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

Last change on this file since 7021 was 2211, checked in by Nicklas Nordborg, 10 years ago

Fixes #568: Update to MEV 4.9

Changed to MeV 4.9. There was an issue with MeV trying to download missing files from which causes the loading to stop with a NullPointerException. Fixed this by adding the files to this extension (in resources directory) and pointing MeV to the BASE server instead of

Also updated java requirements to 1.7 since that seems what is needed although not directly mentioned (the MeV site is a bit of a mess with lots of information relating to old version).

  • Property svn:mime-type set to text/x-trac-wiki
File size: 3.4 KB
[666]1== Requirements ==
[2211]3 1. BASE 3.3 or later.
5== Introduction ==
7This package is an extension package to BASE that installs an action that
8opens TIGR MultiExperiment Viewer (MEV) as a Java webstart application and
9automatically imports data from the currently selected bioassay set. This
[2211]10extension uses the standard MEV 4.9.0 distribution (windows version) that
[1703]11has been Java Webstart enabled. For more information:
13 * The homepage for this extension:
15 * The official MEV homepage:
17== Installation ==
[690]19 1. Download the mev-launcher-*.tar.gz file.
[666]20 2. Unpack the downloaded file to a directory of your choice.
[1383]21 3. Copy the mev-launcher.jar file to your BASE plug-ins directory. Look in
[1395]22   your 'base.config' file if you don't know where this is.
[1442]23 4. Go to 'Administrate->Plug-ins & Extensions->Overview' page.
[1383]24 5. Run the installation wizard and select to install 'mev-launcher.jar'.
[1159]25 6. Run the 'MeV package installer' plug-in. Find this plug-in on the
26    'Administrate -> Plugins -> Definitions' page, click on it, and then
27    on the 'Run plugin' button. Complete the installation wizard. This will
28    install required items, eg. data file types, that are required by MeV.
29 7. The 'MeV CGH exporter' plug-in requires that an admin configures the
30    reporter annotations that corresponds to the CGH file columns. Go to the
[1082]31    'Administrate -> Plugins -> Definitions' page and click on the
[1099]32    'MeV CGH exporter' plug-in. Click on 'New configuration...' and
[1082]33    enter a name and optionally a description. Then, click on 'Save and
34    configure' and select the corresponding reporter annotation columns
35    for the four CGH file columns (chromosome, start, end and description).
[1159]36    Finish the configuration.
[1395]37 8. The TDMS and CGH exporter plug-ins are shared to everyone by default. If
38    that isn't desired, you may want to change this at this stage.
[1182]39 9. Done.
41 The MeV Launcher appears as an action in the "Tools" column when
42 viewing bioassay sets of an experiment. Some (per-user) options can be
43 specified by opening the 'Extensions -> MeV Launcher options' menu.
[1068]45The MeV export plug-ins appears in the 'Export' dialog when viewing
46bioassay sets of an experiment.
[666]48== Known issues ==
[2211]50MeV modules that use R will not work.
52== Compiling ==
54To compile this package you also need:
[1442]56 1. Ant 1.8
[2211]57 2. Java 1.7
59Follow these instructions:
61 1. Download the source code from the subversion repository. See
62 for instructions.
[1191]64 2. Type `ant download-lib` to automatically download the BASE core JAR files that
[690]65    are neeed for compilation. You can also do this manually by copying the
[2211]66    base-core-3.3.0.jar, base-webclient-3.3.0.jar, base-coreplugins-3.3.0.jar and
67    base-webservices-client-3.3.0.jar from the BASE installation directory
[1395]68    (<basedir>/www/WEB-INF/lib/) to the ./lib/compile directory.
70 3. Type 'ant' to compile the code and generate the 'mev-launcher.jar' file
71    in the project directory.
73 4. Use 'ant package' to create a downloadable tar.gz package.
75Tip: If you need different values for any of the properties defined in
76the 'build.xml' file, create a file named '' and set
77the values there.
79Note! If upgrading MeV to a new version, the new JAR files needs to
80be signed. See `./jarsign/readme.txt` for more information.
83== Contributions ==
85 * David Waring, for helping out with MeV 4.3 integration.
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