# HG changeset patch
# User jeremie
# Date 1403863366 14400
# Node ID fff5d75555e26646af0a68e69316bf05e5f17802
# Parent  145d09fbd0141c98c7561ce91cd6afdba9d49467
Uploaded

diff -r 145d09fbd014 -r fff5d75555e2 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jun 27 05:59:25 2014 -0400
+++ b/tool_dependencies.xml	Fri Jun 27 06:02:46 2014 -0400
@@ -2,19 +2,46 @@
 <tool_dependency>
     <package name="breakdancer" version="1.2.6">
         <install version="1.0">
-            <actions>
-                <action type="download_by_url" target_filename="bin.tar.gz">https://www.dropbox.com/s/6fpm0vqmn0vu5m2/1_2_6.tar.gz?dl=1</action>
-                <action type="move_directory_files">
-                    <source_directory>.</source_directory>
-                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                </action>
+            <actions_group>
+                <actions architecture="i386" os="linux">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/freebayes/freebayes-0.9.6_9608597d-Linux-i686.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>       
+                </actions>                
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/freebayes/freebayes-0.9.6_9608597d-Linux-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>       
+                </actions>                
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/freebayes/freebayes-0.9.6_9608597d-Darwin-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>       
+                </actions>         
+                <actions>
+                    <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 || ( 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>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                 </action>
-            </actions>
+            </actions_group>
         </install>
         <readme>
+FreeBayes requires g++ and the standard C and C++ development libraries.
+Additionally, cmake is required for building the BamTools API.
         </readme>
     </package>
-</tool_dependency>
-
+</tool_dependency>
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