# HG changeset patch
# User fubar
# Date 1371095884 14400
# Node ID bbc8a94b53119a663fe2051579729565643b488b
# Parent  0e69aefbbfa4dcda8355e91170364c8aef840512
Uploaded

diff -r 0e69aefbbfa4 -r bbc8a94b5311 rgedgeR/tool_dependencies.xml
--- a/rgedgeR/tool_dependencies.xml	Wed Jun 12 23:55:21 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Wed Jun 12 23:58:04 2013 -0400
@@ -1,5 +1,8 @@
 <?xml version="1.0"?>
 <tool_dependency>
+     <set_environment version="1.0">
+        <environment_variable action="set_to" name="R_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>   
+    </set_environment>
     <package name="package_r3" version="3.0.1">
         <repository changeset_revision="addf8c9c778a" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
@@ -11,7 +14,7 @@
                         <package name="r3" version="3.0.1" />
                     </repository>
                 </action>
-                <action type="shell_command">R CMD BATCH $REPOSITORY_INSTALL_DIR/installBioC.R </action>
+                <action type="shell_command">R CMD BATCH $R_SCRIPT_PATH/installBioC.R </action>
             </actions>
         </install>
         <readme>Installs some basic bioc packages for the edgeR tool