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

Last change on this file since 1082 was 1082, checked in by Nicklas Nordborg, 13 years ago

References #212: Add support for exporting CGH data to MeV

The exporter and plug-in is in place. The plug-in is configurable with respect to which reporter annotations to use for 'chromosome', 'start', 'end' and 'description'. Values are logged if the bioassay set uses logged values, otherwise the pure ratios are exported.

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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:

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.

  1. 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.
  1. Type 'ant' to compile the code and generate the 'mev-launcher.jar' file in the project directory.
  1. 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.
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