Changeset 576


Ignore:
Timestamp:
Feb 7, 2008, 4:43:04 PM (13 years ago)
Author:
Martin Svensson
Message:

References #89 Changed to wiki format and configured some svn properties

File:
1 edited

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  • trunk/net/sf/basedb/illumina/INSTALL

    • Property svn:eol-style set to native
    • Property svn:mime-type set to text/x-trac-wiki
    r553 r576  
    11----------------------------------------------------------------------
    2 How to install the Illumina plug-ins package for BASE.
     2{{{
     3Copyright (C) 2008
     4
     5This file is part of Illumina plug-in package for BASE.
     6Available at http://baseplugins.thep.lu.se/
     7BASE main site: http://base.thep.lu.se/
     8
     9This is free software; you can redistribute it and/or
     10modify it under the terms of the GNU General Public License
     11as published by the Free Software Foundation; either version 2
     12of the License, or (at your option) any later version.
     13
     14The software is distributed in the hope that it will be useful,
     15but WITHOUT ANY WARRANTY; without even the implied warranty of
     16MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     17GNU General Public License for more details.
     18
     19You should have received a copy of the GNU General Public License
     20along with this program; if not, write to the Free Software
     21Foundation, Inc., 59 Temple Place - Suite 330,
     22Boston, MA  02111-1307, USA.
     23}}}
    324----------------------------------------------------------------------
    425
    5 ------------
    6 Requirements
    7 ------------
    8 
    9 1. BASE 2.6.0 or later.
     26== How to install the Illumina plug-ins package for BASE. ==
    1027
    1128
    12 ------------
    13 Installation
    14 ------------
     29== Requirements ==
     30
     31 1. BASE 2.6.0 or later.
     32
     33
     34== Installation ==
    1535
    1636This is preliminary instructions only. The final installation
    1737procedure is not yet completed.
    1838
    19 1. Unpack the tar.gz file to a directory of your choice.
    20 
    21 2. Stop your Tomcat server that is running BASE and all job agents, if any.
    22 
    23 3. Copy the illumina-plugins-xxx.jar (where xxx depends on the version number)
     39 1. Unpack the tar.gz file to a directory of your choice.
     40 2. Stop your Tomcat server that is running BASE and all job agents, if any.
     41 3. Copy the illumina-plugins-xxx.jar (where xxx depends on the version number)
    2442   to your BASE plug-ins directory. This directory is specified by the
    2543   'plugins.dir' option in your base.config file and defaults to
    26    <basedir>/plugins.
    27    
     44   <basedir>/plugins.[[BR]]   
    2845   If you have job agents that are running from another location, copy
    29    the jar file to a location the job agents has access to.
    30    
    31 4. From the 'config' directory, copy:
    32  
    33    * 'illumina-extended-properties.xml' to <basedir>/www/WEB-INF/classes/extended-properties
    34    * 'illumina-raw-data-types-xml' to <basedir>/www/WEB-INF/classes/raw-data-types
    35    
    36    If you have job agents that are running from another location, copy
    37    the configuration files to a location the job agents has access to.
    38    
    39 5. Update the database with Illumina-specific tables and columns by running the
    40    'updatedb.sh' script, located in the <basedir>/bin directory.
    41 
    42 6. Restart the Tomcat server.
    43    
    44 7. Run the auto-installation wizard by going to
    45    Administrate -> Plugins -> Definitions
    46    and click on the 'New' button.
    47    
    48 8. Select the 'Automatical' option.
    49 
    50 9. The auto-detection should find the plug-ins listed below. You should
     46   the jar file to a location the job agents has access to.   
     47 4. From the ''config'' directory, copy:
     48   * ''illumina-extended-properties.xml'' to <basedir>''/www/WEB-INF/classes/extended-properties/''
     49   * ''illumina-raw-data-types-xml'' to <basedir>''/www/WEB-INF/classes/raw-data-types/''[[BR]]
     50    '''Notice: Do you have job agents that are running from another location, copy the
     51   configuration files to a location the job agents has access to.'''   
     52 5. Update the database with Illumina-specific tables and columns by running the
     53   ''updatedb.sh'' script, located in the <basedir>''/bin'' directory.
     54 6. Restart the Tomcat server.   
     55 7. Run the auto-installation wizard by going to ''Administrate -> Plugins ->
     56   Definitions''
     57   and click on the 'New' button.   
     58 8. Select the 'Automatical' option.
     59 9. The auto-detection should find the plug-ins listed below. You should
    5160   change the 'Install' value to 'yes' for all of them.
    52    
    53   * Illumina plug-in package installer
    54   * BGX feature/reporter importer
    55    * Scandata importer
    56    * ... and some more... TODO
    57 
    58    The 'Illumina plug-in package installer' should have the 'Allow immediate
    59    execution' option set to 'allow'.
    60    
    61 10. Find the 'Illumina plug-in package installer' in the list of plug-ins and
    62     click on it.
    63 
    64 11. Click on the 'Run plugin' button.
    65 
    66 11. Accept the default options.
    67 
    68 12. Wait for the plug-in to finish.
    69 
    70 13. Done. The Illumina plug-ins are now installed. You can now restart any job
    71     agents as well.
     61  * Illumina plug-in package installer (set 'Allow immediate execution' to 'allow')
     62  * Illumina BGX feature importer
     63  * Illumina BGX reporter importer
     64  * Illumina Bead Summary importer 
     65 10. Find the 'Illumina plug-in package installer' in the list of plug-ins and click on it.
     66 11. Click on the 'Run plugin' button.
     67 12. Accept the default options.
     68 13. Wait for the plug-in to finish.
     69 14. Done. The Illumina plug-ins are now installed. You can now restart any job
     70    agents as well.
    7271   
    73     Make sure that the job agents have access to the illumina-plugins-xxx.jar file,
    74     and to the same raw data types and extended property configurations files as
    75     the Tomcat web server. If the job agents are not running from the same BASE
    76     installation directory, you may need to copy the files to a proper location.
    77     You may also have to configure the path the jar file for each job agent using the
    78     web interface.
    79 
     72Make sure that the job agents have access to the illumina-plugins-xxx.jar file,
     73and to the same raw data types and extended property configurations files as
     74the Tomcat web server. If the job agents are not running from the same BASE
     75installation directory, you may need to copy the files to a proper location.
     76You may also have to configure the path the jar file for each job agent using the
     77web interface.
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