# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1348258609 18000
# Node ID d57983929080fbe98d94e4ed558644bd8d793d71
# Parent  57c46f7fe70b278622eab1edb33533057486030f
tool_dependencies.xml changes

diff -r 57c46f7fe70b -r d57983929080 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Sep 21 14:42:09 2012 -0500
+++ b/tool_dependencies.xml	Fri Sep 21 15:16:49 2012 -0500
@@ -1,8 +1,5 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/snpEff</environment_variable>
-    </set_environment>
     <package name="snpEff" version="3.0">
         <install version="1.0">
             <actions>
@@ -13,7 +10,10 @@
                 </action>
 
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/snpEff</environment_variable>
+                    <environment_variable name="JAVA_JAR_PATH" action="prepend_to">$INSTALL_DIR/snpEff</environment_variable>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/snpEff/scripts</environment_variable>
                 </action>
             </actions>
         </install>