--- a/tool_dependencies.xml	Thu Nov 28 12:49:25 2013 -0500
+++ b/tool_dependencies.xml	Thu Jan 22 17:36:16 2015 -0500
@@ -1,11 +1,18 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="python" version="2.7">
+        <repository changeset_revision="dffe84445ebd" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
     <package name="pysam" version="0.7.7">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">https://pypi.python.org/packages/source/p/pysam/pysam-0.7.7.tar.gz</action>
-                <action type="make_directory">$INSTALL_DIR/lib/python</action>
-                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
+                <action type="setup_python_environment">
+                   <repository changeset_revision="dffe84445ebd" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                       <package name="python" version="2.7" />
+                   </repository>
+                    <!-- allow downloading and installing an Python package from https://pypi.org/ -->
+                    <package>https://pypi.python.org/packages/source/p/pysam/pysam-0.7.7.tar.gz</package>
+                </action>
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>