Oct 24, 2006, 4:03:46 PM (16 years ago)
Jari Häkkinen

Added info.

1 edited


  • trunk/doc/user/short.html

    r2756 r2799  
    5151      <b>Contents</b>
    5252      <ol>
    53         <li><a href="#first">First section</a></li>
     53        <li><a href="#administative">Admintrative tasks</a></li>
     54        <li><a href="#user">User tasks</a></li>
    5455      </ol>
    6263    </div>
    64     <a name="first"></a>
    65     <h2>1. First section</h2>
     65    <ol>
    67     <p>
    68       To be written.
    69     </p>
     67      <li>
     68        <a name="administrative"></a>
     69        <h2>Administrative tasks</h2>
    71 Update doc/affymetrix.txt!
     71        <p> Most of the task in this section requires more privileges
     72        than the normal user credentials. You should log in as an
     73        administrator when you perform these tasks. As always, there
     74        are many ways to do things and what is presented here is the
     75        path to get going with BASE as fast as possible without
     76        creating havoc in future use of the BASE server. </p>
    73 Log in and create your first users of which one must be a administrator. You should use the root user in normal situations.
     78        <ol type=a>
    75 Add you first plug-in to BASE.
     80          <li>
     81            <p> Log in as 'root' using the password you set during
     82            BASE initialization. Create an adminstrator account. Log
     83            out, and use the admin account for all administrative
     84            tasks. The root account should not be used as the
     85            administrator account. </p>
     86          </li>
    77 Create reporter import configuration. Create reporter map config
    78 (optional, affy does not need it.).
     88          <li>
     89            <p> Create user accounts using the newly created
     90            administrator account. You should give your users
     91            appropriate roles, most of them should be assigned to the
     92            'User' role. (Link to role docs?) You can create new roles
     93            if the default ones does not fit your needs. </p>
     94          </li>
    80 Upload files: Array design and reporter annotations.
     96          <li>
     97            <p> Create needed plug-in configurations. Some plug-ins
     98            need to be configured before use, whereas other works out
     99            of the box. Some external plug-ins as the
     100            <a
     101            href=http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress>RMAExpress
     102            plug-in for BASE</a> has to be compiled before including
     103            them into your BASE server.</p>
    82 Import reporters.
     105            <p> Core plug-ins are a set of plug-ins that are
     106            automatically installed during setup. As pointed out
     107            above, these may need a configuration to work. The way to
     108            find out which plug-ins need a configuration is to choose
     109            Administrate -> Plugins -> Definitions. This will display
     110            a list all plug-ins available for your BASE
     111            server. Nothing is shown? The reason for this is that your
     112            newly created administrator does not own the definitions,
     113            change the view/preset to show shared items as well. By
     114            clicking on the 'Columns' tab you can select what
     115            information should be displayed in the list. Please select
     116            'Requires config' in the 'Columns' tab, and move it up in
     117            the left panel. Finalize by clicking 'Ok'. The list now
     118            has an extra column with yes and no's. Mark the 'true'
     119            radio button in the 'Requires config' column to only list
     120            plug-ins that need a configuration.
     122            <p> The exercise above had two important aims. i) To show
     123            you what plug-ins already exists, and ii) find three
     124            essential plug-ins that needs a configuration each. Before
     125            any raw data can be stored in BASE some information has to
     126            be available in BASE. The slide design (reporter map) and
     127            reporter information (probeset information in Affymetrix
     128            vocabulary). For these we need to create configurations
     129            for the "Reporter map importer" and "Reporter importer"
     130            respectively, and a configuration is needed for the raw
     131            data import plugin, "Raw data importer", as well. </p>
     132          </li>
     134        </ol>
     135      </li>
     137      <li>
     138        <a name="user"></a>
     139        <h2>User tasks</h2>
     140      </li>
     142    </ol>
    84144  </body>
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