# HG changeset patch
# User fubar
# Date 1371037486 14400
# Node ID 13b7fdf4cba9b0fbf020a41f032da0b9989344ff
# Parent  d28ce4e0e3af9257fd3a89ede49c46babca8d798
Uploaded

diff -r d28ce4e0e3af -r 13b7fdf4cba9 rgedgeR/tool_dependencies.xml
--- a/rgedgeR/tool_dependencies.xml	Wed Jun 12 06:33:34 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Wed Jun 12 07:44:46 2013 -0400
@@ -1,15 +1,15 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>   
-    </set_environment>
     <package name="package_BioCBasics" version="2.12">
         <install version="1.0">
             <actions>
                 <action type="set_environment_for_install">
-                    <repository name="package_R3" owner="fubar" prior_installation_required="True"  toolshed="http://testtoolshed.g2.bx.psu.edu/"/>
+                    <repository name="package_R3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+                    <set_environment toolshed="http://testtoolshed.g2.bx.psu.edu" version="1.0">
+                        <environment_variable action="set_to" name="R_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>   
+                    </set_environment>
                 </action>
-                <action type="shell_command">$R3_BINARY/R CMD BATCH $R_SCRIPT_PATH/installBioC.R </action>
+                <action type="shell_command">R CMD BATCH installBioC.R </action>
             </actions>
         </install>
         <readme>R is a free software environment for statistical computing and graphics