# HG changeset patch
# User mzeidler
# Date 1380560060 14400
# Node ID cb323c0ab13daef7c5bd2423d7f192f7f2e7f17d
# Parent  9c533ff4b392d999214e6810839c09fdd0b13005
Uploaded

diff -r 9c533ff4b392 -r cb323c0ab13d vhom_region.xml
--- a/vhom_region.xml	Mon Sep 30 12:50:27 2013 -0400
+++ b/vhom_region.xml	Mon Sep 30 12:54:20 2013 -0400
@@ -6,7 +6,6 @@
         <requirement type="package" version="1.02.00">lastz</requirement>
         <requirement type="package" version="1.0">virana_python</requirement>
         <requirement type="package" version="2.8">jalview</requirement>
-        <requirement type="set_environment">JALVIEW_DIR</requirement>
     </requirements>
 
     <command interpreter="python">vhom_regionplot.py --html_file $hom_output --directory ${hom_output.files_path} --stats $stat_output
@@ -45,7 +44,7 @@
     
     --output_dir ${hom_output.files_path}
     
-    --jalview_jar_dir $JALVIEW_DIR
+    --jalview_jar_dir \$JALVIEW_DIR
     
     
     --region_stats $stat_output