# HG changeset patch
# User fubar
# Date 1371020496 14400
# Node ID 515a5e61874c1ed8d7196c2bf7d2818e978f1615
# Parent  34cbb9e749dab792812b22a356840a00506e1fcc
Uploaded

diff -r 34cbb9e749da -r 515a5e61874c rgedgeR/datatypes_conf_xml.sample
--- a/rgedgeR/datatypes_conf_xml.sample	Wed Jun 12 03:00:31 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-<datatype extension="gseagmt" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" mimetype="application/vnd.ms-excel"/>
-<datatype extension="gseachip" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" mimetype="application/vnd.ms-excel"/>
diff -r 34cbb9e749da -r 515a5e61874c rgedgeR/tool_dependencies.xml
--- a/rgedgeR/tool_dependencies.xml	Wed Jun 12 03:00:31 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Wed Jun 12 03:01:36 2013 -0400
@@ -1,9 +1,10 @@
 
 <?xml version="1.0"?>
+
+<tool_dependency>
 <!--
 blame Boris - Ross stole it from his old 2.15 one
 -->
-<tool_dependency>
     <package name="readline" version="6.2">
         <repository  name="package_readline_6_2" owner="boris" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
diff -r 34cbb9e749da -r 515a5e61874c rgedgeR/tool_dependencies.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgedgeR/tool_dependencies.xml~	Wed Jun 12 03:01:36 2013 -0400
@@ -0,0 +1,47 @@
+
+<?xml version="1.0"?>
+<!--
+blame Boris - Ross stole it from his old 2.15 one
+-->
+<tool_dependency>
+    <package name="readline" 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 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>