annotate tool_dependencies.xml @ 5:be94ae8dac28

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<?xml version="1.0"?>
<tool_dependency>
    <package name="bedtools" version="2.17.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action>
                <action type="shell_command">tar -zxvf BEDTools.v2.17.0.tar.gz </action>
                <action type="shell_command">cd BEDTools.v2.17.0</action>
                <action type="shell_command">make clean</action>
                <action type="shell_command">make all</action>
                <action type="shell_command">cp bin/* $INSTALL_DIR/bin</action>
                
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools
        </readme>
    </package>
</tool_dependency>