source: tags/arb-6.0/arb_README.txt

Last change on this file was 12332, checked in by westram, 8 years ago
  • merge bugfixes from 'trunk' into 'rc'
    • installation @ debian
    • more detailed compile instructions
    • fix 'make clean' in tarball builds
    • font detection failure resulted in missing font selection buttons
  • adds:
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1
2Welcome to the 'ARB' Sequence Database Tools
3
4
5System Requirements
6-------------------
7
8
9        ARB is currently developed for Linux and OSX.
10
11        Hardware Requirements (Linux):
12
13                                Good                    We use
14        Real memory :           1 Gb                    4 Gb   
15        Free discspace :        1 Gb                    more   
16        Computer speed :        2 GHz Cpu               2 GHz Dual Cpu
17                               
18
19        Note : Memory is more important than a fast processor!
20
21
22Files needed to install ARB
23---------------------------
24
25        File                   
26
27                'arb_install.sh'        // install script
28                'arb-*.tgz'             // ARB program
29
30
31        Available ARB versions:
32
33                arb-*.centos5-amd64.tgz
34                arb-*.centos6-amd64.tgz
35                arb-*.ubuntu1004-amd64.tgz
36                arb-*.ubuntu1204-amd64.tgz
37                arb-*.ubuntu1304-amd64.tgz
38                arb-*.osx.tgz
39
40        You need exactly ONE of the available 'arb-*.tgz'!
41
42        Notes:
43
44        * all versions are 64bit versions
45          (if you really need a 32bit version, see http://download.arb-home.de/release/arb_5.5/)
46
47        * all versions are compiled without OPENGL
48          (if you rely on OPENGL features, either stick with arb_5.5 or compile arb from source)
49
50        * OSX version is available as arb-*.osx.tgz
51          and via MacPorts (see arb_OS_X_MacPorts.txt included inside arb-*.osx.tgz)
52
53        * debian users should either use the arb package in 'non-free' or
54          install one of the centos versions (see also arb_INSTALL.txt)
55
56
57Install/Update ARB
58------------------
59
60        ARB consists of more than 1400 files which are installed into a single
61        directory. Creating this directory, copying all data into it, and setting
62        the permissions correctly is done by the installation script
63
64                'arb_install.sh'
65
66        Open a terminal, change to the directory where you have saved the
67        files needed for installation:
68
69                'arb_install.sh'                // install script
70                'arb_README.txt'                // this file
71                'arb-*.tgz'                     // your chosen ARB version
72
73
74        and type
75
76                '/bin/sh arb_install.sh'
77
78        (to install arb for all users call the script as root or via sudo)
79
80
81        Answer all questions asked by the script.
82
83        Notes:- The script will ask about a pt_server directory. This is a
84                directory where arb will store big index files.
85                You should enter a different path as you do not want to
86                recreate those files after an ARB update.
87              - Normally pressing enter will be a good choice.
88              - You can rerun the script many times, it can be used to
89                change an existing installation.
90
91        Change your .cshrc/.profile files:
92
93                Set the environment variable ARBHOME
94                to the ARB installation directory
95                Append   $ARBHOME/bin   to your PATH
96
97        reread it,      (logout+login)
98
99        goto a directory with a demo database 'eg demo.arb'
100        and start 'ARB' with
101
102                        'arb'
103
104Compile ARB from source
105-----------------------
106
107        * See arb_INSTALL.txt for information about how to compile
108          arb from source.
109
110
111Additional information
112----------------------
113
114        * See arb_INSTALL.txt for additional software needed and/or useful
115          together with ARB.
116
117
118PT_server
119---------
120
121        To Install 'ARB' you have to know that some modules use a so
122        called 'pt_server' (prefix tree server).
123
124        ARB needs a writeable directory to store the pt_server files.
125        Those files are needed for fast database search
126        (by probe_design, probe_match and the automatic aligner)
127        and need a lot of disc space (up to several 100 mega bytes,
128        e.g. 4000 16S RNA sequences require about 40 MB).
129        This files are not created now. They can be build by any user via
130                <ARB_NTREE/Probes/PT_SERVER admin/Build server>
131        You may define a special directory as the pt_server files location.
132        This prevents any loss of data installing a new version of
133        ARB.
134        To minimize the use of ressources in a workstation cluster
135        only one pt_server for each database is started on a user defined
136        host. The first user starts the pt_server, and all other users
137        can connect to it.
138
139
140What you should know: Swap
141--------------------------
142
143        Arb needs a lot of virtual memory
144        (about 50 Mbyte for 5000 Sequences, Length = 3000).
145        You can find out about installed swap space by typing:
146
147                Linux                   'top'
148                SunOS 1.x:              'pstat -s'
149                System V / SGI          'swap -s'
150                OSF                     'swapon -sv'
151
152        Call your system administrator or local guru to increase your
153        swap. (If you don't have such a nice person, try to read the
154        man pages: 'man -k swap')
155
156
157The Database
158------------
159
160        In the current release a small dataset (demo.arb) is provided.
161        This database contains a selection of artificial and real-life
162        sequences.
163
164        The intention of providing this small dataset first is to give
165        you the opportunity to get familiar with the program and to
166        test the performance of your computer system as well as the
167        stability of ARB on your system.
168
169
170Bugs
171----
172
173        ARB is running properly and stably on our systems. However, it
174        may be that there are bugs never detected by us or never
175        appearing on our systems. Please don't hesitate to inform us
176        about any bugs. A detailed description of the steps performed
177        before the problem was evident and of the number and types of
178        modules running at the same time would be extremely helpful to
179        our computer scientists.
180
181        Please report bugs into our bug tracker at
182               http://bugs.arb-home.de/
183
184
185Support
186-------
187
188        Please send any comments, bug reports or questions to
189
190                arb@arb-home.de
191
192
193Copyright Notice
194----------------
195
196        Please see the file
197
198               arb_LICENSE.txt
199
200        in the ARB installation directory.
201
202
203Disclaimer
204----------
205
206        THE AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED OR IMPLIED
207        FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT
208        NOT LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF
209        FITNESS FOR A PARTICULAR PURPOSE.
210
211
212Have fun!
213
214
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