source: plugins/base2/net.sf.basedb.agilent/trunk/INSTALL

Last change on this file was 1213, checked in by Jari Häkkinen, 12 years ago

Updated install instructions and added upgraded instructions.

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[1199]1$Id: INSTALL 1213 2010-03-26 11:28:21Z jari $
2
3= Install and upgrade instructions for the Agilent plug-ins package for BASE. =
4
5
6== Requirements ==
7
8 1. BASE 2.14.0 or later.
9
10
11== Installation ==
12
[1200]13 1. Unpack the tar.gz file to a directory inside your BASE plug-in
14    installations directory structure (defined in
15    `<basedir>/www/WEB-INF/classes/base.config' parameter
16    ''plugins.dir''.
[1199]17    [[br]]
18    '''Note''' If the job agents are running from a different
19    directory than the BASE server you must copy the jar file to the
20    directory used by the job agents.
[1200]21 2. Stop the Tomcat server running BASE and all associated job agents.
22 3. From the `config` directory, copy `agilent-raw-data-types-xml`
[1199]23    to `<basedir>/www/WEB-INF/classes/raw-data-types/`
[1200]24 4. Update the database with Agilent specific tables and columns by
[1199]25    running the `updatedb.sh` script, located in directory
26    `<basedir>/bin`.
[1200]27 5. The display name of the Agilent 1-channel raw data type is
[1199]28    `AgilentGE1ch` and the unique ID is
29    `RawDataAgilent1ch`. You can change the display name of the
30    Agilent 2-channel data from the generic `Agilent` to more
31    specific `AgilentGE2ch` by change the name attribute for the
32    Agilent 2-channel tag in file
33    `<basedir>/www/WEB-INF/classes/raw-data-types.xml`. Loog for
34    {{{
35    <raw-data-type
36      id="agilent"
37      channels="2"
38      name="Agilent"
39      table="RawDataAgilent"
40      >
41    }}}
42    and replace `Agilent` with `AgilentGE2ch`.
[1200]43 6. Restart the Tomcat server.
44 7. Log in to BASE with administrator privileges and run the plug-in
[1199]45    auto-installation wizard by selecting ''Administrate -> Plugins ->
46    Definitions'' in the menu and click on the 'New' button.
[1200]47 8. Select the 'Automatically' option.
[1213]48 9. The auto-detection should find the plug-in listed below. Change
49    the 'Install' value to 'yes' and click on the 'Save' button.
[1199]50     * Agilent 1 channel expression background correction
[1213]51 10. Verify that the 'Use permissions' option for the plug-ins is set
52    to 'no' and remember to share the plug-in appropriately.
53 11. Install the 'Raw data importer' plug-in configuration included in
[1199]54    this package.
55    - Upload the configuration file
56      (`config/Agilen1chFull-plugin-configuration.xml`) to BASE.
57    - Select ''Administrate -> Plugins -> Configurations'' and click on
58      the 'Import...' button. Select 'Plugin configuration importer'
59      in the Plugin list, click 'Next', select the uploaded file for
60      'XML file'. Run the plug-in.
61    - In the plugin configuration list view find 'Agilent 1 channel
62      raw data import (full format files)'
63    - Share the new configuration (and the 'Raw data importer'
[1200]64      plug-in) appropriately, e.g, to an Agilent group or group
[1199]65      Everyone with 'RU' privileges.
[1213]66 12. If applicable restart job agents.
67 13. Done. The Agilent plug-ins are now installed.
[1199]68
69
70== Upgrade ==
71
[1213]72 1. Unpack the tar.gz file to a directory inside your BASE plug-in
73    installations directory structure (defined in
74    `<basedir>/www/WEB-INF/classes/base.config' parameter
75    ''plugins.dir''.
76    [[br]]
77    '''Note''' If the job agents are running from a different
78    directory than the BASE server you must copy the jar file to the
79    directory used by the job agents.
80 2. Remove or move away the already installed version of the plug-in.
81 3. Log in to BASE with administrator privileges and run the plug-in
82    auto-installation wizard by selecting ''Administrate -> Plugins ->
83    Definitions'' in the menu and click on the 'New' button.
84 4. Select the 'Automatically' option.
85 5. The auto-detection should find the plug-in listed below and
86    highlight it as new. Change the 'Install' value to 'yes' and click
87    on the 'Save' button.
88     * Agilent 1 channel expression background correction
89 6. Verify that the 'Use permissions' option for the plug-ins is set
90    to 'no'.
91 7. If applicable restart job agents.
92 8. Done. The Agilent plug-ins are now upgraded.
[1199]93
94
95== Important ==
96
97Make sure that the job agents have access to the same (or an identical
98copy) agilent-plugins.jar file as the Tomcat server. If the job agents
99are not running from the same BASE installation directory, you must
100copy the files to a proper location. We recommend that you always put
101the agilent-plugins.jar inside the BASE server plug-in directory as
102defined by `plugins.dir` in the `base.config` configuration file. If
103you do BASE will automatically find the JAR file for the job agents,
104otherwise you may have to configure the JAR path manually for each job
105agent.
106
107----------------------------------------------------------------------
108{{{
109Copyright (C) 2010 Jari Häkkinen
110
111This file is part of the Agilent plug-in package for BASE
112(net.sf.based.agilent).
113The package is available at http://baseplugins.thep.lu.se/
114BASE main site is http://base.thep.lu.se/
115
116This is free software; you can redistribute it and/or
117modify it under the terms of the GNU General Public License
118as published by the Free Software Foundation; either version 3
119of the License, or (at your option) any later version.
120
121The software is distributed in the hope that it will be useful,
122but WITHOUT ANY WARRANTY; without even the implied warranty of
123MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
124GNU General Public License for more details.
125
126You should have received a copy of the GNU General Public License
127along with this program. If not, see <http://www.gnu.org/licenses/>.
128}}}
129----------------------------------------------------------------------
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