use Getopt::Long;
use Pod::Usage;
-use File::Basename;
+use FindBin;
+use lib $FindBin::Bin;
use strict;
+use rsem_perl_utils;
+
my $k = 25;
my $help = 0;
pod2usage(-verbose => 2) if ($help == 1);
pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 2);
-my ($fn, $dir, $suf) = fileparse($0);
+my $dir = "$FindBin::Bin/";
my $command = "";
-$command = $dir."rsem-for-ebseq-calculate-clustering-info $k $ARGV[0] $ARGV[1].ump";
+$command = $dir."EBSeq/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 = $dir."EBSeq/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
=head1 SYNOPSIS
-=over
-
- rsem-generate-ngvector [options] input_fasta_file output_name
-
-=back
+rsem-generate-ngvector [options] input_fasta_file output_name
=head1 ARGUMENTS