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view tool_dependencies.xml @ 4:796814f16b12

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Add tool_dependencies.xml and update to new augustus version. Thanks to James Johnson for the patch.
author bjoern-gruening
date Tue, 30 Oct 2012 06:29:50 -0400
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children a4fab0c1ae1a
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<?xml version="1.0"?>
<tool_dependency>
    <package name="augustus" version="2.6.1">
        <install version="1.0">
            <actions>
                <!-- the first command puts us in the dir for the package name: "augustus"-->
                <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.6.1.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>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
                <action type="set_environment">
                    <environment_variable name="AUGUSTUS_CONFIG_PATH" action="set_to">$INSTALL_DIR/config</environment_variable>
                </action>
            </actions>
        </install>
        <readme>http://augustus.gobics.de/binaries/README.TXT</readme>
    </package>
</tool_dependency>