source: plugins/base2/net.sf.basedb.illumina/trunk/INSTALL @ 1386

Last change on this file since 1386 was 1386, checked in by Nicklas Nordborg, 10 years ago

Fixes #311: Updates required for BASE 3 support

BGX and SNP manifest file validation seems to be working. Updated readme and installation instructions.

  • Property svn:eol-style set to native
  • Property svn:mime-type set to text/x-trac-wiki
File size: 4.3 KB

How to install or upgrade the Illumina plug-ins package for BASE.


  1. BASE 3.0 or later.


  1. Unpack the tar.gz file to a directory of your choice.
  2. Stop your Tomcat server that is running BASE and all job agents, if any.
  3. Copy the illumina-plugins.jar to your BASE plug-ins directory. Look in your 'base.config' file if you don't know where this is.
    If you have job agents that are running from another location, you must also copy the jar file to the plug-in directory that the job agents use (if that is different).
  4. From the config directory, copy (Notice: If you have job agents running from another location, copy the configuration files to a location the job agents has access to.):
    • illumina-extended-properties.xml to <basedir>/www/WEB-INF/classes/extended-properties/
    • illumina-raw-data-types-xml to <basedir>/www/WEB-INF/classes/raw-data-types/
  5. Update the database with Illumina-specific tables and columns by running the script, located in the <basedir>/bin directory.
  6. Restart the Tomcat server.
  7. Go to 'Administrate->Plug-ins & Extensions->Overview' page.
  8. Run the installation wizard and select to install 'illumina-plugins.jar'.
  9. Find the 'Illumina plug-in package installer' in the list of plug-ins and click on it.
  10. Click on the 'Run plugin' button.
  11. Decide which Illumina variants to install and if you want the installation

program to create a scanner and/or software entry.

  1. Finish the job registration and wait for the plug-in to finish.
  2. Done. The Illumina plug-ins and extensions are now installed. You can

now restart any job agents as well.

  1. Optionally, if not already done, disable use of the 'Illumina' raw data type provided by a standard BASE installation; Simply remove, or comment out, the <raw-data-type> entry for id='illumina' in configuration file /path/to/base/WEB-INF/classes/raw-data-types.xml and restart the BASE server. If a user already used the 'Illumina' raw data type, BASE will display an error message in the GUI. Either restore the use of 'Illumina' raw data type or remove the data using 'Illumina' raw data type.

Make sure that the job agents have access to the illumina-plugins.jar file, and to the same raw data types and extended property configurations files as the Tomcat web server. If the job agents are not running from the same BASE installation directory, you may need to copy the files to a proper location. Notice: you may have to configure the JAR path manually for each job agent.


The instructions below are comments how to follow the steps in installation section when upgrading an already installed Illumina package.

  1. Do the step 1-3 as described in the installation instructions.
  2. Then proceed with step 4.
    Caution: Any changes in the files on the local server must be transferred to the new configuration-files before they are copied. Copying the new files will overwrite the existing files.
  3. Do step 5-8 as described.
  4. Step 9-12 is optional and only needed if the release comes with new Illumina variants that you want to create.
  5. Done. The Illumina package is now updated. You can restart any job-agents as well.

Copyright (C) 2008 Jari Häkkinen, Nicklas Nordborg
Copyright (C) 2009 Jari Häkkinen, Martin Svensson
Copyright (C) 2010 Jari Häkkinen, Nicklas Nordborg
This file is part of Illumina plug-in package for BASE.
Available at
BASE main site:
This is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 3
of the License, or (at your option) any later version.
The software is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with BASE. If not, see <>.

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