--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Feb 05 14:15:40 2013 -0500
@@ -0,0 +1,40 @@
+<?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>
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