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<?xml version="1.0"?>
<tool_dependency>
    <package name="segemehl" version="0.1.6">
        <install version="1.0">
            <actions>
                <action type="download_by_url" target_filename="segemehl_0_1_6_1.tar.gz">http://www.bioinf.uni-leipzig.de/Software/segemehl/segemehl_0_1_6.tar.gz</action>
                <action type="change_directory">segemehl</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>segemehl.x</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Short read mapping with gaps.
            To compile segemehl a C-compiler is needed, usually GCC.
            http://www.bioinf.uni-leipzig.de/Software/segemehl/
            
            Please note that segemehl loads the whole index and genome files into memory.
            Segemehl's index is around 45GB in size, so the memory usage of that tool is huge.
        </readme>
    </package>
</tool_dependency>