# HG changeset patch
# User fubar
# Date 1393819279 18000
# Node ID e7d02e6b253c215466d5d7cb26eb133f62ae8cbf
# Parent  8c96a2d95436aae9f9fe14909bc7583f7d04a63d
Uploaded

diff -r 8c96a2d95436 -r e7d02e6b253c tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Mar 02 22:35:18 2014 -0500
+++ b/tool_dependencies.xml	Sun Mar 02 23:01:19 2014 -0500
@@ -9,6 +9,9 @@
     <package name="r303" version="3.0.3">
         <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="RUNME_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>   
+    </set_environment>
     <package name="biocbasics" version="2.14">
         <install version="1.0"> 
             <actions>
@@ -18,9 +21,8 @@
                     </repository>
                 </action>
                 <action type="make_directory">$INSTALL_DIR</action>     
-                <action type="shell_command">echo `ls -l`</action>
-                          
-                <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH ./runme.R </action>
+                <action type="shell_command">ls -l</action>
+                <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $RUNME_PATH/runme.R </action>
             </actions>
         </install>
         <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs