# HG changeset patch
# User nilesh
# Date 1373915369 18000
# Node ID aad08b24baffe3ba2cd8f2a98550a2f41331c905
# Parent  6baaaaa1f8588a2ce4e37b258d0da2023160cfd5
switched to git

diff -r 6baaaaa1f858 -r aad08b24baff tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jul 15 14:00:46 2013 -0500
+++ b/tool_dependencies.xml	Mon Jul 15 14:09:29 2013 -0500
@@ -11,10 +11,11 @@
                         <package name="zlib" version="1.2.8" />
                    </repository>
                 </action>
-    			<action type="download_by_url">http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.5a.tar.bz2</action>
+    			<action type="shell_command">git clone https://github.com/lh3/bwa.git</action>
+    			<action type="shell_command">cd ./bwa &amp;&amp; make LIBS="-L$ZLIB_PATH -lm -lz -lpthread"</action>
     			<action type="move_file">
-                    <source>.</source>
-                    <destination>$INSTALL_DIR</destination>
+                    <source>bwa/bwa</source>
+                    <destination>$INSTALL_DIR/bin</destination>
                 </action>
     			<action type="set_environment">
     				<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>