# HG changeset patch
# User fubar
# Date 1371101782 14400
# Node ID d110c5bb0ad32d85e81233b92b37c4ee06d526d6
# Parent  ba361e7ebc17590de666e924f23cb8e6fca1cb64
Uploaded

diff -r ba361e7ebc17 -r d110c5bb0ad3 rgedgeR/tool_dependencies.xml
--- a/rgedgeR/tool_dependencies.xml	Thu Jun 13 01:09:25 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Thu Jun 13 01:36:22 2013 -0400
@@ -11,7 +11,12 @@
                         <package name="r3" version="3.0.1" />
                     </repository>
                 </action>
-                <action type="shell_command">R CMD BATCH rgedgeR/installBioC.R </action>
+                <action type="make_directory">$INSTALL_DIR</action>
+                <action type="shell_command">echo source('http://bioconductor.org/biocLite.R') &gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo installme=c('edgeR','limma','DESeq','DEXSeq','ggplot2','gplots') &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo biocLite() &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo biocLite(installme) &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R  </action>
             </actions>
         </install>
         <readme>Installs some basic bioc packages for the edgeR tool