source: extensions/net.sf.basedb.mev/trunk/README @ 1540

Requirements

1. BASE 3.1 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 4.7.3 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 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. See the "Known issues" section at ​http://www.tm4.org/mev/features/releases for more information.

Compiling

To compile this package you also need:

1. Ant 1.8
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 files that are neeed for compilation. You can also do this manually by copying the base-core-3.0.0.jar, base-webclient-3.0.0.jar, base-coreplugins-3.0.0.jar and base-webservices-client-3.0.0.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.