source: trunk/doc/user/getting_started.html @ 2800

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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: getting_started.html 2800 2006-10-24 14:11:42Z 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: Getting started</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      Getting started
40    </div>
41
42    <h1>BASE 2.0 - User documentation: Getting started</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">Administrative 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 14:11:42 +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    <p> This description will take you from uploading raw data to
66    running the first analysis plug-ins. Both Affymetrix and Genepix
67    data will be used as examples. </p>
68
69    <ol>
70
71      <li>
72        <a name="administrative"></a>
73        <h2>Administrative tasks</h2>
74
75        <p> Most of the task in this section requires more privileges
76        than the normal user credentials. You should log in as an
77        administrator when you perform these tasks. As always, there
78        are many ways to do things and what is presented here is the
79        path to get going with BASE as fast as possible without
80        creating havoc in future use of the BASE server. </p>
81
82        <ol type=a>
83
84          <li>
85            <p> Log in as 'root' using the password you set during
86            BASE initialization. Create an administrator account. Log
87            out, and use the admin account for all administrative
88            tasks. The root account should not be used as the
89            administrator account. </p>
90          </li>
91
92          <li>
93            <p> Create user accounts using the newly created
94            administrator account. You should give your users
95            appropriate roles, most of them should be assigned to the
96            'User' role. (Link to role docs?) You can create new roles
97            if the default ones does not fit your needs. </p>
98          </li>
99
100          <li>
101            <p> Create needed plug-in configurations. Some plug-ins
102            need to be configured before use, whereas other works out
103            of the box. Some external plug-ins as the
104            <a
105            href=http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress>RMAExpress
106            plug-in for BASE</a> has to be compiled before including
107            them into your BASE server.</p>
108
109            <p> Core plug-ins are a set of plug-ins that are
110            automatically installed during setup. As pointed out
111            above, these may need a configuration to work. The way to
112            find out which plug-ins need a configuration is to choose
113            Administrate -> Plugins -> Definitions. This will display
114            a list all plug-ins available for your BASE
115            server. Nothing is shown? The reason for this is that your
116            newly created administrator does not own the definitions,
117            change the view/preset to show shared items as well. By
118            clicking on the 'Columns' tab you can select what
119            information should be displayed in the list. Please select
120            'Requires config' in the 'Columns' tab, and move it up in
121            the left panel. Finalize by clicking 'Ok'. The list now
122            has an extra column with yes and no's. Mark the 'true'
123            radio button in the 'Requires config' column to only list
124            plug-ins that need a configuration.
125
126            <p> The exercise above had two important aims. i) To show
127            you what plug-ins already exists, and ii) find three
128            essential plug-ins that needs a configuration each. Before
129            any raw data can be stored in BASE some information has to
130            be available in BASE. The slide design (reporter map) and
131            reporter information (probeset information in Affymetrix
132            vocabulary). For these we need to create configurations
133            for the "Reporter map importer" and "Reporter importer"
134            respectively, and a configuration is needed for the raw
135            data import plug-in, "Raw data importer", as well. </p>
136          </li>
137
138        </ol>
139      </li>
140
141      <li>
142        <a name="user"></a>
143        <h2>User tasks</h2>
144      </li>
145
146    </ol>
147
148  </body>
149</html>
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