comparison tool_dependencies.xml @ 0:80ed79e80b4a draft

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0:80ed79e80b4a

<?xml version="1.0"?>
<tool_dependency>
    <package name="sambamba" version="0.3.3">
        <install version="1.0">
            <actions>
				<action type="shell_command">git clone --recursive https://github.com/lomereiter/sambamba</action>
                <action type="shell_command">git checkout v0.3.3</action>
                <action type="shell_command">git submodule update --recursive</action>
                <action type="shell_command">make</action>
                <action type="move_directory_files">
                    <source_directory>build</source_directory>
                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
			Sambamba requires a D2 compiler (dmd >= 2.062).  The automated installation will attempt to use the dmd compiler and thus will not be optimized.  
            
            For performance reasons, the sambamba developers recommend you use either GDC or LDC as they use GCC and LLVM backends and do a much better job at optimization.You should then use the sambamba-ldmd2-64 make target.  See https://github.com/lomereiter/sambamba/wiki/Command-line-tools for more information.

            You may wish to simply use a precompiled binary of sambamba available at https://www.dropbox.com/sh/v05fsb5aarob3xe/iUHgyud31a/sambamba.  This may be installed as a "Managed Dependency" in Galaxy's "tool_dependency_dir".  See http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies. 

            See the sambamba repository on github for complete details: https://github.com/lomereiter/sambamba.
        </readme>
    </package>
</tool_dependency>