source: plugins/base2/net.sf.basedb.illumina/tags/1.0/INSTALL

Last change on this file was 629, checked in by Nicklas Nordborg, 14 years ago

References #89: Installation program and documentation

Preparing for release. Added some more information to README_SNP.

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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 2
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 this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330,
Boston, MA  02111-1307, USA.

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


  1. BASE 2.6.0 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 BGX reporter importer
    • Illumina BGX feature importer
    • Illumina Bead Summary importer
    • Illumina SNP raw data importer
    • Illumina SNP root bioassayset creator
    • Illumina SNP reporter importer
  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.

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