wiki:net.sf.basedb.illumina

Version 4 (modified by Nicklas Nordborg, 13 years ago) (diff)

New location for the subversion repository

Illumina plug-ins package for BASE

This package contains plug-ins for the Illumina platform. The plug-ins require BASE 2.6.0 or later and that you have data in the form of Illumina Bead Summary (IBS) and Illumina Sentrix® Array binary manifest (BGX) files. Currently, the plug-ins in this package are:

  • BGX reporter importer: Import reporter annotations from BGX files
  • BGX feature importer: Create array designs from BGX files
  • Bead summary importer: Import Illumina Bead Summary files as raw bioassay data

README contains general information about the plug-ins and hints on how to use them.

INSTALL describes how to install the plug-in package. It is important that you read this document. The plug-ins require additional raw data tables and reporter annotation columns in the database before they can be used.

License

GNU General Public License version 2.

Download

This package has not been released yet.

Subversion Access

The latest development (maybe unstable) revision can be checked out from the repository using the following command:

svn co http://baseplugins.thep.lu.se/svn/plugins/base2/net.sf.basedb.illumina/trunk illumina-devel

Contribute

After making modifications to the source code, compose a clear and concise log message to describe those changes and the reasons for them. Then, send an email to the developers list containing your log message and the output of svn diff (from the top of your subversion working copy). If the community members consider your changes acceptable, someone who has commit privileges will add your changes to the public source code tree. Recall that permission to directly commit changes to the repository is granted on merit - if you demonstrate comprehension of subversion, programming competency, and a team spirit, you will likely be awarded that permission.

TODO

#463
Illumina expression background correction (version 1.7) does not ask for required permissions to write file

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