# HG changeset patch
# User deepakjadmin
# Date 1443001560 14400
# Node ID e91bfaad34599bd9f425894070fec52aba529c83

Uploaded

diff -r 000000000000 -r e91bfaad3459 testing.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/testing.xml	Wed Sep 23 05:46:00 2015 -0400
@@ -0,0 +1,15 @@
+<tool id="kunv02rt90uis" name="R-3-2-0" version="1.0.0">
+  <description>R version and installation test</description>
+<requirements>
+     <requirement type="set_environment">R_ROOT_DIR</requirement>
+    <requirement type="package" version="3.2.0">R</requirement>
+</requirements>
+  <command> /bin/which R > $output_file;
+            /bin/which \$R_ROOT_DIR/bin/R >> $output_file;
+            echo \$R_ROOT_DIR >> $output_file;
+            echo \$PATH >> $output_file;
+   </command>
+  <outputs>
+    <data type="data" format="txt" name="output_file" label ="output_r_3_2_0.env" />
+  </outputs>
+</tool>
diff -r 000000000000 -r e91bfaad3459 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 23 05:46:00 2015 -0400
@@ -0,0 +1,38 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.2.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.2.0.tar.gz</action>
+                <action type="shell_command">./configure</action>
+                <action type="shell_command">make</action>
+                <action type="shell_command">make install</action>
+                <action type="move_file">
+                    <source>R.3.2.0</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+R-3.2.0 installed now try edgeR
+        </readme>
+    </package>
+    <package name="limma" version="3.24.12">
+        <install version="1.0">
+            <actions>
+				<action type="setup_r_environment">
+					<package name="R" version="3.2.0" />
+                <action type="download_by_url">http://bioconductor.org/packages/release/bioc/src/contrib/limma_3.24.12.tar.gz</action>
+                <action type="shell_command">R CMD INSTALL tar.gz</action>
+                </action>
+              </actions>
+        </install>
+        <readme>
+limma_3.24.12 installed now try edgeR
+        </readme>
+    </package>
+    
+</tool_dependency>