# HG changeset patch
# User fubar
# Date 1371098069 14400
# Node ID faf413433dcaa521766042b8201e584a569e9b53
# Parent  46c91da1351eaec470495562737c43587b0416c5
Uploaded

diff -r 46c91da1351e -r faf413433dca rgedgeR/tool_dependencies.xml
--- a/rgedgeR/tool_dependencies.xml	Thu Jun 13 00:01:11 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Thu Jun 13 00:34:29 2013 -0400
@@ -1,20 +1,17 @@
 <?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/" />
+        <repository changeset_revision="6344ee60d0cf" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="biocbasics" version="2.12">
         <install version="1.0"> 
             <actions>
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="addf8c9c778a" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                    <repository changeset_revision="6344ee60d0cf" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                         <package name="r3" version="3.0.1" />
                     </repository>
                 </action>
-                <action type="shell_command">R CMD BATCH $R_SCRIPT_PATH/rgedgeR/installBioC.R </action>
+                <action type="shell_command">R CMD BATCH ${REPOSITORY_INSTALL_DIR}/rgedgeR/installBioC.R </action>
             </actions>
         </install>
         <readme>Installs some basic bioc packages for the edgeR tool