Changeset 549


Ignore:
Timestamp:
Jan 22, 2008, 2:41:08 PM (13 years ago)
Author:
Nicklas Nordborg
Message:

References #89: Installation program and documentation

Updated installation procedure to something that might actually work when BASE 2.6 is released.

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

Legend:

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

    • Property svn:ignore
      •  

        old new  
        11dist
        22build
         3package
         4.classpath
         5.project
  • trunk/net/sf/basedb/illumina/README

    r546 r549  
    19191. Unpack the tar.gz file to a directory of your choice.
    2020
    21 2. Copy the illumina-plugins-xxx.jar (where xxx depends on the version number)
    22    to your BASE plug-ins directory. We recommend that you have set the
    23    'plugins.dir' option in your base.config and copy the JAR file to a
    24    subdirectory.
     212. Stop your Tomcat server that is running BASE and all job agents, if any.
     22
     233. 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.
    2527   
    26 3. Run the auto-installation wizard by gioing to
     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   
     314. 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   
     395. Update the database with Illumina-specific tables and columns by running the
     40   'updatedb.sh' script, located in the <basedir>/bin directory.
     41
     426. Restart the Tomcat server.
     43   
     447. Run the auto-installation wizard by going to
    2745   Administrate -> Plugins -> Definitions
    2846   and click on the 'New' button.
    2947   
    30 4. Select the 'Automaticall' option.
     488. Select the 'Automatical' option.
    3149
    32 5. The auto-detection should find the plug-ins listed below. You should
     509. The auto-detection should find the plug-ins listed below. You should
    3351   change the 'Install' value to 'yes' for all of them.
    3452   
     
    3654  * BGX feature/reporter importer
    3755   * Scandata importer
     56   * ... and some more... TODO
    3857
    3958   The 'Illumina plug-in package installer' should have the 'Allow immediate
    4059   execution' option set to 'allow'.
    4160   
    42 6. Find the 'Illumina plug-in package installer' in the list of plug-ins and
    43    click on it.
     6110. Find the 'Illumina plug-in package installer' in the list of plug-ins and
     62    click on it.
    4463
    45 7. Click on the 'Run plugin' button.
     6411. Click on the 'Run plugin' button.
    4665
    47 8. Accept the default options.
     6611. Accept the default options.
    4867
    49 9. TODO
     6812. Wait for the plug-in to finish.
    5069
     7013. 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.
    5179
  • trunk/net/sf/basedb/illumina/build.xml

    r546 r549  
    4343    <copy todir="${dist}">
    4444      <fileset dir="." includes="README,LICENSE" />
     45      <fileset dir="." includes="config/*" />
    4546    </copy>
    4647  </target>
  • trunk/net/sf/basedb/illumina/config/illumina-extended-properties.xml

    r546 r549  
    88-->
    99<extended-properties>
     10  <!--  TODO
    1011  <class name="ReporterData">
    1112   
    1213  </class>
     14  -->
    1315</extended-properties>
    1416
  • trunk/net/sf/basedb/illumina/config/illumina-raw-data-types.xml

    r546 r549  
    33<!--
    44  Definition for raw data types needed by the Illumina plug-ins.
    5   You should manually copy the raw data types from this file into
    6   your main raw-data-types.xml file.
     5  Place this file in the WEB-INF/classes/raw-data-types directory.
     6  For detailed installation instructions see the README file.
    77-->
    88<raw-data-types>
    99  <raw-data-type
    10     id="iluminascandata"
     10    id="illumina_scandata"
    1111    channels="1"
    1212    name="Illumina scandata"
     
    2727      column="mean"
    2828      type="float"
    29       averagemethod="mean"
     29      averagemethod="arithmetic_mean"
    3030    />
    3131    <property
Note: See TracChangeset for help on using the changeset viewer.