# HG changeset patch
# User jeremyjliu
# Date 1413567686 14400
# Node ID 5d9014614d2827c3c9cc4c97d50da0e48eab77b6
# Parent  baf68a0e7cf47d7b948f1dabe91c430103554ea7
Uploaded

diff -r baf68a0e7cf4 -r 5d9014614d28 region_motif_intersect.xml
--- a/region_motif_intersect.xml	Wed Aug 06 15:37:03 2014 -0400
+++ b/region_motif_intersect.xml	Fri Oct 17 13:41:26 2014 -0400
@@ -1,7 +1,10 @@
 <tool id="region_motif_intersect" name="Region Motif Intersect">
   <description>for computing the motifs that lie inside a region set</description>
-  <command interpreter="bash">
-    /usr/bin/R --slave --vanilla -f $GALAXY_ROOT_DIR/tools/my_tools/region_motif_intersect.r --args $GALAXY_ROOT_DIR $db_type $in_bed $out_tab
+  <requirements>
+    <requirement type="set_environment">MOTIF_DB_PATH</requirement>
+  </requirements>
+  <command interpreter="Rscript">
+    region_motif_intersect.r --args $MOTIF_DB_PATH $db_type $in_bed $out_tab
   </command>
   <inputs>
     <param name="in_bed" type="data" format="bed" label="Input BED File" />