Mercurial > repos > cjav > package_bwa_0_7_5a

view tool_dependencies.xml @ 0:df10a1254304 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author cjav
date Tue, 24 Sep 2013 13:09:58 -0400
parents
children
line wrap: on
line source

<?xml version="1.0"?>
<tool_dependency>
    <package name="bwa" version="0.7.5a">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.5a.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: 0.7.5a-r405
Contact: Heng Li &lt;lh3@sanger.ac.uk&gt;

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

Command: index         index sequences in the FASTA format
         mem           BWA-MEM algorithm
         fastmap       identify super-maximal exact matches
         pemerge       merge overlapping paired ends (EXPERIMENTAL)
         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
         bwt2sa        generate SA from BWT and Occ
        </readme>
    </package>
</tool_dependency>