<?xml version="1.0"?>
<tool_dependency>
    <package name="msgfplus" version="20140210">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://proteomics.ucsd.edu/Software/MSGFPlus/MSGFPlus.20140210.zip</action>
                <action type="move_file">
                    <source>MSGFPlus.jar</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                
                <!-- This is purely so we can find it using which -->
                <action type="shell_command">chmod u+x $INSTALL_DIR/MSGFPlus.jar</action>
                <action type="set_environment">
                    <environment_variable name="MSGFPLUS_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
                    <environment_variable name="PROTK_MSGFPLUS_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Downloads and installs MSGF+.
            https://proteomics.ucsd.edu/
            Java 1.6 is required to run MSGF+.
        </readme>
    </package>
</tool_dependency>