<?xml version="1.0"?>
<tool_dependency>
    <package name="bowtie" version="0.12.7">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>bowtie</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bowtie-build</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bowtie-inspect</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
Compiling Bowtie requires libpthread to be present on your system.
        </readme>
    </package>
</tool_dependency>