Mercurial > repos > deepakjadmin > limmatest

diff tool_dependencies.xml @ 0:31eb67db059b draft default tip

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author deepakjadmin
date Wed, 23 Sep 2015 05:54:53 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 23 05:54:53 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 limma_3.24.12.tar.gz</action>
+                </action>
+             </actions>
+        </install>
+        <readme>
+limma_3.24.12 installed now try edgeR 
+        </readme>
+    </package>
+    
+</tool_dependency>