From f0aa264bd96a2e742cfe186767db69270b896899 Mon Sep 17 00:00:00 2001
From: Bo Li <bli@cs.wisc.edu>
Date: Sun, 27 Jan 2013 09:19:02 -0600
Subject: [PATCH] Fixed a bug that will lead perl scripts fail to find the perl
 module they use

---
 convert-sam-for-rsem         | 4 +++-
 rsem-calculate-expression    | 5 +++--
 rsem-generate-ngvector       | 5 +++--
 rsem-plot-transcript-wiggles | 5 +++--
 rsem-prepare-reference       | 5 +++--
 5 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/convert-sam-for-rsem b/convert-sam-for-rsem
index 94b7965..eb34c54 100755
--- a/convert-sam-for-rsem
+++ b/convert-sam-for-rsem
@@ -2,6 +2,8 @@
 
 use Getopt::Long;
 use Pod::Usage;
+use FindBin;
+use lib $FindBin::Bin;
 use File::Basename;
 use File::Path 'rmtree';
 use strict;
@@ -31,7 +33,7 @@ $suf = lc(substr($suf, 1));
 pod2usage(-msg => "Input file's suffix is neither sam nor bam!", -exitval => 2, -verbose => 2) if (($suf ne "sam") && ($suf ne "bam"));
 my $isSam = ($suf eq "sam");
 
-($fn, $dir, $suf) = fileparse($0);
+$dir = "$FindBin::Bin/";
 
 my $temp_dir = "$out_file.temp";
 if (-d $temp_dir) { print "Warning: $temp_dir exists, convert-sam-for-rsem will write temporary files into this folder and delete it after it finishes!\n"; }
diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index 4fbb4a5..fec2e31 100755
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -2,7 +2,8 @@
 
 use Getopt::Long;
 use Pod::Usage;
-use File::Basename;
+use FindBin;
+use lib $FindBin::Bin;
 use strict;
 
 use rsem_perl_utils qw(runCommand collectResults showVersionInfo);
@@ -109,7 +110,7 @@ GetOptions("keep-intermediate-files" => \$keep_intermediate_files,
 	   "q|quiet" => \$quiet,
 	   "h|help" => \$help) or pod2usage(-exitval => 2, -verbose => 2);
 
-my ($fn, $dir, $suf) = fileparse($0);
+my $dir = "$FindBin::Bin/";
 
 pod2usage(-verbose => 2) if ($help == 1);
 &showVersionInfo($dir) if ($version == 1);
diff --git a/rsem-generate-ngvector b/rsem-generate-ngvector
index 0f44fd4..137fa03 100755
--- a/rsem-generate-ngvector
+++ b/rsem-generate-ngvector
@@ -2,7 +2,8 @@
 
 use Getopt::Long;
 use Pod::Usage;
-use File::Basename;
+use FindBin;
+use lib $FindBin::Bin;
 use strict;
 
 use rsem_perl_utils;
@@ -16,7 +17,7 @@ GetOptions("k=i" => \$k,
 pod2usage(-verbose => 2) if ($help == 1);
 pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 2);
 
-my ($fn, $dir, $suf) = fileparse($0);
+my $dir = "$FindBin::Bin/";
 my $command = "";
 
 $command = $dir."EBSeq/rsem-for-ebseq-calculate-clustering-info $k $ARGV[0] $ARGV[1].ump";
diff --git a/rsem-plot-transcript-wiggles b/rsem-plot-transcript-wiggles
index 35dfd75..11027a1 100755
--- a/rsem-plot-transcript-wiggles
+++ b/rsem-plot-transcript-wiggles
@@ -2,7 +2,8 @@
 
 use Getopt::Long;
 use Pod::Usage;
-use File::Basename;
+use FindBin;
+use lib $FindBin::Bin;
 use strict;
 
 use rsem_perl_utils;
@@ -18,7 +19,7 @@ GetOptions("gene-list" => \$gene_list,
 pod2usage(-verbose => 2) if ($help == 1);
 pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 3);
 
-my ($fn, $dir, $suf) = fileparse($0);
+my $dir = "$FindBin::Bin/";
 my $command = "";
 
 unless (-e "$ARGV[0].transcript.sorted.bam") {
diff --git a/rsem-prepare-reference b/rsem-prepare-reference
index 5d954a1..223d79d 100755
--- a/rsem-prepare-reference
+++ b/rsem-prepare-reference
@@ -2,7 +2,8 @@
 
 use Getopt::Long;
 use Pod::Usage;	
-use File::Basename;
+use FindBin;
+use lib $FindBin::Bin;
 use strict;
 
 use rsem_perl_utils;
@@ -60,7 +61,7 @@ elsif ($subsetFile ne "") { $polyAChoice = 2; }
 
 if ($bowtie_path ne "") { $bowtie_path .= "/"; }
 
-my ($fn, $dir, $suf) = fileparse($0); 
+my $dir = "$FindBin::Bin/";
 my $command = "";
 
 if ($type == 0) {
-- 
2.39.2