<?xml version="1.0"?>
<tool_dependency>
    <package name="sortmerna" version="1.7">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://bioinfo.lifl.fr/RNA/sortmerna/code/sortmerna-1.7.tar.gz</action>
                <action type="shell_command">./configure</action>
                <action type="shell_command">make</action>
                <action type="shell_command">make check</action>
                <action type="move_file">
                    <source>sortmerna</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>buildtrie</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>scripts/merge-paired-reads.sh</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_directory_files">
                    <source_directory>rRNA_databases</source_directory>
                    <destination_directory>$INSTALL_DIR/rRNA_databases</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>automata</source_directory>
                    <destination_directory>$INSTALL_DIR/automata</destination_directory>
                </action>
                <action type="set_environment">
		    <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR</environment_variable>
                </action>
                <action type="set_environment">
		    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
SortMeRNA requires g++ 4.3 or later. Installation may take a moment since ribosomal databases have to be indexed.
	</readme>
    </package>
</tool_dependency>