source: plugins/base2/net.sf.basedb.illumina/tags/1.3/INSTALL

Last change on this file was 959, checked in by Martin Svensson, 12 years ago

Fixes #164 Improve documentation on how to upgrade the illumina plug-in package

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Copyright (C) 2008
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 <>.

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


  1. BASE 2.9.0 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. This directory is specified by the 'plugins.dir' option in your base.config file and defaults to <basedir>/plugins.
    If you have job agents that are running from another location, you must also copy the jar file to a location the job agents has access to.
  4. From the config directory, copy:
    • 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/
      Notice: If you have job agents that are running from another location, copy the configuration files to a location the job agents has access to.
  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. Log in to BASE as an administrator and run the plug-in auto-installation wizard by going to Administrate -> Plugins -> Definitions and click on the 'New' button.
  8. Select the 'Automatically' option.
  9. The auto-detection should find the plug-ins listed below. You should change the 'Install' value to 'yes' or 'plugin+configurations' for all of them.
    • Illumina plug-in package installer
    • Illumina Bead Summary importer
    • Illumina BGX reporter importer
    • Illumina BGX feature importer
    • Illumina detection P-value calculation
    • Illumina expression background correction
    • Illumina SNP raw data importer
    • Illumina SNP reporter importer
    • Illumina SNP root bioassayset creator
  10. Find the 'Illumina plug-in package installer' in the list of plug-ins and click on it.
  11. Click on the 'Run plugin' button.
  12. Decide which Illumina variants to install and if you want the installation program to create a scanner and/or software entry.
  13. Finish the job registration and wait for the plug-in to finish.
  14. Done. The Illumina plug-ins are now installed. You can now restart any job agents as well.

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. We recommend that you always put the illumina-plugins.jar inside the plugins.dir directory. If you do, BASE will automatically find the JAR file in job agents. Otherwise, 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 transfered

to the new configuration-files before they are copied. Copying the new files will overwrite the existing files.

  1. Do step 5-6 as described.
  2. Step 7-9 are optional and only needed if the new release contains plugins or changed/new pluginconfigurations that you want to install.
    Notice1: Already installed plugins do not need to be re-installed, but updated configurations do.
    Notice2: If the existing configuration is not first removed you will end up with two configurations with the same name.
  3. Step 10-13 are also optional and only necessary when the release comes with new Illumina variants that you want to create.
  4. Done. The Illumina package is now updated. You can restart any job-agents as well.
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