--- a/tool_dependencies.xml	Tue Sep 16 13:46:05 2014 -0400
+++ b/tool_dependencies.xml	Tue Oct 20 14:43:12 2015 -0400
@@ -1,101 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="samtools" version="0.1.19">
-        <repository changeset_revision="923adc89c666" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="numpy" version="1.7.1">
-        <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="matplotlib" version="1.2.1">
-        <repository changeset_revision="fe60617380df" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="scipy" version="0.12.0">
-        <repository changeset_revision="984d208b0808" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="pysam" version="0.7.7">
-        <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bx-python" version="12-2013">
-        <repository changeset_revision="55bd96a1c3b3" name="package_bx_python_12_2013" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="python" version="2.7">
+        <repository changeset_revision="eb37ce21eef1" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.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="1.5.9.1">
-        <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="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="pysam" version="0.7.7" />
-                    </repository>
-                    <repository changeset_revision="55bd96a1c3b3" name="package_bx_python_12_2013" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="bx-python" version="12-2013" />
-                    </repository>
-                    <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="numpy" version="1.7.1" />
-                    </repository>
-                    <repository changeset_revision="fe60617380df" name="package_matplotlib_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="matplotlib" version="1.2.1" />
-                    </repository>
-                    <repository changeset_revision="984d208b0808" name="package_scipy_0_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="scipy" version="0.12.0" />
-                    </repository>
-                </action>
-                <action type="shell_command">git reset --hard 351890e3db9a443484c5c349791b7247163cc94f</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>
+    <package name="deepTools" version="1.5.11">
+        <repository changeset_revision="01eb49da8dcf" name="package_python_2_7_deeptools_1_5_11" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
 </tool_dependency>