry = <SEQFILE> )
+ 
+     print
+         "Performing BLAST search for sequence number $seqCount ($sequenceTitle).\n";
++    print "DEBUG: $blast_command\ncontent of $filename is:\n";
++    `cat $filename` ;
+ 
+     my $result = `$blast_command`;
++    print "DEBUG: result = $result\n";
+ 
+     my $hitFound = 0;
+     my $HSPCount = 0;

debian/patches/series

+cgview_path.patch
 testscripts.patch
+debug.patch