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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[666]1== Requirements ==
2
[1061]3 1. BASE 2.12.0 or later.
[666]4 
5== Introduction ==
6
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
[976]10extension uses the standard MEV 4.3.02 distribution that has been
11Java Webstart enabled. For more information:
[666]12
13 * The homepage for this extension:
14   http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev
15 * The official MEV homepage: http://www.tm4.org/mev.html
16
17== Installation ==
18
[690]19 1. Download the mev-launcher-*.tar.gz file.
[666]20 2. Unpack the downloaded file to a directory of your choice.
21 3. Copy the mev-launcher.jar file to your BASE extensions directory:
22    WEB-INF/extensions.
23 4. Run the 'Extensions -> Manual scan' command if you have disabled automatic
24    installation. Otherwise, just wait a bit and the automatic installation will
[690]25    find and install the new extension.
[1068]26 5. Run the plug-in installation wizard by clicking the 'New' button on the
[1082]27    'Administrate -> Plugins -> Definitions' page. Make sure the option for
[1068]28    the 'Extensions directory' is selected. Install all plug-ins found in
29    the mev-launcher.jar file.
[1082]30 6. The 'MeV CGH exporter' requires that an admin configures the reporter
31    annotations that corresponds to the CGH file columns. Go to the
32    'Administrate -> Plugins -> Definitions' page and click on the
33    'MeV CGH exporter' plug-in. Click on 'New configuration...' and give
34    enter a name and optionally a description. Then, click on 'Save and
35    configure' and select the corresponding reporter annotation columns
36    for the four CGH file columns (chromosome, start, end and description).
37    Finish the configuration. Note! This step will also register a file
38    type for CGH. Make sure the logged in user has enough permissions to
39    create new file types.
40 7. Done.
[1068]41 
42 The MeV Launcher appears as an action in the "Tools" column when
43 viewing bioassay sets of an experiment. Some (per-user) options can be
44 specified by opening the 'Extensions -> MeV Launcher options' menu.
[666]45
[1068]46The MeV export plug-ins appears in the 'Export' dialog when viewing
47bioassay sets of an experiment.
48
[666]49== Known issues ==
50
[976]51None.
[666]52
53== Compiling ==
54
55To compile this package you also need:
56 
57 1. Ant 1.6
58 2. Java 1.6
59
60Follow these instructions:
61
62 1. Download the source code from the subversion repository. See
63    http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev for instructions.
64 
[690]65 2. Type `ant download-lib` to automatically download the BASE core JAR file that
66    are neeed for compilation. You can also do this manually by copying the
[976]67    BASE2Core.jar, BASE2Webclient.jar, BASE2CorePlugins.jar and BASE2WSClient.jar
[974]68    from the BASE installation directory (<basedir>/www/WEB-INF/lib/) to the
[666]69    ./lib/compile directory.
70
71 3. Type 'ant' to compile the code and generate the 'mev-launcher.jar' file
72    in the project directory.
73
74 4. Use 'ant package' to create a downloadable tar.gz package.
[690]75 
76Tip: If you need different values for any of the properties defined in
77the 'build.xml' file, create a file named 'build.properties' and set
78the values there.
[976]79
80Note! If upgrading MeV to a new version, the new JAR files needs to
81be signed. See `./jarsign/readme.txt` for more information.
82
83
84== Contributions ==
85
86 * David Waring, for helping out with MeV 4.3 integration.
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