$Id: INSTALL 1213 2010-03-26 11:28:21Z jari $

Install and upgrade instructions for the Agilent plug-ins package for BASE.

Requirements

1. BASE 2.14.0 or later.

Installation

1. Unpack the tar.gz file to a directory inside your BASE plug-in installations directory structure (defined in `<basedir>/www/WEB-INF/classes/base.config' parameter plugins.dir.
   Note If the job agents are running from a different directory than the BASE server you must copy the jar file to the directory used by the job agents.
2. Stop the Tomcat server running BASE and all associated job agents.
3. From the config directory, copy agilent-raw-data-types-xml to <basedir>/www/WEB-INF/classes/raw-data-types/
4. Update the database with Agilent specific tables and columns by running the updatedb.sh script, located in directory <basedir>/bin.
5. The display name of the Agilent 1-channel raw data type is AgilentGE1ch and the unique ID is RawDataAgilent1ch. You can change the display name of the Agilent 2-channel data from the generic Agilent to more specific AgilentGE2ch by change the name attribute for the Agilent 2-channel tag in file <basedir>/www/WEB-INF/classes/raw-data-types.xml. Loog for

   <raw-data-type
     id="agilent"
     channels="2"
     name="Agilent"
     table="RawDataAgilent"
     >
   

   and replace Agilent with AgilentGE2ch.
6. Restart the Tomcat server.
7. Log in to BASE with administrator privileges and run the plug-in auto-installation wizard by selecting Administrate -> Plugins -> Definitions in the menu and click on the 'New' button.
8. Select the 'Automatically' option.
9. The auto-detection should find the plug-in listed below. Change the 'Install' value to 'yes' and click on the 'Save' button.
   • Agilent 1 channel expression background correction
10. Verify that the 'Use permissions' option for the plug-ins is set to 'no' and remember to share the plug-in appropriately.
11. Install the 'Raw data importer' plug-in configuration included in this package.
    • Upload the configuration file (config/Agilen1chFull-plugin-configuration.xml) to BASE.
    • Select Administrate -> Plugins -> Configurations and click on the 'Import...' button. Select 'Plugin configuration importer' in the Plugin list, click 'Next', select the uploaded file for 'XML file'. Run the plug-in.
    • In the plugin configuration list view find 'Agilent 1 channel raw data import (full format files)'
    • Share the new configuration (and the 'Raw data importer' plug-in) appropriately, e.g, to an Agilent group or group Everyone with 'RU' privileges.
12. If applicable restart job agents.
13. Done. The Agilent plug-ins are now installed.

Upgrade

1. Unpack the tar.gz file to a directory inside your BASE plug-in installations directory structure (defined in `<basedir>/www/WEB-INF/classes/base.config' parameter plugins.dir.
   Note If the job agents are running from a different directory than the BASE server you must copy the jar file to the directory used by the job agents.
2. Remove or move away the already installed version of the plug-in.
3. Log in to BASE with administrator privileges and run the plug-in auto-installation wizard by selecting Administrate -> Plugins -> Definitions in the menu and click on the 'New' button.
4. Select the 'Automatically' option.
5. The auto-detection should find the plug-in listed below and highlight it as new. Change the 'Install' value to 'yes' and click on the 'Save' button.
   • Agilent 1 channel expression background correction
6. Verify that the 'Use permissions' option for the plug-ins is set to 'no'.
7. If applicable restart job agents.
8. Done. The Agilent plug-ins are now upgraded.

Important

Make sure that the job agents have access to the same (or an identical copy) agilent-plugins.jar file as the Tomcat server. If the job agents are not running from the same BASE installation directory, you must copy the files to a proper location. We recommend that you always put the agilent-plugins.jar inside the BASE server plug-in directory as defined by plugins.dir in the base.config configuration file. If you do BASE will automatically find the JAR file for the job agents, otherwise you may have to configure the JAR path manually for each job agent.

Copyright (C) 2010 Jari Häkkinen
This file is part of the Agilent plug-in package for BASE
(net.sf.based.agilent).
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/>.