--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jun 24 12:39:12 2013 -0400
@@ -0,0 +1,48 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="SearchGUI" version="1.13.1">
+        <install version="1.0">
+            <actions>
+              <action type="download_by_url">http://searchgui.googlecode.com/files/SearchGUI-1.13.1_mac_and_linux.zip</action>
+	      <action type="shell_command">tar -xf SearchGUI-1.13.1_mac_and_linux.tar</action>
+	      <action type="shell_command">cd SearchGUI-1.13.1_mac_and_linux</action>
+	      <action type="shell_command">chmod -R o+w resources</action>
+              <action type="move_directory_files">
+                <source_directory>.</source_directory>
+                <destination_directory>$INSTALL_DIR/</destination_directory>
+              </action>
+	      <action type="shell_command">mkdir -p $BIN_DIR</action>
+              <action type="set_environment">
+                <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+              </action>                
+            </actions>
+        </install>
+        <readme>
+          This package downloads and installs the SearchGUI scripts develped as part of the Peptideshaker tool.
+          (https://github.com/jmchilton/peptide-shaker).
+
+        </readme>
+    </package>
+    
+    <package name="PeptideShaker" version="0.20.1">
+        <install version="1.0">
+            <actions>
+              <action type="download_by_url">http://peptide-shaker.googlecode.com/files/PeptideShaker-0.20.1.zip</action>
+	      <action type="shell_command">chmod -R o+w resources</action>
+              <action type="move_directory_files">
+                <source_directory>.</source_directory>
+                <destination_directory>$INSTALL_DIR/</destination_directory>
+              </action>
+              <action type="shell_command">mkdir -p $BIN_DIR</action>
+              <action type="set_environment">
+                <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+              </action>                
+            </actions>
+        </install>
+        <readme>
+          This package downloads and installs the peptideshaker tool as a part of the peptideshaker framework.
+          (https://github.com/jmchilton/peptide-shaker).
+
+        </readme>
+    </package>
+</tool_dependency>