--- a/tool_dependencies.xml	Thu Jul 11 12:33:27 2013 -0400
+++ b/tool_dependencies.xml	Wed Oct 02 02:20:04 2013 -0400
@@ -1,14 +1,40 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="R" version="2.15.1">
+    <package name="R" version="2.11.0">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz</action>
-                <action type="shell_command">./configure --prefix=$INSTALL_DIR/lib</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>bin/R</source>
-                    <destination>$INSTALL_DIR/lib/bin</destination>
+                <action type="download_by_url">http://cran.rstudio.com/src/base/R-2/R-2.11.0.tar.gz</action>
+                <action type="shell_command">
+                    ./configure --enable-R-shlib \
+                    --with-readline=no \
+                    --with-x=no \
+                    --prefix=$INSTALL_DIR \
+                    --libdir=$INSTALL_DIR/lib \
+                    --disable-R-framework
+                </action>
+                <action type="shell_command">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.
+            NOTE: See custom compilation options above 
+        </readme>
+    </package>
+    <package name="numpy" version="1.7.1">
+        <repository toolshed="http://toolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="iuc" changeset_revision="74c21f9bdc39" />
+    </package>
+    <package name="rseqc" version="2.3.7">
+        <install version = "1.0">
+            <actions>
+                <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
+                <action type="shell_command">python setup.py install --root $INSTALL_DIR --prefix . --install-lib lib</action>
+                <action type="set_environment">
+                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
                 </action>
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
@@ -16,45 +42,9 @@
             </actions>
         </install>
         <readme>
-            You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R.
+            RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html#.
+            Requires gcc, python, numpy, and R
         </readme>
     </package>
-    <package name="samtools" version="0.1.18">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>samtools</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>bcftools/bcftools</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Both BCFTools and Samtools installed in this dependency.Compiling SAMtools requires the ncurses and zlib development libraries.</readme>
-    </package>
-    <package name="rseqc" version="2.3.7">
-        <install version = "1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
-                <action type="shell_command">python setup.py install --root $INSTALL_DIR/lib/rseqc</action>
-                <action type="set_environment">
-                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/rseqc/usr/local/lib/python2.7/site-packages</environment_variable>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/lib/rseqc/usr/local/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        	RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html#.
-        </readme>
-    </package>
-    
+
 </tool_dependency>