X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rsem-prepare-reference;h=5d954a1fc7b7f411fa8fe46d43b5cda1cb181fa6;hb=52f1bd6f44f9b2630b839f192fb9ece18581983b;hp=6c5d5f31ad1dcfc98bec5f999b1bcc7d6eb3eaae;hpb=a1dc3c6c442d288c7f4218cbb8b7a54f08e9d980;p=rsem.git

diff --git a/rsem-prepare-reference b/rsem-prepare-reference
index 6c5d5f3..5d954a1 100755
--- a/rsem-prepare-reference
+++ b/rsem-prepare-reference
@@ -5,6 +5,8 @@ use Pod::Usage;
 use File::Basename;
 use strict;
 
+use rsem_perl_utils;
+
 my $status;
 
 my $gtfF = "";
@@ -93,20 +95,6 @@ if (!$no_bowtie) {
     &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! Please check if you provide correct parameters/options for the pipeline!\n";
-        print $errmsg;
-        exit(-1);
-    }
-    print "\n";
-}
-
 __END__
 
 =head1 NAME