--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Feb 06 18:50:26 2015 -0500
@@ -0,0 +1,56 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <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="scipy" version="0.14">
+       <repository changeset_revision="a257ce4d82ad" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <!--package name="rpy2" version="2.3.6">
+       <repository name="package_rpy2_2_3_6" owner="bgruening" prior_installation_required="True" />
+    </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="msproteomicstools" version="0.3.2">
+        <install version="1.0">
+            <actions>
+                <!-- populate the environment variables from the dependend repos -->
+                <action type="set_environment_for_install">
+                   <repository changeset_revision="21afd61aae1e" name="package_pandas_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="pandas" version="0.14" />
+                    </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>
+                    <!--repository name="package_rpy2_2_3_6" owner="bgruening">
+                        <package name="rpy2" version="2.3.6" />
+                    </repository>-->
+                    <repository changeset_revision="a257ce4d82ad" name="package_scipy_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="scipy" version="0.14" />
+                    </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/l/lxml/lxml-3.4.1.tar.gz</package>
+                    <package>https://pypi.python.org/packages/source/x/xlwt/xlwt-0.7.5.tar.gz</package>
+                    <package>https://pypi.python.org/packages/source/X/XlsxWriter/XlsxWriter-0.6.6.tar.gz</package>
+                    <package>https://pypi.python.org/packages/source/s/scikits.datasmooth/scikits.datasmooth-0.61.tar.gz</package>
+                    <package>https://pypi.python.org/packages/source/p/pyteomics/pyteomics-2.5.5.tar.gz</package>
+                    <package>https://pypi.python.org/packages/source/c/cluster/cluster-1.2.2.tar.gz</package>
+                    <package>https://pypi.python.org/packages/source/m/msproteomicstools/msproteomicstools-0.3.2.tar.gz</package>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
+                    <environment_variable action="set_to" name="MSPROTEOMICSTOOLS_ROOT">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Installing msproteomicstools.</readme>
+    </package>
+</tool_dependency>