Changeset 1082


Ignore:
Timestamp:
May 18, 2009, 11:22:03 AM (12 years ago)
Author:
Nicklas Nordborg
Message:

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.

Location:
extensions/net.sf.basedb.mev/trunk
Files:
2 added
2 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.mev/trunk/META-INF/base-plugins.xml

    r1068 r1082  
    66    <hasconfigurations/>
    77  </pluginclass>
     8  <pluginclass classname="net.sf.basedb.mev.plugin.CghExporterPlugin">
     9    <minbaseversion>2.12</minbaseversion>
     10    <hasconfigurations/>
     11  </pluginclass>
    812</plugins>
  • extensions/net.sf.basedb.mev/trunk/README

    r1068 r1082  
    2525    find and install the new extension.
    2626 5. Run the plug-in installation wizard by clicking the 'New' button on the
    27     'Administration -> Plugins -> Definitions' page. Make sure the option for
     27    'Administrate -> Plugins -> Definitions' page. Make sure the option for
    2828    the 'Extensions directory' is selected. Install all plug-ins found in
    2929    the mev-launcher.jar file.
    30  6. Done.
     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.
    3141 
    3242 The MeV Launcher appears as an action in the "Tools" column when
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