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<?xml version="1.0"?>
<tool_dependency>
    <package name="kent" version="283">
        <install version="1.0">
            <actions>
                <action type="download_by_url" target_filename="kent.zip">http://hgdownload.cse.ucsc.edu/admin/jksrc.v283.zip</action>
                <action type="shell_command">
                    export MACHTYPE=`uname -m`; 
                    export BINDIR=$INSTALL_DIR/bin; mkdir $INSTALL_DIR/bin; 
                    cd src/lib; make; 
                    cd ../jkOwnLib; make; 
                    cd ../blat; make;
                    cd ../gfClient; make;
                    cd ../gfServer; make;
                    cd ../utils; mv makefile makefile.orig; grep -v -E 'pslLiftSubrangeBlat|raSqlQuery|scaffoldFaToAgp' makefile.orig > makefile;  make
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
This only handles blat for a non-commercial linux system.

Please note that the Blat source and executables are freely available for
academic, nonprofit and personal use. Commercial licensing information is
available on the Kent Informatics website (http://www.kentinformatics.com/).
        </readme>
    </package>

</tool_dependency>