# HG changeset patch
# User geert-vandeweyer
# Date 1406555350 14400
# Node ID e4000df38772ff0431c49860242f878a233f1907
# Parent  1850675b00d20513c688cefd0d0b559c719ebf7c
Uploaded

diff -r 1850675b00d2 -r e4000df38772 run_cf0611.pl
--- a/run_cf0611.pl	Mon Jul 28 09:48:25 2014 -0400
+++ b/run_cf0611.pl	Mon Jul 28 09:49:10 2014 -0400
@@ -30,8 +30,16 @@
 my $partnerfile='';
 
 my $cwd = getcwd();
-my $scriptspath="$cwd/cf_scripts";
-my $cffile="$cwd/cf_v1.1.jar";
+my $scriptspath = $cffile = '';
+# Galaxy installer puts scripts and jar into a folder, which is available under the environment variable CF_PATH
+if (defined($ENV{'CF_PATH'}) && -d $ENV{'CF_PATH'}) {
+	$scriptspath = $ENV{'CF_PATH'}."/cf_scripts";
+	$cffile = $ENV{'CF_PATH'}."/cf_v1.1.jar";
+}
+else {
+	$scriptspath="$cwd/cf_scripts";
+	$cffile="$cwd/cf_v1.1.jar";
+}
 my $help='';