Author: Andreas Tille <tille@debian.org>
Last-Update: Wed, 20 Jan 2016 09:10:18 +0100
Description: To run build time tests enable running the scripts
 from build path

--- a/NAST-iEr/run_NAST-iEr.pl
+++ b/NAST-iEr/run_NAST-iEr.pl
@@ -8,6 +8,13 @@ use Getopt::Long;
 #use FindBin;
 ##Hack needed because FindBin is braindead.
 BEGIN{ $FindBin::Bin = "/usr/lib/NAST-iEr" };
+if ( ! -d $FindBin::Bin ) {
+	if ( -d "../../NAST-iEr" ) {
+		$FindBin::Bin = "../../NAST-iEr" ;
+	} else {
+		die("Directory $FindBin::Bin does not exist.");
+	}
+}
 use lib ("$FindBin::Bin/PerlLib");
 use Fasta_reader;
 use CdbTools;
@@ -15,8 +22,21 @@ use Nuc_translator;
 
 
 my $db_FASTA = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta";
+if ( ! -e $db_FASTA ) {
+	if ( -e "../../RESOURCES/rRNA16S.gold.fasta" ) {
+		$db_FASTA = "../../RESOURCES/rRNA16S.gold.fasta" ;
+	} else {
+		die("File $db_FASTA does not exist.");
+	}
+}
 my $db_NAST = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta";
-
+if ( ! -e $db_NAST ) {
+        if ( -e "../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta" ) {
+                $db_NAST = "../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta" ;
+        } else {
+                die("File $db_NAST does not exist.");
+        }
+}
 
 my $usage = <<_EOUSAGE_;
 
--- a/NAST-iEr/sample_data/runMe.sh
+++ b/NAST-iEr/sample_data/runMe.sh
@@ -12,9 +12,9 @@ echo "../NAST-iEr -b template_seqs.NAST
 
 echo "converting NAST mfasta to multi-alignment output highlighting differences"
 echo "../show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign\n\n"
-../util/show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign
+perl -I../PerlLib ../util/show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign
 
 
 echo "Run via the megablast wrapper"
-../run_NAST-iEr.pl --query_FASTA query_seq.fasta > tmp.mb_select.NAST
+perl -I../PerlLib ../run_NAST-iEr.pl --query_FASTA query_seq.fasta > tmp.mb_select.NAST
 
--- a/ChimeraSlayer/sample_data/runMe.sh
+++ b/ChimeraSlayer/sample_data/runMe.sh
@@ -1,9 +1,9 @@
 #!/bin/sh
 
 # remove any preexisting outputs from an earlier run.
-rm chims.NAST.CPS*
-rm tmp.*
+rm -f chims.NAST.CPS*
+rm -f tmp.*
 
-../ChimeraSlayer.pl --query_NAST chims.NAST --printCSalignments --printFinalAlignments 
+perl -I../PerlLib ../ChimeraSlayer.pl --query_NAST chims.NAST --printCSalignments --printFinalAlignments 
 
 
--- a/ChimeraSlayer/ChimeraSlayer.pl
+++ b/ChimeraSlayer/ChimeraSlayer.pl
@@ -7,6 +7,13 @@ use Getopt::Long qw(:config no_ignore_ca
 #use FindBin;
 #Hack needed because FindBin is braindead.
 BEGIN{ $FindBin::Bin = "/usr/lib/ChimeraSlayer" };
+if ( ! -d $FindBin::Bin ) {
+	if ( -d "../../ChimeraSlayer" ) {
+		$FindBin::Bin = "../../ChimeraSlayer" ;
+	} else {
+		die("Directory $FindBin::Bin does not exist.");
+	}
+}
 
 use lib ("$FindBin::Bin/PerlLib");
 use Fasta_reader;
@@ -14,7 +21,21 @@ use CdbTools;
 use File::Basename;
 
 my $db_NAST = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta";
+if ( ! -e $db_NAST ) {
+	if ( -e "../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta" ) {
+		$db_NAST = "../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta" ;
+	} else {
+		die("File $db_NAST does not exist.");
+	}
+}
 my $db_FASTA = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta";
+if ( ! -e $db_FASTA ) {
+	if ( -e "../../RESOURCES/rRNA16S.gold.fasta" ) {
+		$db_FASTA = "../../RESOURCES/rRNA16S.gold.fasta" ;
+	} else {
+		die("File $db_FASTA does not exist.");
+	}
+}
 
 
 my $usage = <<_EOUSAGE_;
--- a/ChimeraSlayer/util/CS_add_taxonomy.pl
+++ b/ChimeraSlayer/util/CS_add_taxonomy.pl
@@ -13,7 +13,15 @@ use Fasta_reader;
 my %acc_to_taxonomy;
 
 {
-	my $fasta_reader = new Fasta_reader("/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta");
+	my $db_FASTA = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta";
+	if ( ! -e $db_FASTA ) {
+		if ( -e "../../RESOURCES/rRNA16S.gold.fasta" ) {
+			$db_FASTA = "../../RESOURCES/rRNA16S.gold.fasta" ;
+		} else {
+			die("File $db_FASTA does not exist.");
+		}
+	}
+	my $fasta_reader = new Fasta_reader($db_FASTA);
 	while (my $seq_obj = $fasta_reader->next()) {
 		my $acc = $seq_obj->get_accession;
 		
--- a/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl
+++ b/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl
@@ -655,7 +655,7 @@ sub report_alignment_trace {
 			}
 			
 			#print(  (" " x 26) . join ("", @$error_profile_aref) . "\n");
-			printf("%-25s $align_region\n", substr("$alignment_counter $acc", 0, 25), $align_region);
+			printf("%-25s $align_region\n", substr("$alignment_counter $acc", 0, 25));
 		}
 		
 		print "\n";