# HG changeset patch
# User bgruening
# Date 1372620898 14400
# Node ID 4e9dce1105cdad620db126e0598d951372ee943e
# Parent  5b253fafd35a6ec8c89f503f756e7672215122e3
Uploaded

diff -r 5b253fafd35a -r 4e9dce1105cd tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 06 02:44:50 2013 -0400
+++ b/tool_dependencies.xml	Sun Jun 30 15:34:58 2013 -0400
@@ -1,6 +1,53 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="fastqc_dist_0_10_1" version="0.10.1">
-        <repository changeset_revision="7d57dba74532" name="upload_testing" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <!--
+    <package name="lapack" version="3.4.2">
+        <repository name="package_lapack_3_4" owner="bgruening" prior_installation_required="True" />
+    </package>
+    <package name="atlas" version="3.10.1">
+        <repository name="package_atlas_3_10" owner="bgruening" prior_installation_required="True" />
+    </package>
+
+    <package name="readline" version="6.2">
+        <repository name="package_readline_6_2" owner="boris" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    </package>
+    -->
+
+    <package name="R_3_0_1" 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="25dc49b0d6d5" name="package_atlas_3_10" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="atlas" version="3.10.1" />
+                    </repository>
+                    <repository changeset_revision="a6b8f46acca7" name="package_lapack_3_4" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="lapack" version="3.4.2" />
+                    </repository>
+                </action>
+                <!--
+                with-blas="$LAPACK_LIB_DIR"
+                with-lapack="-L$ATLAS_LIB_DIR -llapack -lcblas"
+
+                export BLAS=$LAPACK_LIB_DIR/libblas.a &amp;&amp; 
+                export LAPACK=$LAPACK_LIB_DIR/liblapack.a &amp;&amp; 
+                export ATLAS=$ATLAS_LIB_DIR/libatlas.a &amp;&amp; 
+                -->
+
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="1301ec7705a8" name="package_readline_6_2" owner="boris" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                        <package name="readline" version="6.2" />
+                    </repository>
+                </action>
+                <action type="shell_command">./configure  --enable-R-shlib  --with-x=no --with-readline=no --prefix=$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 />
     </package>
 </tool_dependency>