comparison tool_dependencies.xml @ 0:af307d3285c5 draft

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0:af307d3285c5

<?xml version="1.0"?>
<tool_dependency>
    <set_environment version="1.0">
        <environment_variable name="AUGUSTUS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>
    <package name="augustus" version="2.7">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.7.tar.gz</action>
                <action type="shell_command">make</action>
                <action type="move_directory_files">
                    <source_directory>bin</source_directory>
                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>scripts</source_directory>
                    <destination_directory>$INSTALL_DIR/scripts</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>config</source_directory>
                    <destination_directory>$INSTALL_DIR/config</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable name="AUGUSTUS_CONFIG_PATH" action="set_to">$INSTALL_DIR/config</environment_variable>
                </action>
            </actions>
        </install>
        <readme>AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller.
It can be used as an ab initio program, which means it bases its prediction purely on the
sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
such as EST, MS/MS, protein alignments and synthenic genomic alignments.
http://augustus.gobics.de/binaries/README.TXT</readme>
    </package>
</tool_dependency>