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<?xml version="1.0"?>
<tool_dependency>
    <package name="bowtie" version="1.0.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/bowtie-bio/files/bowtie/1.0.0/bowtie-1.0.0-src.zip</action>
                <action type="shell_command">make BITS=64</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>
Program: bowtie (ultrafast, memory-efficient short read aligner)
Version: 1.0.0 
http://bowtie-bio.sourceforge.net/manual.shtml

Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. It aligns 35-base-pair reads to the human genome at a rate of 25 million reads per hour on a typical workstation. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: for the human genome, the index is typically about 2.2 GB (for unpaired alignment) or 2.9 GB (for paired-end or colorspace alignment). Multiple processors can be used simultaneously to achieve greater alignment speed. Bowtie can also output alignments in the standard SAM format, allowing Bowtie to interoperate with other tools supporting SAM, including the SAMtools consensus, SNP, and indel callers. Bowtie runs on the command line under Windows, Mac OS X, Linux, and Solaris.
        </readme>
    </package>
</tool_dependency>