Modified RSEM perl scripts so that RSEM directory will be added in the beginning...

diff --git a/convert-sam-for-rsem b/convert-sam-for-rsem
index a7300f272ea127121dfc9592c76ed612d53ce798..812c8b9ca6ce1e295d62752974588a419182b195 100755 (executable)
--- 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 9040272a68c592a4a9cd7c7d532add78e448f942..03811afb0c8b79c1ae348ce01883820908e0c4b8 100755 (executable)
--- 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 44066b70e14811bbc0749c9fed84f5ccdd8802be..93f1a799d27df5ea89d9c3d1b9198bacb267dc33 100755 (executable)
--- 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 1d14a22a26ce7d0f8bceb4249abb8024bf8571c1..5bd89f2ffecb2d0d55818bd77a8363f71de461c2 100755 (executable)
--- 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 211e086a659d0539444275f925051a96679ab4d4..d696c68b00f9d3d6023cb8dd76869de5ab5d2bf0 100755 (executable)
--- 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 59d35c87279a62721954f2b2c63f81dc45ec17ae..47f767859a51f97c070f6c134c216159e5da2b79 100755 (executable)
--- 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;