From 810375ef69e0de93188c6fa3819cfc584a32ff34 Mon Sep 17 00:00:00 2001
From: Bo Li <bli@cs.wisc.edu>
Date: Thu, 5 Jun 2014 14:46:52 -0500
Subject: [PATCH] Modified RSEM perl scripts so that RSEM directory will be
 added in the beginning of PATH variable

---
 convert-sam-for-rsem         | 2 +-
 rsem-calculate-expression    | 2 +-
 rsem-generate-ngvector       | 2 +-
 rsem-plot-transcript-wiggles | 2 +-
 rsem-prepare-reference       | 2 +-
 rsem-run-ebseq               | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/convert-sam-for-rsem b/convert-sam-for-rsem
index a7300f2..812c8b9 100755
--- a/convert-sam-for-rsem
+++ b/convert-sam-for-rsem
@@ -10,7 +10,7 @@ use lib $FindBin::RealBin;
 use rsem_perl_utils;
 
 use Env qw(@PATH);
-push(@PATH, $FindBin::RealBin, "$FindBin::RealBin/sam");
+@PATH = ($FindBin::RealBin, "$FindBin::RealBin/sam", @PATH);
 
 use strict;
 
diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index 9040272..03811af 100755
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -8,7 +8,7 @@ use lib $FindBin::RealBin;
 use rsem_perl_utils qw(runCommand collectResults showVersionInfo);
 
 use Env qw(@PATH);
-push(@PATH, $FindBin::RealBin, "$FindBin::RealBin/sam");
+@PATH = ($FindBin::RealBin, "$FindBin::RealBin/sam", @PATH);
 
 use strict;
 
diff --git a/rsem-generate-ngvector b/rsem-generate-ngvector
index 44066b7..93f1a79 100755
--- a/rsem-generate-ngvector
+++ b/rsem-generate-ngvector
@@ -8,7 +8,7 @@ use lib $FindBin::RealBin;
 use rsem_perl_utils;
 
 use Env qw(@PATH);
-push(@PATH, "$FindBin::RealBin/EBSeq");
+@PATH = ("$FindBin::RealBin/EBSeq", @PATH);
 
 use strict;
 
diff --git a/rsem-plot-transcript-wiggles b/rsem-plot-transcript-wiggles
index 1d14a22..5bd89f2 100755
--- a/rsem-plot-transcript-wiggles
+++ b/rsem-plot-transcript-wiggles
@@ -8,7 +8,7 @@ use lib $FindBin::RealBin;
 use rsem_perl_utils;
 
 use Env qw(@PATH);
-push(@PATH, $FindBin::RealBin, "$FindBin::RealBin/sam");
+@PATH = ($FindBin::RealBin, "$FindBin::RealBin/sam", @PATH);
 
 use strict;
 
diff --git a/rsem-prepare-reference b/rsem-prepare-reference
index 211e086..d696c68 100755
--- a/rsem-prepare-reference
+++ b/rsem-prepare-reference
@@ -7,7 +7,7 @@ use lib $FindBin::RealBin;
 use rsem_perl_utils;
 
 use Env qw(@PATH);
-push(@PATH, $FindBin::RealBin);
+@PATH = ($FindBin::RealBin, @PATH);
 
 use strict;
 
diff --git a/rsem-run-ebseq b/rsem-run-ebseq
index 59d35c8..47f7678 100755
--- a/rsem-run-ebseq
+++ b/rsem-run-ebseq
@@ -8,7 +8,7 @@ use lib $FindBin::RealBin;
 use rsem_perl_utils;
 
 use Env qw(@PATH);
-push(@PATH, "$FindBin::RealBin/EBSeq");
+@PATH = ("$FindBin::RealBin/EBSeq", @PATH);
 
 use strict;
 
-- 
2.39.2