--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Dec 10 10:09:39 2013 -0500
@@ -0,0 +1,92 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="numpy" version="1.7.1">
+        <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="matplotlib" version="1.2.1">
+        <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="scipy" version="0.12.0">
+        <repository changeset_revision="3c1bf479158c" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pysam" version="0.7.7">
+        <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bx-python" version="12-2013">
+        <repository changeset_revision="efba2bb75ac8" name="package_bx_python_12_2013" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="ucsc_tools" version="0.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_binary">
+                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
+                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
+                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
+                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
+                </action>
+                <action type="chmod">
+                    <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
+                </action>
+                <action type="download_binary">
+                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
+                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
+                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
+                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
+                </action>
+                <action type="chmod">
+                    <file mode="755">$INSTALL_DIR/bigWigInfo</file>
+                </action>
+                <action type="download_binary">
+                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph</url_template>
+                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
+                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
+                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph</url_template>
+                </action>
+                <action type="chmod">
+                    <file mode="755">$INSTALL_DIR/bigWigToBedGraph</file>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+                </action>
+             </actions>
+         </install>
+         <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
+     </package>
+
+    <package name="deepTools" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
+                <!-- populate the environment variables from the dependend repos -->
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="pysam" version="0.7.7" />
+                    </repository>
+                    <repository changeset_revision="efba2bb75ac8" name="package_bx_python_12_2013" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="bx-python" version="12-2013" />
+                    </repository>
+                </action>
+                <action type="shell_command">git reset --hard fada41ab04f78c4c78d10c7a216e5c3160e8c36e</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 $INSTALL_DIR/bin
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <!-- disable the config file of deepTools -->
+                    <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
+                </action>
+             </actions>
+         </install>
+         <readme>
+            Installation of deepTools from Fidel Ramirez.
+            https://github.com/fidelram/deepTools
+         </readme>
+     </package>
+</tool_dependency>