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view tool_dependencies.xml @ 6:fb61d175ab99 draft

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Fix tool_dependencies.xml install.
author Jim Johnson <jj@umn.edu>
date Wed, 24 Oct 2012 11:08:05 -0500
parents 6d288b228c6d
children bf047bff79df
line wrap: on
line source

<?xml version="1.0"?>
<tool_dependency>
    <package name="augustus" version="2.6.1">
        <install version="1.0">
            <actions>
                <action type="shell_command">mkdir augustus</action>
                <!-- the first command puts us in the dir for the package name: "augustus"-->
                <action type="shell_command">wget --quiet http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.6.1.tar.gz</action>
                <action type="shell_command">tar zxf ../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>