<?xml version="1.0"?>
<tool_dependency>
    <set_environment version="1.0">
        <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>
    <package name="samtools" version="0.1.12">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://github.com/modENCODE-DCC/Galaxy/blob/master/toolshed/dependencies/bamedit/samtoolspkg.tar?raw=true</action>
                <action type="shell_command">chmod ago+x samtools</action>
                <action type="shell_command">chmod ago+x maq2sam-long</action>
                <action type="move_file">
                    <source>samtools</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>maq2sam-long</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Compiling SAMtools requires the ncurses and zlib development libraries.</readme>
    </package>
</tool_dependency>