<?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 openmp=yes</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>