view tool_dependencies.xml @ 1:e2b822d7408f draft

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author bgruening
date Thu, 05 Dec 2013 09:44:17 -0500
parents af307d3285c5
children a77a4e9921e0
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<?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>