source: extensions/net.sf.basedb.mev/trunk/README @ 7021

== Requirements ==

 1. BASE 3.3 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 4.9.0 distribution (windows version) 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 plug-ins directory. Look in
   your 'base.config' file if you don't know where this is.
 4. Go to 'Administrate->Plug-ins & Extensions->Overview' page.
 5. Run the installation wizard and select to install 'mev-launcher.jar'. 
 6. Run the 'MeV package installer' plug-in. Find this plug-in on the 
    'Administrate -> Plugins -> Definitions' page, click on it, and then
    on the 'Run plugin' button. Complete the installation wizard. This will
    install required items, eg. data file types, that are required by MeV.
 7. The 'MeV CGH exporter' plug-in 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 
    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.
 8. The TDMS and CGH exporter plug-ins are shared to everyone by default. If
    that isn't desired, you may want to change this at this stage.
 9. 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 ==

MeV modules that use R will not work. 

== Compiling ==

To compile this package you also need:
 
 1. Ant 1.8
 2. Java 1.7

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 files that
    are neeed for compilation. You can also do this manually by copying the 
    base-core-3.3.0.jar, base-webclient-3.3.0.jar, base-coreplugins-3.3.0.jar and 
    base-webservices-client-3.3.0.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.