--- a/tool_dependencies.xml	Mon Apr 25 18:00:02 2016 -0400
+++ b/tool_dependencies.xml	Tue Apr 26 07:03:26 2016 -0400
@@ -29,9 +29,9 @@
         <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="download_file" sha256sum="beb3445cfc3a0f9a36df7de6489d2a488a5ac113c471c448e46e6d9c47cb7840">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">
           <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
             <package name="readline" version="6.3" />
@@ -48,7 +48,9 @@
         <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="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>
         <action type="set_environment_for_install">
           <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
             <package name="zlib" version="1.2.8" />