--- a/tool_dependencies.xml	Sat Apr 12 07:25:47 2014 -0400
+++ b/tool_dependencies.xml	Mon Jan 26 13:10:16 2015 -0500
@@ -1,12 +1,103 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="PEPTIDESHAKER_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-    <package name="searchgui" version="1.18.0">
-      <repository changeset_revision="3bcfc0d7275b" name="package_searchgui_1_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="c35b30122eb6" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="matplotlib" version="1.4">
+        <repository changeset_revision="6424ce261dab" name="package_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="scipy" version="0.14">
+        <repository changeset_revision="38e76888714c" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pysam" version="0.8.1">
+        <repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bx-python" version="0.7.2">
+        <repository changeset_revision="b9a2fe72b835" name="package_bx_python_0_7_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="python" version="2.7">
+        <repository changeset_revision="dffe84445ebd" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="peptide_shaker" version="0.28.0">
-      <repository changeset_revision="aa0a836dfaa9" name="package_peptideshaker_0_28" owner="iuc" 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="1.5.9.1">
+        <install version="1.0">
+            <actions>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="pysam" version="0.8.1" />
+                    </repository>
+                    <repository changeset_revision="b9a2fe72b835" name="package_bx_python_0_7_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="bx-python" version="0.7.2" />
+                    </repository>
+                    <repository changeset_revision="c35b30122eb6" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.9" />
+                    </repository>
+                    <repository changeset_revision="6424ce261dab" name="package_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="matplotlib" version="1.4" />
+                    </repository>
+                    <repository changeset_revision="38e76888714c" 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="dffe84445ebd" 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/d/deepTools/deepTools-1.5.9.1.tar.gz</package>
+                </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>