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<?xml version="1.0"?>
<tool_dependency>
    <package name="blat_server" version="latest">
        <install version="1.0">
            <actions_group>

                <actions os="linux" architecture="x86_64">
                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action>
                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfServer</action>
                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfClient</action>
                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit</action>
                    <action type="shell_command">chmod ugo+x *</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </actions>

                <actions os="darwin" architecture="x86_64">
                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/blat</action>
                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gfClient</action>
                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gfServer</action>
                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faToTwoBit</action>
                    <action type="shell_command">chmod ugo+x *</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </actions>

            <actions>
                <action type="download_by_url" target_filename="kent.zip">http://hgdownload.cse.ucsc.edu/admin/jksrc.zip</action>
                <action type="shell_command">
                    export MACHTYPE=`uname -m`; 
                    export BINDIR=$INSTALL_DIR/bin; mkdir $INSTALL_DIR/bin; 
                    cd src/lib; make; 
                    cd ../jkOwnLib; make; 
                    cd ../blat; make;
                    cd ../gfClient; make;
                    cd ../gfServer; make;
                    cd ../utils; mv makefile makefile.orig; grep -v -E 'pslLiftSubrangeBlat|raSqlQuery|scaffoldFaToAgp' makefile.orig > makefile;  make
                </action>
            </actions>
            <action type="set_environment">
                <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
Downloads and installs the latest kent blat server tools (blat, gfServer, gfClient, faToTwoBit).
It will try to install executable files from:  UCSC ftp://hgdownload.cse.ucsc.edu/admin/exe/
otherwise it will try to compile from source from:  UCSC at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
( The website doesn't offer previously released versions. )

NOTE: A license is required for use in a COMMERCIAL system.

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>