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Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
author devteam
date Mon, 16 Dec 2013 16:30:37 -0500
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<?xml version="1.0"?>
<tool_dependency>
    <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">
        <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="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_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>