source: plugins/base2/net.sf.basedb.normalizers/trunk/INSTALL @ 1087

Last change on this file since 1087 was 1087, checked in by Martin Svensson, 12 years ago

Fixes #195 net.sf.basedb.normalizers: Normalizers should ask user for how to calculate averages

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
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File size: 3.6 KB

$Id: INSTALL 1087 2009-05-19 12:30:34Z martin $


Copyright (C) 2008, 2009 Jari Häkkinen, Martin Svensson
This file is part of the Normalizers plug-in package for BASE
(net.sf.based.normalizers). The package is available at
http://baseplugins.thep.lu.se/ BASE main site is
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 this program. If not, see <http://www.gnu.org/licenses/>.

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

Requirements

  1. BASE 2.12.0 or later.
  2. (Optional) The qQuantile normalization requires a C++ standards compliant compiler and the yat library available at http://dev.thep.lu.se/yat. The package can be used without the qQuantile normalization algorithm, simply de-select the plug-in when making BASE aware of the plug-ins.

Installation/Upgrade?

  1. Unpack the tar.gz file to a directory of your choice.
  2. Copy the normalization-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. In case of upgrading to a newer package-release the old jar-file should be overwritten.

    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.

    If you are upgrading and not want to install new plugins or configurations - go to step 7, otherwise continue with the next step.
  3. 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.
  4. Select the 'Automatically' option.
  5. The auto-detection should find plug-ins for the algorithms listed below. You should change the 'Install' value to 'yes' for those which should be installed.
    • Average normalization
    • qQuantile normalization
    • Quantile Normalization
    Do NOT select qQuantile if you do not plan to build the underlying binary (step 8 below).
  6. Finish the installation wizard.
  7. Done. The normalization plug-ins are now installed.
  1. (Optional step) Building the qQuantile binary. Unpack the qqn-version.tar.gz file and change direcotry to qqn-version. Follow the instructions in the README file included in the qQN package. Remember to copy file bin/qQN to the same location as the normalization jar files.

Make sure that the job agents have access to the same normalization-plugins.jar file 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 normalization-plugins.jar inside the BASE server plug-in directory as defiend by plugins.dir in the base.config configuration file. 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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