# HG changeset patch
# User fubar
# Date 1404693439 14400
# Node ID 86bd60bea4d83ccf115b3868a7ce5096ba485202
# Parent  96ebf676f6c02e4763034359b7a5b52aafc83caf
Uploaded

diff -r 96ebf676f6c0 -r 86bd60bea4d8 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Jul 06 02:36:47 2014 -0400
+++ b/tool_dependencies.xml	Sun Jul 06 20:37:19 2014 -0400
@@ -24,10 +24,8 @@
                 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "install.packages(c(\"stringr\",\"gplots\"),dependencies=T,repos=\"http://cran.us.r-project.org\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo "quit(save=\"no\")" &gt;&gt; $INSTALL_DIR/runme.R</action>                
-                <action type="shell_command">echo "PATH=$PATH 1&gt;&amp;2"</action>                
-                <action type="shell_command">echo "R_PATH=$R_PATH 1&gt;&amp;2"</action>                
-                <action type="shell_command">export PATH=$PATH &amp;&amp; $R_PATH/R CMD BATCH $INSTALL_DIR/runme.R </action>
+                <action type="shell_command">echo "quit(save=\"no\")" &gt;&gt; $INSTALL_DIR/runme.R</action>          
+                <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/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