view bismark_wrapper/tool_dependencies.xml @ 4:a4bd52c4ed46 draft

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<?xml version="1.0"?>
<tool_dependency>
    <!-- http://www.bioinformatics.babraham.ac.uk/projects/bismark/bismark_v0.7.7.tar.gz -->
    <package name="bowtie2" version="2.0.0-beta7">
        <install version="1.1">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.0.0-beta7/bowtie2-2.0.0-beta7-source.zip</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>bowtie2</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bowtie2-align</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
Compiling bowtie2 requires zlib and libpthread to be present on your system.
        </readme>
    </package>
    <!-- We ship bismark with that wrapper, so we only need to set the PATH variable -->
    <package name="bismark">
        <install version="1.1">
                <action type="move_file">
                    <source>bismark</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bismark_genome_preparation</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bismark_methylation_extractor</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">./</environment_variable>
                </action>
            </actions>
        </install>
    </package>
</tool_dependency>