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view tool_dependencies.xml @ 5:6d288b228c6d draft

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tool_dependecy debugging
author Jim Johnson <jj@umn.edu>
date Tue, 23 Oct 2012 11:33:18 -0500
parents 06b5da1079d8
children fb61d175ab99
line wrap: on
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<?xml version="1.0"?>
<tool_dependency>
    <package name="augustus" version="2.6.1">
        <install version="1.0">
            <actions>
                <action type="shell_command">wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.6.1.tar.gz</action>
                <!-- with the first command of with type shell_command a dir will be created with the package name, and we'll operate from there. -->
                <action type="shell_command">pwd</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>