--- a/tool_dependencies.xml	Sat Feb 15 15:41:04 2014 -0500
+++ b/tool_dependencies.xml	Sat Feb 15 15:43:39 2014 -0500
@@ -1,101 +1,54 @@
 <?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" />
+       <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="scipy" version="0.12.0">
-        <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+       <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" 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 name="R_3_0_1" version="3.0.1">
+        <repository changeset_revision="4666f68ad4d5" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="bx-python" version="12-2013">
-        <repository changeset_revision="5457e32b427c" name="package_bx_python_12_2013" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="gnu_awk" version="4.1.0">
+       <repository changeset_revision="cbe9f1c8c98b" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-
-    <package name="ucsc_tools" version="0.1">
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="MACS2_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+    <!-- 2.0.10 12162013 -->
+    <package name="macs2" version="2.0.10.3">
         <install version="1.0">
             <actions>
-                <action type="download_binary">
-                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
-                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
-                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
-                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
-                </action>
-                <action type="chmod">
-                    <file mode="755">$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>
+                <action type="shell_command">git clone --recursive https://github.com/taoliu/MACS.git</action>
+                <!-- Galaxy tries to change automatically to the directory "macs2" (name of the package). 
+                But we need to change to MACS. Go one level back and enter MACS -->
+                <action type="change_directory">../MACS</action>
+                <action type="shell_command">git checkout 7ccb571d2f2dcb5be1d75f323b1d17a59b926deb</action>
+                <action type="shell_command">git submodule update --recursive</action>
 
-    <package name="deepTools" version="1.5.4_3268f7e1458f3a520ab6fea3039971ee9d7a6d5b">
-        <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="5457e32b427c" name="package_bx_python_12_2013" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="bx-python" version="12-2013" />
-                    </repository>
                     <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="numpy" version="1.7.1" />
                     </repository>
-                    <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="matplotlib" version="1.2.1" />
-                    </repository>
                     <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="scipy" version="0.12.0" />
                     </repository>
                 </action>
-                <action type="shell_command">git reset --hard 3268f7e1458f3a520ab6fea3039971ee9d7a6d5b</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 $INSTALL_DIR/bin
                 </action>
                 <action type="set_environment">
+                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
                     <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>
+                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
+                    <environment_variable action="set_to" name="PYTHONPATH_MACS2">$INSTALL_DIR/lib/python</environment_variable>
+                    </action>
+            </actions>
+        </install>
+        <readme>Macs2 installation instructions. MACS2 can be found at https://github.com/taoliu/MACS</readme>
+    </package>
 </tool_dependency>