--- a/tool_dependencies.xml	Tue Apr 26 11:21:43 2016 -0400
+++ b/tool_dependencies.xml	Tue Apr 26 15:27:13 2016 -0400
@@ -26,20 +26,19 @@
         <!-- 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 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="shell_command">tar -xjf setuptools_18.2_src_all.tar.bz2</action>
         <action type="change_directory">pypa-setuptools-1a981f2e5031</action>
-        <action type="shell_command">python3 setup.py install</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="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">python3 setup.py install</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 -->
@@ -57,7 +56,7 @@
         <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
+          $INSTALL_DIR/MiModD_venv/bin/python3 setup.py install
         </action>
         <action type="change_directory">$TMP_WORK_DIR</action>
 
@@ -71,11 +70,11 @@
           </repository>
         </action>
       <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
-        <action type="shell_command">python3 setup.py install</action>
+        <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 -->
-        <action type="shell_command">python3 -m MiModD.__first_run__</action>
+        <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action>
                 
         <action type="set_environment">
       <!-- make the mimodd entry script discoverable -->