# HG changeset patch
# User jeremie
# Date 1403863649 14400
# Node ID 8fe9a085639985c4a3ea366f52f6f52eda35eda1
# Parent  fff5d75555e26646af0a68e69316bf05e5f17802
Uploaded

diff -r fff5d75555e2 -r 8fe9a0856399 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jun 27 06:02:46 2014 -0400
+++ b/tool_dependencies.xml	Fri Jun 27 06:07:29 2014 -0400
@@ -4,36 +4,19 @@
         <install version="1.0">
             <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="download_by_url" target_filename="bin.tar.gz">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="download_by_url" target_filename="bin.tar.gz">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>$INSTALL_DIR/bin</destination_directory>
                     </action>       
-                </actions>         
-                <actions>
-                    <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
-                    <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action>
-                    <action type="shell_command">git submodule update --recursive</action>
-                    <action type="shell_command">make || ( make clean &amp;&amp; sed -i.bak -e &apos;s:LIBS = -lz -lm -L./ -L../vcflib/tabixpp/ -L$(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>
+                </actions>                       
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                 </action>