Added .gitignore file back

[rsem.git] / rsem-generate-ngvector

diff --git a/rsem-generate-ngvector b/rsem-generate-ngvector
index cd184b69ecfe5e1ccc69735add06d2ffaa74c7f4..93f1a799d27df5ea89d9c3d1b9198bacb267dc33 100755 (executable)
--- a/rsem-generate-ngvector
+++ b/rsem-generate-ngvector
@@ -1,8 +1,15 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Getopt::Long;
 use Pod::Usage;
-use File::Basename;
+
+use FindBin;
+use lib $FindBin::RealBin;
+use rsem_perl_utils;
+
+use Env qw(@PATH);
+@PATH = ("$FindBin::RealBin/EBSeq", @PATH);
+
 use strict;
 
 my $k = 25;
@@ -14,29 +21,14 @@ GetOptions("k=i" => \$k,
 pod2usage(-verbose => 2) if ($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."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."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);
 
-# command, {err_msg}
-sub runCommand {
-    print $_[0]."\n";
-    my $status = system($_[0]);
-    if ($status != 0) {
-        my $errmsg = "";
-        if (scalar(@_) > 1) { $errmsg .= $_[1]."\n"; }
-        $errmsg .= "\"$_[0]\" failed! Plase check if you provide correct parameters/options for the pipeline!\n";
-        print $errmsg;
-        exit(-1);
-    }
-    print "\n";
-}
-
 __END__
 
 =head1 NAME
@@ -45,11 +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