--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgedgeR/tool_dependencies.xml	Fri Jul 26 22:04:58 2013 -0400
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="package_r3" version="3.0.1">
+        <repository changeset_revision="6f249fadd4ec" 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="6f249fadd4ec" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                        <package name="r3" version="3.0.1" />
+                    </repository>
+                </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','DESeq2','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">echo "quit(save='no')" &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 wrapper
+        It's clunky but this is the only way I could get anything installed into the package_r3 R
+       </readme>
+    </package>
+</tool_dependency>