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view tool_dependencies.xml @ 15:baab049d3aff draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
author bebatut
date Wed, 10 Feb 2016 04:02:18 -0500
parents 011ec5258e71
children
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<?xml version="1.0"?>
<tool_dependency>
    <package name="sortmerna" version="2.0">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                        <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
                        <action type="shell_command"><![CDATA[
                            ./build.sh --prefix=$INSTALL_DIR
                        ]]>
                        </action>
                        <action type="change_directory">../</action>
                        <action type="make_directory">$INSTALL_DIR/bin/</action>
                        <action type="move_file">
                            <source>sortmerna-2.0/sortmerna</source>
                            <destination>$INSTALL_DIR/bin</destination>
                        </action>
                        <action type="move_file">
                            <source>sortmerna-2.0/indexdb_rna</source>
                            <destination>$INSTALL_DIR/bin</destination>
                        </action>
                        <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
                        <action type="move_directory_files">
                            <source_directory>sortmerna-2.0/rRNA_databases/</source_directory>
                            <destination_directory>$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-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
                        <action type="shell_command"><![CDATA[
                            export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./configure && make && make install
                        ]]>
                        </action>
                        <action type="change_directory">../</action>
                        <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
                        <action type="move_directory_files">
                            <source_directory>sortmerna-2.0/rRNA_databases/</source_directory>
                            <destination_directory>$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>