--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Dec 14 04:19:46 2015 -0500
@@ -0,0 +1,37 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="cd-hit" version="4.6.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://cdhit.googlecode.com/files/cd-hit-v4.6.1-2012-08-27.tgz</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                     <source>cd-hit</source>
+                     <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="move_file">
+                      <source>cd-hit-est</source>
+                      <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="CDHIT_SITE_OPTIONS" action="set_to">"-M 4000 -T 0"</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+These links provide information for building the cdhit package:
+
+http://weizhong-lab.ucsd.edu/cd-hit/
+
+https://code.google.com/p/cdhit/
+
+https://code.google.com/p/cdhit/source/browse/README
+
+Change the CDHIT_SITE_OPTIONS variable in the installed env.sh file to adjust 
+the maximum memory Mb (-M) or to limit the number of threads (-T)
+to match your site 
+        </readme>
+    </package>
+</tool_dependency>
+