--- a/tool_dependencies.xml	Tue Apr 26 15:27:13 2016 -0400
+++ b/tool_dependencies.xml	Fri Apr 29 06:01:46 2016 -0400
@@ -10,7 +10,7 @@
     <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="python3" version="3.4">
-    <repository changeset_revision="3956f4688295" name="package_python_3_4_x_lean" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="5e5653b689ca" name="package_python_3_4_x_lean" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
     
   <package name="mimodd" version="0.1.7.2">
@@ -18,7 +18,7 @@
       <actions>
       <!-- prepare a python3 venv to install into -->
         <action type="set_environment_for_install">
-          <repository changeset_revision="3956f4688295" name="package_python_3_4_x_lean" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
+          <repository changeset_revision="5e5653b689ca" name="package_python_3_4_x_lean" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
             <package name="python3" version="3.4" />
           </repository>
         </action>
@@ -28,21 +28,22 @@
         <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>
 
       <!-- download and install setuptools (required to install rpy2) -->
-        <action type="download_file" sha256sum="7b2a76ec3aeb6dc95ae66eab173e7b46e26436c5ba4ee94744f2360bce493b25">https://depot.galaxyproject.org/software/setuptools/setuptools_18.2_src_all.tar.bz2</action>
+        <action type="change_directory">$TMP_WORK_DIR</action>
+        <action sha256sum="7b2a76ec3aeb6dc95ae66eab173e7b46e26436c5ba4ee94744f2360bce493b25" type="download_file">https://depot.galaxyproject.org/software/setuptools/setuptools_18.2_src_all.tar.bz2</action>
         <action type="shell_command">tar -xjf setuptools_18.2_src_all.tar.bz2</action>
         <action type="change_directory">pypa-setuptools-1a981f2e5031</action>
         <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
-        <action type="change_directory">$TMP_WORK_DIR</action>
 
       <!-- download and install six (required by rpy2) -->
-        <action type="download_file" sha256sum="e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5">https://depot.galaxyproject.org/software/six/six_1.9.0_src_all.tar.gz</action>
+        <action type="change_directory">$TMP_WORK_DIR</action>
+        <action sha256sum="e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5" type="download_file">https://depot.galaxyproject.org/software/six/six_1.9.0_src_all.tar.gz</action>
         <action type="shell_command">tar -xzf six_1.9.0_src_all.tar.gz</action>
         <action type="change_directory">six-1.9.0</action>
         <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
-        <action type="change_directory">$TMP_WORK_DIR</action>
 
       <!-- download and install rpy2 -->
-        <action type="download_file" sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action>
+        <action type="change_directory">$TMP_WORK_DIR</action>
+        <action sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441" type="download_file">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action>
         <action type="shell_command">tar -xzf rpy2_2.7.5_src_all.tar.gz</action>
         <action type="change_directory">rpy2-2.7.5</action>
         <action type="set_environment_for_install">
@@ -58,9 +59,9 @@
           export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &amp;&amp;
           $INSTALL_DIR/MiModD_venv/bin/python3 setup.py install
         </action>
-        <action type="change_directory">$TMP_WORK_DIR</action>
 
       <!-- download and install MiModD -->
+        <action type="change_directory">$TMP_WORK_DIR</action>
         <action type="download_file">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action>
         <action type="shell_command">tar -xzf MiModD-0.1.7.2.tar.gz</action>
         <action type="change_directory">MiModD-0.1.7.2</action>
@@ -69,25 +70,19 @@
             <package name="zlib" version="1.2.8" />
           </repository>
         </action>
-      <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
+        <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
         <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
-      <!-- make MiModD's wrapped binaries executable -->
-        <action type="chmod"><file mode="755">$INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</file></action>
-      <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself -->
+        <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself -->
         <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action>
-                
+        
+      <!-- configure environment -->
         <action type="set_environment">
-      <!-- make the mimodd entry script discoverable -->
+          <!-- make the mimodd entry script discoverable -->
           <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
-      <!-- clear $PYTHONPATH and $PYTHONHOME -->
-          <environment_variable action="set_to" name="PYTHONPATH" />
-          <environment_variable action="set_to" name="PYTHONHOME" />
-      <!-- propagate $LD_LIBRARY_PATH -->    
-          <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
         </action>
-        
       </actions>
     </install>
+    
     <readme>
 Summary: Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
 Home-page: http://sourceforge.net/projects/mimodd/
@@ -108,12 +103,10 @@
 MiModD is designed for good performance on standard hardware and enables WGS 
 data analysis for most model organisms on regular desktop PCs.
 
-MiModD can be installed under Linux and Mac OS with minimal software 
-requirements and a simple setup procedure. As a standalone package it can be 
-used from the command line, but can also be integrated seamlessly and easily 
-into any local installation of a Galaxy bioinformatics server providing a 
-graphical user interface, database management of results and simple composition 
-of analysis steps into workflows.
+Detailed documentation of the software can be found at:
+
+  http://mimodd.readthedocs.io
+
     </readme>
   </package>
 </tool_dependency>