Changeset 5178


Ignore:
Timestamp:
Nov 2, 2009, 3:47:32 PM (12 years ago)
Author:
Jari Häkkinen
Message:

Restructured Base1PluginExecuter configuration and BASE1 plug-in installation section.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/src/docbook/admindoc/plugin_installation.xml

    r4936 r5178  
    77
    88  Copyright (C) 2007 Johan Enell, Jari Häkkinen, Peter Johansson, Nicklas Nordborg, Martin Svensson
    9   Copyright (C) 2007 Jari Häkkinen, Nicklas Nordborg
     9  Copyright (C) 2008 Jari Häkkinen, Nicklas Nordborg
     10  Copyright (C) 2009 Jari Häkkinen, Nicklas Nordborg, Martin Svensson
    1011
    1112  This file is part of BASE - BioArray Software Environment.
     
    458459        the <emphasis>Base1PluginExecuter</emphasis> plug-in. This is
    459460        itself a plug-in and BASE version 1 plug-ins are added as
    460         configurations to this plug-in. See
    461         <xref linkend="plugins.configuration" />. To install a BASE
     461        configurations to this plug-in (cf.
     462        <xref linkend="plugins.configuration" />). To install a BASE
    462463        version 1 plug-in follow these instructions:
    463464      </para>
     
    466467        <listitem>
    467468        <para>
    468           Install the BASE version 1 plug-in executable and any
    469           other files needed by it on the BASE server. Check the documentation
    470           for the plug-in for information about what is needed.
     469          Install the BASE version 1 plug-in executable and any other
     470          files needed by it on the BASE server. Check the
     471          documentation for the plug-in for information about what is
     472          needed.
    471473        </para>
    472474        </listitem>
     
    474476        <listitem>
    475477        <para>
    476           Upload the <filename>*.base</filename> file for the BASE
    477           version 1 plug-in. If you cannot find the file, you can let
    478           your BASE version 1 server create one for you. In your BASE
    479           version 1 installation go to
    480           <menuchoice>
    481             <guimenu>Analyze data</guimenu>
    482             <guimenuitem>Plug-ins</guimenuitem>
    483           </menuchoice>
    484           and use the <guilabel>Export</guilabel> function. This will create a
    485           configuration file for your BASE version 1 plug-in that you
    486           can upload to your new BASE server.
     478          Follow the instructions in
     479          <xref linkend="plugins.configuration.base1" /> to configure
     480          Base1PluginExecuter for use of the BASE1 plug-in.
    487481        </para>
    488         </listitem>
    489        
    490         <listitem>
    491           <para>
    492             Create a new plug-in configuration using, for example,
    493             the <guibutton>New configuration</guibutton> button
    494             in single-item view for the <emphasis>Base1PluginExecuter</emphasis>
    495             plug-in.
    496           </para>
    497         </listitem>
    498        
    499         <listitem>
    500           <para>
    501             Start the configuration wizard and select the <filename>*.base</filename>
    502             file describing the BASE version 1 plug-in and enter the path and
    503             file name to the location of the executable.
    504           </para>
    505         </listitem>
    506        
    507         <listitem>
    508           <para>
    509             To check that the new plug-in works correctly, you need
    510             to have an experiment with some data. Go to the single-item
    511             view for a bioassayset and click on the <guibutton>Run analysis</guibutton>
    512             button. Select the <emphasis>Base1PluginExecuter</emphasis>
    513             plug-in. The list of configurations should include the newly
    514             installed plug-in. Select it and click on &gbNext;.
    515           </para>
    516         </listitem>
    517        
    518         <listitem>
    519           <para>
    520             This will enter regular plug-in execution wizard and you
    521             will have to enter parameters needed by the plug-in.
    522           </para>
    523482        </listitem>
    524483       
     
    15031462     
    15041463    </sect2>
     1464
     1465    <sect2 id="plugins.configuration.base1">
     1466      <title>Configuring Base1PluginExecuter</title>
     1467      <para>
     1468        BASE version 1 plug-ins are supported through the use of
     1469        the <emphasis>Base1PluginExecuter</emphasis> plug-in. Each
     1470        BASE version 1 plug-in must have at least one
     1471        Base1PluginExecuter configuration to work. To install a BASE
     1472        version 1 plug-in follow these instructions:
     1473      </para>
     1474     
     1475      <orderedlist>
     1476        <listitem>
     1477        <para>
     1478          Install the BASE version plug-in package as outlined in
     1479          <xref linkend="plugins.installation.base1" />
     1480        </para>
     1481        </listitem>
     1482
     1483        <listitem>
     1484        <para>
     1485          Upload the <filename>*.base</filename> file for the BASE
     1486          version 1 plug-in. If you cannot find the file, you can let
     1487          your BASE version 1 server create one for you. In your BASE
     1488          version 1 installation go to
     1489          <menuchoice>
     1490            <guimenu>Analyze data</guimenu>
     1491            <guimenuitem>Plug-ins</guimenuitem>
     1492          </menuchoice>
     1493          and use the <guilabel>Export</guilabel> function. This will
     1494          create a configuration file for your BASE version 1 plug-in
     1495          that you can upload to your new BASE server.
     1496        </para>
     1497        </listitem>
     1498
     1499        <listitem>
     1500          <para>
     1501            Create a new plug-in configuration using, for example,
     1502            the <guibutton>New configuration</guibutton> button in
     1503            single-item view for
     1504            the <emphasis>Base1PluginExecuter</emphasis> plug-in.
     1505          </para>
     1506        </listitem>
     1507
     1508        <listitem>
     1509          <para>
     1510            Start the configuration wizard and select
     1511            the <filename>*.base</filename> file describing the BASE
     1512            version 1 plug-in and enter the path and file name to the
     1513            location of the executable.
     1514          </para>
     1515        </listitem>
     1516
     1517        <listitem>
     1518          <para>
     1519            To check that the new plug-in works correctly, you need to
     1520            have an experiment with some data. Go to the single-item
     1521            view for a bioassay set and click on the <guibutton>Run
     1522            analysis</guibutton> button. Select
     1523            the <emphasis>Base1PluginExecuter</emphasis> plug-in. The
     1524            list of configurations should include the newly installed
     1525            plug-in. Select it and click on &gbNext;.
     1526          </para>
     1527        </listitem>
     1528
     1529        <listitem>
     1530          <para>
     1531            This will enter regular plug-in execution wizard and you
     1532            will have to enter parameters needed by the plug-in.
     1533          </para>
     1534        </listitem>
     1535
     1536      </orderedlist>
     1537
     1538    </sect2>
    15051539 
    15061540  </sect1>
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