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

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[909]1$Id: INSTALL 1087 2009-05-19 12:30:34Z martin $
2
[733]3----------------------------------------------------------------------
4{{{
[964]5Copyright (C) 2008, 2009 Jari Häkkinen, Martin Svensson
[733]6
[909]7This file is part of the Normalizers plug-in package for BASE
8(net.sf.based.normalizers). The package is available at
9http://baseplugins.thep.lu.se/ BASE main site is
10http://base.thep.lu.se/
[733]11
12This is free software; you can redistribute it and/or
13modify it under the terms of the GNU General Public License
[910]14as published by the Free Software Foundation; either version 3
[733]15of the License, or (at your option) any later version.
16
17The software is distributed in the hope that it will be useful,
18but WITHOUT ANY WARRANTY; without even the implied warranty of
19MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
20GNU General Public License for more details.
21
22You should have received a copy of the GNU General Public License
[910]23along with this program. If not, see <http://www.gnu.org/licenses/>.
[733]24}}}
25----------------------------------------------------------------------
26
[909]27
[958]28== How to install or upgrade the Normalization plug-ins package for BASE. ==
[733]29
30
31== Requirements ==
32
[1087]33 1. BASE 2.12.0 or later.
[952]34 2. (Optional) The qQuantile normalization requires a C++ standards
[964]35    compliant compiler and the yat library available at
36    http://dev.thep.lu.se/yat. The package can be used without the
37    qQuantile normalization algorithm, simply de-select the plug-in
38    when making BASE aware of the plug-ins.
[733]39
40
[958]41== Installation/Upgrade ==
[733]42
43 1. Unpack the tar.gz file to a directory of your choice.
[932]44 2. Copy the normalization-plugins.jar to your BASE plug-ins
45    directory. This directory is specified by the 'plugins.dir' option
[958]46    in your base.config file and defaults to <basedir>/plugins. In case
47    of upgrading to a newer package-release the old jar-file should be
48    overwritten.
[932]49    [[br]][[br]]
50    If you have job agents that are running from another location, you
51    must also copy the jar file to a location the job agents has
52    access to.
[958]53    [[br]][[br]]
54    If you are upgrading and not want to install new plugins or
55    configurations - go to step 7, otherwise continue with the next step.
[932]56 3. Log in to BASE as an administrator and run the plug-in
57    auto-installation wizard by going to ''Administrate -> Plugins ->
58    Definitions'' and click on the 'New' button.
[733]59 4. Select the 'Automatically' option.
[932]60 5. The auto-detection should find plug-ins for the algorithms listed
61    below. You should change the 'Install' value to 'yes' for those
62    which should be installed.
[733]63     * Average normalization
[952]64     * qQuantile normalization
[931]65     * Quantile Normalization
[964]66    Do ''NOT'' select qQuantile if you do not plan to build the
67    underlying binary (step 8 below).
[733]68 6. Finish the installation wizard.
69 7. Done. The normalization plug-ins are now installed.
[735]70
[964]71 8. (Optional step) Building the qQuantile binary. Unpack the
[1042]72    qqn-version.tar.gz file and change direcotry to
73    qqn-version. Follow the instructions in the README file included
[1009]74    in the qQN package. Remember to copy file bin/qQN to the same
75    location as the normalization jar files.
[964]76
[932]77Make sure that the job agents have access to the same
78normalization-plugins.jar file as the Tomcat web server. If the job
79agents are not running from the same BASE installation directory, you
[1008]80may need to copy the files to a proper location. We recommend that you
81always put the normalization-plugins.jar inside the BASE server
82plug-in directory as defiend by `plugins.dir` in the `base.config`
83configuration file. If you do, BASE will automatically find the JAR
84file in job agents. Otherwise, you may have to configure the JAR path
85manually for each job agent.
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