X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=rsem-generate-ngvector;h=93f1a799d27df5ea89d9c3d1b9198bacb267dc33;hp=137fa03db354e8e7078a8dd16b535549034f949e;hb=910250881a4c3e48a33aa427b82131acda914da3;hpb=f0aa264bd96a2e742cfe186767db69270b896899

diff --git a/rsem-generate-ngvector b/rsem-generate-ngvector
index 137fa03..93f1a79 100755
--- a/rsem-generate-ngvector
+++ b/rsem-generate-ngvector
@@ -1,13 +1,17 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Getopt::Long;
 use Pod::Usage;
-use FindBin;
-use lib $FindBin::Bin;
-use strict;
 
+use FindBin;
+use lib $FindBin::RealBin;
 use rsem_perl_utils;
 
+use Env qw(@PATH);
+@PATH = ("$FindBin::RealBin/EBSeq", @PATH);
+
+use strict;
+
 my $k = 25;
 my $help = 0;
 
@@ -17,13 +21,12 @@ 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 $dir = "$FindBin::Bin/";
 my $command = "";
 
-$command = $dir."EBSeq/rsem-for-ebseq-calculate-clustering-info $k $ARGV[0] $ARGV[1].ump";
+$command = "rsem-for-ebseq-calculate-clustering-info $k $ARGV[0] $ARGV[1].ump";
 &runCommand($command);
 
-$command = $dir."EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info $ARGV[1].ump $ARGV[1].ngvec";
+$command = "rsem-for-ebseq-generate-ngvector-from-clustering-info $ARGV[1].ump $ARGV[1].ngvec";
 &runCommand($command);
 
 __END__
@@ -34,11 +37,7 @@ rsem-generate-ngvector
 
 =head1 SYNOPSIS
 
-=over
-
- rsem-generate-ngvector [options] input_fasta_file output_name
-
-=back
+rsem-generate-ngvector [options] input_fasta_file output_name
 
 =head1 ARGUMENTS