--- a/tool_dependencies.xml	Tue Jan 27 15:15:42 2015 -0500
+++ b/tool_dependencies.xml	Wed Feb 18 11:35:06 2015 -0500
@@ -1,42 +1,39 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="atlas" version="3.10.2">
-        <repository changeset_revision="d5b1c7875b7b" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="numpy" version="1.9">
-        <repository changeset_revision="dd91d64330d4" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="python" version="2.7">
-        <repository changeset_revision="2c52c900e56a" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="scipy" version="0.14">
-        <install version="1.0">
-            <actions>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="d5b1c7875b7b" name="package_atlas_3_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="atlas" version="3.10.2" />
-                    </repository>
-                    <repository changeset_revision="dd91d64330d4" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="numpy" version="1.9" />
-                    </repository>
-                </action>
-                <action type="setup_python_environment">
-                   <repository changeset_revision="2c52c900e56a" 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/s/scipy/scipy-0.14.0.tar.gz</package>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
-                    <environment_variable action="set_to" name="PYTHONPATH_SCIPY">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable action="set_to" name="PATH_SCIPY">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Compiling scipy requires a C and Fortran compiler (typically gcc and gfortran). The PYTHONPATH for scipy can be accessed through PYTHONPATH_SCIPY and the binaries with PATH_SCIPY.</readme>
-    </package>
+        <package name="atlas" version="3.10.2">
+            <repository changeset_revision="d5b1c7875b7b" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        </package>
+        <package name="numpy" version="1.9">
+            <repository changeset_revision="266529386609" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        </package>
+        <package name="scipy" version="0.14">
+            <install version="1.0">
+                <actions>
+                    <action type="download_by_url">https://pypi.python.org/packages/source/s/scipy/scipy-0.14.0.tar.gz#md5=d7c7f4ccf8b07b08d6fe49d5cd51f85d</action>
+                    <action type="set_environment_for_install">
+                        <repository changeset_revision="d5b1c7875b7b" name="package_atlas_3_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                            <package name="atlas" version="3.10.2" />
+                        </repository>
+                        <repository changeset_revision="266529386609" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                            <package name="numpy" version="1.9" />
+                        </repository>
+                    </action>
+                    <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                    <action type="shell_command">
+                        export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
+                        export ATLAS=$ATLAS_ROOT_PATH &amp;&amp;
+                        python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
+                    </action>
+                    <action type="set_environment">
+                        <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                        <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
+                        <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
+                        <environment_variable action="set_to" name="PYTHONPATH_SCIPY">$INSTALL_DIR/lib/python</environment_variable>
+                        <environment_variable action="set_to" name="PATH_SCIPY">$INSTALL_DIR/bin</environment_variable>
+                        </action>
+                </actions>
+            </install>
+            <readme>Compiling scipy requires a C and Fortran compiler (typically gcc and gfortran). The PYTHONPATH for scipy can be accessed through PYTHONPATH_SCIPY and the binaries with PATH_SCIPY.</readme>
+        </package>
 </tool_dependency>