== Requirements ==

 1. BASE 2.12.0 or later.
 
== Introduction ==

This package is an extension package to BASE that integrates BASE
with GenePattern. ......... 

For more information:

 * The homepage for this extension: 
   http://baseplugins.thep.lu.se/wiki/net.sf.basedb.genepattern
 * The GenePattern homepage: http://www.broad.mit.edu/cancer/software/genepattern/index.html

== Installation ==

 1. Download the gp-integration-*.tar.gz file.
 2. Unpack the downloaded file to a directory of your choice.
 3. Copy the gp-integration.jar file to your BASE extensions directory: 
    WEB-INF/extensions. 
 4. Run the 'Extensions -> Manual scan' command if you have disabled automatic
    installation. Otherwise, just wait a bit and the automatic installation will
    find and install the new extension.
 5. Run the plug-in installation wizard by clicking the 'New' button on the
    'Administrate -> Plugins -> Definitions' page. Make sure the option for
    the 'Extensions directory' is selected. Install all plug-ins found in 
    the gp-integration.jar file.
 6. TODO....
 7. Done. 

 
== Known issues ==

None.

== Compiling ==

To compile this package you also need:
 
 1. Ant 1.6
 2. Java 1.6

Follow these instructions:

 1. Download the source code from the subversion repository. See
    http://baseplugins.thep.lu.se/wiki/net.sf.basedb.genepattern
    for instructions.
 
 2. Type `ant download-lib` to automatically download the BASE core JAR files that
    are needed for compilation. You can also do this manually by copying the 
    BASE2Core.jar, BASE2Webclient.jar, BASE2CorePlugins.jar and BASE2WSClient.jar 
    from the BASE installation directory (<basedir>/www/WEB-INF/lib/) to the 
    ./lib/compile directory.

 3. Type 'ant' to compile the code and generate the 'gp-integration.jar' file
    in the project directory.

 4. Use 'ant package' to create a downloadable tar.gz package.
 
Tip: If you need different values for any of the properties defined in
the 'build.xml' file, create a file named 'build.properties' and set
the values there.