# HG changeset patch
# User Daniel Blankenberg <dan@bx.psu.edu>
# Date 1370458803 14400
# Node ID d291dc763c4c95aa53de762665ec405bf119868f
# Parent  28e422c589ac11151b2af386a510a9c4d86a728b
Add an optional alternative make route for compiling FreeBayes; solves issues seen installing under certain architectures.

diff -r 28e422c589ac -r d291dc763c4c tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Sep 12 13:06:51 2012 -0400
+++ b/tool_dependencies.xml	Wed Jun 05 15:00:03 2013 -0400
@@ -6,7 +6,7 @@
                 <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
                 <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action>
                 <action type="shell_command">git submodule update --recursive</action>
-                <action type="shell_command">make</action>
+                <action type="shell_command">make || ( make clean &amp;&amp; sed -i.bak -e &apos;s:LIBS = -lz -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix:LIBS = -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz:g&apos; src/Makefile &amp;&amp; make )</action>
                 <action type="move_directory_files">
                     <source_directory>bin</source_directory>
                     <destination_directory>$INSTALL_DIR/bin</destination_directory>