<?xml version="1.0"?>
<tool_dependency>
    <package name="cd-hit" version="4.6.4">
        <install version="1.0">
            <actions>
                <action type="download_by_url" md5="d4baba1e95ba9c831a763c6b8a19ce21">https://github.com/weizhongli/cdhit/releases/download/V4.6.4/cd-hit-v4.6.4-2015-0603.tar.gz</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"</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).
        </readme>
    </package>
</tool_dependency>