X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rsem-generate-ngvector;h=fc97b84e83dfdb058ef2bbe048b56cfc68342507;hb=a1dc3c6c442d288c7f4218cbb8b7a54f08e9d980;hp=c4d26a8f067efead6eb652e04a9cb31bfe6bf9ea;hpb=4496388fd52d4354c746f36b1998477f31c2b0dd;p=rsem.git

diff --git a/rsem-generate-ngvector b/rsem-generate-ngvector
index c4d26a8..fc97b84 100755
--- a/rsem-generate-ngvector
+++ b/rsem-generate-ngvector
@@ -17,10 +17,10 @@ pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2)
 my ($fn, $dir, $suf) = fileparse($0);
 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}
@@ -28,10 +28,10 @@ sub runCommand {
     print $_[0]."\n";
     my $status = system($_[0]);
     if ($status != 0) {
-        my $errmsg;
-        if (scalar(@_) > 1) { $errmsg = $_[1]; }
-        else { $errmsg = "\"$command\" failed! Plase check if you provide correct parameters/options for the pipeline!"; }
-        print $errmsg."\n";
+        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";