source: tags/arb_5.5/arb_README.txt

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1
2Welcome to the 'ARB' Sequence Database Tools
3
4
5System Requirements
6-------------------
7
8
9        ARB is currently developed on Linux PCs only.
10
11        Compiling ARB using the gcc compiler (3.x and 4.x series)
12        as well works on Mac OSX and Sun OS - but we do not publish or support
13        these versions.
14
15
16        Hardware Requirements (Linux):
17
18                                Good                    We use
19        Real memory :           1 Gb                    4 Gb   
20        Free discspace :        1 Gb                    more   
21        Computer speed :        2 GHz Cpu               2 GHz Dual Cpu
22                               
23
24        Note : Memory is more important than a fast processor!
25
26
27Files needed to install ARB
28---------------------------
29
30        File                   
31
32        'arb_install.sh'        // install script
33        'arb.*.tgz'             // ARB program
34
35
36        Available ARB versions:
37
38        'arb.32.*.tgz'          // 32 bit versions
39        'arb.64.*.tgz'          // 64 bit versions
40
41        'arb.*.OPENGL.tgz'      // OPENGL version (contains RNA3D, a 3D-molecule-viewer)
42
43
44        Choose a 32-bit-version, if your system is 32-bit,
45        choose a 64-bit-version, if your system is 64-bit.
46
47        You need only ONE of the available 'arb.*.tgz'!
48
49
50Install/Update ARB
51------------------
52
53        ARB consists of more than 1200 files which are installed into a single
54        directory. Creating this directory, copying all data into it, and setting
55        the permissions correctly is done by the installation script
56
57                'arb_install.sh'
58
59        Goto the directory, where the files
60
61                'arb_install.sh'                // install script
62                'arb_README.txt'                // this file
63                'arb.*.tgz'                     // your chosen ARB version
64
65
66        are located and type
67
68                '/bin/sh arb_install.sh'
69
70        Answer all questions asked by the script.
71
72        Notes:- The script will ask about a pt_server directory. This is a
73                directory where arb will store big index files.
74                You should enter a different path as you do not want to
75                recreate those files after an ARB update.
76              - Normally pressing enter will be a good choice.
77              - You can rerun the script many times, it can be used to
78                change an existing installation.
79
80        Change your .cshrc/.profile files:
81
82                Set the environment variable ARBHOME
83                to the ARB installation directory
84                Append   $ARBHOME/bin   to your PATH
85
86        reread it,      (logout+login )
87
88        goto a directory with a demo database 'eg demo.arb'
89        and start 'ARB' with
90
91                        'arb'
92
93
94Additional information
95----------------------
96
97        * See arb_INSTALL.txt for additional software needed and/or useful
98          together with ARB.
99
100
101PT_server
102---------
103
104        To Install 'ARB' you have to know that some modules use a so
105        called 'pt_server' (prefix tree server).
106
107        ARB needs a writeable directory to store the pt_server files.
108        Those files are needed for fast database search
109        (by probe_design, probe_match and the automatic aligner)
110        and need a lot of disc space (up to several 100 mega bytes,
111        e.g. 4000 16S RNA sequences require about 40 MB).
112        This files are not created now. They can be build by any user via
113                <ARB_NTREE/Probes/PT_SERVER admin/Build server>
114        You may define a special directory as the pt_server files location.
115        This prevents any loss of data installing a new version of
116        ARB.
117        To minimize the use of ressources in a workstation cluster
118        only one pt_server for each database is started on a user defined
119        host. The first user starts the pt_server, and all other users
120        can connect to it.
121
122
123What you should know: Swap
124--------------------------
125
126        Arb needs a lot of virtual memory
127        (about 50 Mbyte for 5000 Sequences, Length = 3000).
128        You can find out about installed swap space by typing:
129
130                Linux                   'top'
131                SunOS 1.x:              'pstat -s'
132                System V / SGI          'swap -s'
133                OSF                     'swapon -sv'
134
135        Call your system administrator or local guru to increase your
136        swap. (If you don't have such a nice person, try to read the
137        man pages: 'man -k swap')
138
139
140The Database
141------------
142
143        In the current release a small dataset (demo.arb) is provided.
144        This database contains a selection of artificial and real-life
145        sequences.
146
147        The intention of providing this small dataset first is to give
148        you the opportunity to get familiar with the program and to
149        test the performance of your computer system as well as the
150        stability of ARB on your system.
151
152
153Bugs
154----
155
156        ARB is running properly and stably on our systems. However, it
157        may be that there are bugs never detected by us or never
158        appearing on our systems. Please don't hesitate to inform us
159        about any bugs. A detailed description of the steps performed
160        before the problem was evident and of the number and types of
161        modules running at the same time would be extremely helpful to
162        our computer scientists.
163
164        Please report bugs into our bug tracker at
165               http://bugs.arb-home.de/
166
167
168Support
169-------
170
171        Please send any comments, bug reports or questions to
172
173                arb@arb-home.de
174
175
176Copyright Notice
177----------------
178
179        Please see the file
180
181               arb_LICENSE.txt
182
183        in the ARB installation directory.
184
185
186Disclaimer
187----------
188
189        THE AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED OR IMPLIED
190        FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT
191        NOT LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF
192        FITNESS FOR A PARTICULAR PURPOSE.
193
194
195Have fun!
196
197
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