annotate tool_dependencies.xml @ 4:1bdb57965c6f draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit b'eebcbcf7ec7804eb97e6be0f417d01fd3422ab32\n'

<?xml version="1.0"?>
<tool_dependency>
    <package name="sortmerna" version="2.1b">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url" target_filename="sortmerna-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action>
                    <action type="shell_command"><![CDATA[
                        ./build.sh --prefix=$INSTALL_DIR
                    ]]>
                    </action>
                    <action type="shell_command">make install</action>
                    <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
                    <action type="move_directory_files">
                        <source_directory>rRNA_databases/</source_directory>
                        <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
                    </action>
                    <action type="set_environment">
                        <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    </action>
                </actions>
                <actions architecture="x86_64" os="darwin">
                    <action type="download_by_url" target_filename="sortmerna-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action>
                    <action type="shell_command"><![CDATA[
                        export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./build.sh --prefix=$INSTALL_DIR && make install
                    ]]>
                    </action>
                    <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
                    <action type="move_directory_files">
                        <source_directory>rRNA_databases/</source_directory>
                        <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
                    </action>
                    <action type="set_environment">
                        <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    </action>
                </actions>
            </actions_group>
        </install>
        <readme>
        SortMeRNA requires g++ 4.8 or later.

        Note: the Clang compiler on Mac (distributed through Xcode) does not
        support multithreading. The user is recommended to install the original
        GCC compiler via MacPorts
        </readme>
    </package>
</tool_dependency>