<?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 release</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>
 This tool uses the sambamba view command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file.

There are a three options for installation of sambamba:

	1) Automated toolshed installation.  This requires that a D2 compiler (dmd >= 2.063) is installed.  The automated installation will attempt to use the dmd compiler and thus **will not be optimized**.  

	2) Manual compilation.  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.

	3) Precompiled binary (recommended).  You may wish to simply use a precompiled binary of sambamba available at https://www.dropbox.com/sh/v05fsb5aarob3xe/iUHgyud31a/sambamba.  

If you choose option 2 or 3, sambamba may be installed as a "Managed Dependency" in Galaxy's "tool_dependency_dir".  See http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies. 

The development repository for the galaxy wrapper is at: https://bitbucket.org/lance_parsons/sambamba_filter_galaxy_wrapper.
The sambamba development repository is at: https://github.com/lomereiter/sambamba.
        </readme>
    </package>
</tool_dependency>