-#!/usr/bin/perl
+#!/usr/bin/env perl
use Getopt::Long;
use Pod::Usage;
use FindBin;
-use lib $FindBin::Bin;
-use strict;
-
+use lib $FindBin::RealBin;
use rsem_perl_utils;
+use Env qw(@PATH);
+push(@PATH, $FindBin::RealBin);
+
+use strict;
+
my $status;
my $gtfF = "";
if ($bowtie_path ne "") { $bowtie_path .= "/"; }
if ($bowtie2_path ne "") { $bowtie2_path .= "/"; }
-my $dir = "$FindBin::Bin/";
my $command = "";
if ($type == 0) {
$"=" ";
- $command = $dir."rsem-extract-reference-transcripts $ARGV[1] $quiet $gtfF";
+ $command = "rsem-extract-reference-transcripts $ARGV[1] $quiet $gtfF";
if ($mappingF ne "") { $command .= " 1 $mappingF"; }
else { $command .= " 0"; }
$command .= " @list";
}
else {
$"=" ";
- $command = $dir."rsem-synthesis-reference-transcripts $ARGV[1] $quiet";
+ $command = "rsem-synthesis-reference-transcripts $ARGV[1] $quiet";
if ($mappingF ne "") { $command .= " 1 $mappingF"; }
elsif ($alleleMappingF ne "") { $command .= " 2 $alleleMappingF"; }
else { $command .= " 0"; }
&runCommand($command);
}
-$command = $dir."rsem-preref $ARGV[1].transcripts.fa $polyAChoice $ARGV[1] -l $polyALen";
+$command = "rsem-preref $ARGV[1].transcripts.fa $polyAChoice $ARGV[1] -l $polyALen";
if ($polyAChoice == 2) { $command .= " -f $subsetFile"; }
if ($no_ntog) { $command .= " --no-ntog"; }
if ($quiet) { $command .= " -q"; }