Changeset 553


Ignore:
Timestamp:
Jan 25, 2008, 2:25:16 PM (13 years ago)
Author:
Nicklas Nordborg
Message:

References #89: Installation program and documentation

Added INSTALL file

Location:
trunk/net/sf/basedb/illumina
Files:
1 added
3 edited

Legend:

Unmodified
Added
Removed
  • trunk/net/sf/basedb/illumina/COMPILE

    r546 r553  
    2525   the ./dist directory.
    2626   
    27 3. See the README file for installation instructions.
     273. See the INSTALL file for installation instructions.
    2828
    2929----------
  • trunk/net/sf/basedb/illumina/README

    r549 r553  
    77------------
    88
    9 1. BASE 2.6
    10 
     91. BASE 2.6.0 or later.
     102. Some Illumina scanner and software
     11   blah blah blah.
    1112
    1213------------
     
    1415------------
    1516
    16 This is preliminary instructions only. The final installation
    17 procedure is not yet completed.
     17See the INSTALL file.
    1818
    19 1. Unpack the tar.gz file to a directory of your choice.
    2019
    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)
    24    to your BASE plug-ins directory. This directory is specified by the
    25    'plugins.dir' option in your base.config file and defaults to
    26    <basedir>/plugins.
    27    
    28    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
    51    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.
    72    
    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 
  • trunk/net/sf/basedb/illumina/build.xml

    r549 r553  
    4242    >
    4343    <copy todir="${dist}">
    44       <fileset dir="." includes="README,LICENSE" />
     44      <fileset dir="." includes="README,LICENSE,INSTALL" />
    4545      <fileset dir="." includes="config/*" />
    4646    </copy>
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