--- a/tool_dependencies.xml	Mon Apr 25 17:26:32 2016 -0400
+++ b/tool_dependencies.xml	Mon Apr 25 17:27:25 2016 -0400
@@ -3,6 +3,12 @@
   <package name="zlib" version="1.2.8">
     <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
+  <package name="R" version="3.2.1">
+    <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="readline" version="6.2">
+    <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
   <package name="python3" version="3.4.1">
     <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
@@ -10,27 +16,50 @@
   <package name="mimodd" version="0.1.7.2">
     <install version="1.0">
       <actions>
-        <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action>
+      <!-- prepare a python3 venv to install into -->
         <action type="set_environment_for_install">
           <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
             <package name="python3" version="3.4.1" />
           </repository>
         </action>
+        <action type="shell_command">python3 -m venv --without-pip $INSTALL_DIR/MiModD_venv</action>
+        <!-- remove the plain python symlink from the venv to avoid its 
+             accidental use by Galaxy, MiModD uses python3 explicitly -->
+        <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>
+        <action type="shell_command">. $INSTALL_DIR/MiModD_venv/bin/activate</action>
+        
+      <!-- download and install rpy2 -->
+        <action sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441" type="download_by_url">
+          https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz
+        </action>
+        <action type="set_environment_for_install">
+          <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+            <package name="readline" version="6.2" />
+          </repository>
+          <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+            <package name="R" version="3.2.1" />
+          </repository>
+        </action>
+        <action type="shell_command">
+          export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" &amp;&amp;
+          export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &amp;&amp;
+          python3 setup.py install
+        </action>
+        <action type="change_directory">$TMP_WORK_DIR</action>
+
+      <!-- download and install MiModD -->
+        <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action>
         <action type="set_environment_for_install">
           <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
             <package name="zlib" version="1.2.8" />
           </repository>
         </action>
-        <action type="shell_command">pyvenv --without-pip $INSTALL_DIR/MiModD_venv</action>
-      <!-- remove the plain python symlink from the venv to avoid its 
-           accidental use by Galaxy, MiModD uses python3 explicitly -->
-        <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>
       <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
-        <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
+        <action type="shell_command">python3 setup.py install</action>
       <!-- make MiModD's wrapped binaries executable -->
-        <action type="shell_command">chmod 755 $INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</action>
+        <action type="chmod"><file mode="755">$INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</file></action>
       <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself -->
-        <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action>
+        <action type="shell_command">python3 -m MiModD.__first_run__</action>
                 
         <action type="set_environment">
       <!-- make the mimodd entry script discoverable -->
@@ -42,7 +71,6 @@
           <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
         </action>
         
-        
       </actions>
     </install>
     <readme>