source: trunk/doc/user/short.html @ 2799

Last change on this file since 2799 was 2799, checked in by Jari Häkkinen, 16 years ago

Added info.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id Date
File size: 4.9 KB
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1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2
3<!--
4    $Id: short.html 2799 2006-10-24 14:03:46Z jari $
5
6    Copyright (C) 2006 Jari Hakkinen
7
8    This file is part of BASE - BioArray Software Environment.
9    Available at http://base.thep.lu.se/
10
11    BASE is free software; you can redistribute it and/or modify it
12    under the terms of the GNU General Public License as published by
13    the Free Software Foundation; either version 2 of the License, or
14    (at your option) any later version.
15
16    BASE is distributed in the hope that it will be useful, but
17    WITHOUT ANY WARRANTY; without even the implied warranty of
18    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19    General Public License for more details.
20
21    You should have received a copy of the GNU General Public License
22    along with this program; if not, write to the Free Software
23    Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
24    02111-1307, USA.
25-->
26
27<html>
28  <head>
29    <title>BASE 2.0 - User documentation: Short introduction</title>
30    <link rel=stylesheet type="text/css" href="../styles.css">
31  </head>
32  <body>
33
34    <div class="navigation">
35      <a href="../index.html">BASE</a>
36      <img src="../next.gif">
37      <a href="index.html">User documentation</a>
38      <img src="../next.gif">
39      Short introduction
40    </div>
41
42    <h1>BASE 2.0 - User documentation: Short introduction</h1>
43
44    <div class="abstract">
45
46      <p>
47        This document describes how to get started with your new shiny
48        BASE box.
49      </p>
50
51      <b>Contents</b>
52      <ol>
53        <li><a href="#administative">Admintrative tasks</a></li>
54        <li><a href="#user">User tasks</a></li>
55      </ol>
56
57      <p class="authors">
58        <b>Last updated:</b> $Date: 2006-10-24 14:03:46 +0000 (Tue, 24 Oct 2006) $ <br>
59        <b>Copyright &copy;</b> 2006 The respective authors. All
60        rights reserved.
61      </p>
62
63    </div>
64
65    <ol>
66
67      <li>
68        <a name="administrative"></a>
69        <h2>Administrative tasks</h2>
70
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>
77
78        <ol type=a>
79
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>
87
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>
95
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>
104
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.
121
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>
133
134        </ol>
135      </li>
136
137      <li>
138        <a name="user"></a>
139        <h2>User tasks</h2>
140      </li>
141
142    </ol>
143
144  </body>
145</html>
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