<?xml version="1.0"?>
<tool_dependency>
    <package name="bwa" version="0.5.9">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>bwa</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: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.5.9-r16
Contact: Heng Li &lt;lh3@sanger.ac.uk&gt;

Usage:   bwa &lt;command&gt; [options]

Command: index         index sequences in the FASTA format
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries

         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         pac2bwtgen    alternative algorithm for generating BWT
         bwtupdate     update .bwt to the new format
         pac_rev       generate reverse PAC
         bwt2sa        generate SA from BWT and Occ
         pac2cspac     convert PAC to color-space PAC
         stdsw         standard SW/NW alignment
        </readme>
    </package>
</tool_dependency>