source: extensions/net.sf.basedb.mev/trunk/README @ 1082

== Requirements ==

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

This package is an extension package to BASE that installs an action that
opens TIGR MultiExperiment Viewer (MEV) as a Java webstart application and
automatically imports data from the currently selected bioassay set. This
extension uses the standard MEV 4.3.02 distribution that has been
Java Webstart enabled. For more information:

 * The homepage for this extension: 
   http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev
 * The official MEV homepage: http://www.tm4.org/mev.html

== Installation ==

 1. Download the mev-launcher-*.tar.gz file.
 2. Unpack the downloaded file to a directory of your choice.
 3. Copy the mev-launcher.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 mev-launcher.jar file.
 6. The 'MeV CGH exporter' requires that an admin configures the reporter
    annotations that corresponds to the CGH file columns. Go to the
    'Administrate -> Plugins -> Definitions' page and click on the 
    'MeV CGH exporter' plug-in. Click on 'New configuration...' and give
    enter a name and optionally a description. Then, click on 'Save and
    configure' and select the corresponding reporter annotation columns
    for the four CGH file columns (chromosome, start, end and description).
    Finish the configuration. Note! This step will also register a file
    type for CGH. Make sure the logged in user has enough permissions to
    create new file types.
 7. Done. 
 
 The MeV Launcher appears as an action in the "Tools" column when
 viewing bioassay sets of an experiment. Some (per-user) options can be 
 specified by opening the 'Extensions -> MeV Launcher options' menu.

The MeV export plug-ins appears in the 'Export' dialog when viewing
bioassay sets of an experiment.

== 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.mev for instructions.
 
 2. Type `ant download-lib` to automatically download the BASE core JAR file that
    are neeed 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 'mev-launcher.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.

Note! If upgrading MeV to a new version, the new JAR files needs to 
be signed. See `./jarsign/readme.txt` for more information.


== Contributions ==

 * David Waring, for helping out with MeV 4.3 integration.