Added .gitignore file back

[rsem.git] / rsem-generate-ngvector

diff --git a/rsem-generate-ngvector b/rsem-generate-ngvector
index 0f44fd4daa2f153e60d3874a09c948aebc606b62..93f1a799d27df5ea89d9c3d1b9198bacb267dc33 100755 (executable)
--- a/rsem-generate-ngvector
+++ b/rsem-generate-ngvector
@@ -1,12 +1,17 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Getopt::Long;
 use Pod::Usage;
-use File::Basename;
-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;
 
@@ -16,13 +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 ($fn, $dir, $suf) = fileparse($0);
 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__
@@ -33,11 +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