# HG changeset patch
# User geert-vandeweyer
# Date 1406565971 14400
# Node ID b9711e16f1484bd917b8954ccf96b0d363e28a0d
# Parent  4d719572fc9e190dcacd7826830f5019b8b5aacf
Uploaded

diff -r 4d719572fc9e -r b9711e16f148 run_cf0611.pl
--- a/run_cf0611.pl	Mon Jul 28 10:28:08 2014 -0400
+++ b/run_cf0611.pl	Mon Jul 28 12:46:11 2014 -0400
@@ -19,6 +19,7 @@
 use File::Path qw(make_path);
 use Cwd ;
 use Cwd 'abs_path';
+use File::Basename;
 
 my ($inbam, $outdir, $targets, $minct1, $minct2, $dist, $novoindex, $rmtmp, $FASTA,$twobit,$refpaths,$bp1,$bp2,$contigs);
 
@@ -33,9 +34,10 @@
 my $scriptspath = '';
 my $cffile = '';
 # Galaxy installer puts scripts and jar into a folder, which is available under the environment variable CF_PATH
+# this is future work (once github of clusterfast gets updated. For now, it's a placeholder.
 if (defined($ENV{'CF_PATH'}) && -d $ENV{'CF_PATH'}) {
-	$scriptspath = $ENV{'CF_PATH'}."/cf_scripts";
-	$cffile = $ENV{'CF_PATH'}."/cf_v1.1.jar";
+	$scriptspath = dirname(abs_path($0))."/cf_scripts";
+	$cffile = dirname(abs_path($0))."/cf_v1.1.jar";
 }
 else {
 	$scriptspath="$cwd/cf_scripts";