<?xml version="1.0"?>
<tool_dependency>
    <package name="tabix" version="0.2.6">
        <install version="1.0">
            <actions>
             <action type="download_by_url">http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>tabix</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bgzip</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable name="TABIX_BIN_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Installs tabix version 0.2.6. Available binaries: tabix, bgzip
            http://samtools.sourceforge.net/tabix.shtml

            Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line.
            The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing,
            tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos".
            Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally.
        </readme>
    </package>
</tool_dependency>