---------------------------------------------------------------------- {{{ Copyright (C) 2008 Jari Häkkinen, Nicklas Nordborg Copyright (C) 2009 Jari Häkkinen, Martin Svensson This file is part of Illumina plug-in package for BASE. Available at http://baseplugins.thep.lu.se/ BASE main site: http://base.thep.lu.se/ 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 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 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. == == Requirements == 1. BASE 2.15.0 or later. == Installation == 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 ''/www/WEB-INF/extensions/''.[[BR]] 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 ''/www/WEB-INF/classes/extended-properties/'' * ''illumina-raw-data-types-xml'' to ''/www/WEB-INF/classes/raw-data-types/''[[BR]] '''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 ''updatedb.sh'' script, located in the ''/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. If the extension auto-installation is disabled a manual scan is necessary to detect/register the new illumina-extensions. Click on menu: ''Extensions -> Manual scan...'' 15. Done. The Illumina plug-ins are now installed. You can now restart any job agents as well. 16. 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 `` 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.''' == Upgrade == 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 5-6 as described. 4. Step 7-9 are optional and only needed if the new release contains plugins or changed/new plugin configurations that you want to install. [[BR]] '''Notice1:''' Already installed plugins do not need to be re-installed(unless the jar-path has been changed), but updated configurations do.[[BR]] '''Notice2:''' If the existing configuration is not first removed you will end up with two configurations with the same name. '''Notice3:''' Upgrading from 1.3.x or less require you to run the installation wizard even for the installed plugins to update their jar-path. 5. Step 10-13 are also optional and only necessary when the release comes with new Illumina variants that you want to create. 6. Do step 14 to update the extensions. 7. Done. The Illumina package is now updated. You can restart any job-agents as well.