# HG changeset patch
# User fubar
# Date 1371023708 14400
# Node ID a6e497d7baa2a1ea659fb0311ee0fba06b0f20bc
# Parent  06e51c47590d8401ae7e701563fe09e9fdf2dd04
Uploaded

diff -r 06e51c47590d -r a6e497d7baa2 rgedgeR/tool_dependencies.xml
--- a/rgedgeR/tool_dependencies.xml	Wed Jun 12 03:51:48 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Wed Jun 12 03:55:08 2013 -0400
@@ -9,7 +9,7 @@
                 <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action>
                 <action type="set_environment_for_install">
                     <repository changeset_revision="1301ec7705a8" name="package_readline_6_2" owner="boris" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-                        <package name="readline" version="6.2" />
+                        <package name="package_readline_6_2" version="6.2" />
                     </repository>
                 </action>
                 <action type="make_directory">$INSTALL_DIR</action>
diff -r 06e51c47590d -r a6e497d7baa2 rgedgeR/tool_dependencies.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgedgeR/tool_dependencies.xml~	Wed Jun 12 03:55:08 2013 -0400
@@ -0,0 +1,43 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="package_readline_6_2" version="6.2">
+        <repository name="package_readline_6_2" owner="boris" prior_installation_required="True" 
+                toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    </package>
+    <package name="package_R" version="3.0.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="1301ec7705a8" name="package_readline_6_2" owner="boris" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                        <package name="readline" version="6.2" />
+                    </repository>
+                </action>
+                <action type="make_directory">$INSTALL_DIR</action>
+                <action type="shell_command">./configure --with-blas --with-lapack --enable-R-shlib --with-readline=no --with-x=no --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
+                    <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>R is a free software environment for statistical computing and graphics
+                WARNING: See custom compilation options above
+                Modified from an older version of R by Boris by Ross Lazarus for R 3.0
+                Added Bioc basics too
+       </readme>
+    </package>
+    <package name="package_BioCBasics" version="2.12">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">$INSTALL_DIR/lib/R/bin/R CMD BATCH installBioC.R </action>
+            </actions>
+        </install>
+        <readme>R is a free software environment for statistical computing and graphics
+                WARNING: See custom compilation options above
+                Modified from an older version of R by Boris by Ross Lazarus for R 3.0
+                Added Bioc basics via this package installBioC.R script
+       </readme>
+    </package>
+</tool_dependency>