<?xml version="1.0"?>
<tool_dependency>
    <set_environment version="1.0">
        <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
    </set_environment>
    <package name="snpEff" version="3.0f">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip</action>
                <action type="shell_command">unzip snpEff_latest_core.zip</action>
                <action type="move_file">
                    <source>snpEff_3_0/SnpSift.jar</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>snpEff_3_0/snpEff.jar</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>snpEff_3_0/snpEff.config</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_directory_files">
                    <source_directory>snpEff_3_0/scripts</source_directory>
                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
        </readme>
    </package>

</tool_dependency>