source: tags/arb-7.0/arb_README.txt

Last change on this file was 18692, checked in by westram, 3 years ago
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1
2Welcome to the ARB 6 Sequence Analysis Suite
3
4
5System Requirements
6-------------------
7
8  Operating System: Linux or OSX
9  Harddrive:        200 MB for arb (+some GB for databases)
10  Memory:           much
11
12  Notes:
13
14      The resources required for ARB to run smoothly depend on the
15      size of the database(s) you intend to work with. Large
16      databases, especially the SSU databases provided by the
17      SILVA project, require large amounts of fast memory.
18
19  Please refer to http://bugs.arb-home.de/wiki/SystemRequirements
20  for details on memory usage.
21
22
23Choose ARB version:
24-------------------
25
26Currently there are two arb versions available:
27 * the frequently updated PRODUCTION version (recommended)
28 * the last stable public RELEASE version (older)
29
30
31Installation using Package Managers:
32----------------------------------
33
34  OSX:
35    For the production version please refer to
36        https://github.com/arb-project/homebrew-arb
37
38    For the release version the approach is to install MacPorts (macports.org) and use
39    the ports command to install arb: "sudo port install arb"
40
41  Debian Linux:
42    The production version has to be installed from Pre-Compiled Binary (see below).
43
44    ARB release is available in Debian Testing in section "non-free". Install ARB
45    using "apt-get install arb" or your preferred GUI front-end to apt-get.
46
47
48Installation from Pre-Compiled Binaries:
49----------------------------------------
50
51  1) Download "arb_install.sh" and the arb-*.tgz matching your distribution
52
53      * for production version from http://download.arb-home.de/special/manual-builds/
54      * for release    version from http://download.arb-home.de/release/latest/
55
56     We currently only provide a few precompiled versions:
57
58          arb-*.debian#-amd64.tgz
59          arb-*.ubuntu#-amd64.tgz
60
61          (here '*' stands for the version or revision number, e.g. '6.0.6' or 'r17491'
62           and  '#' stands for the OS version number)
63
64     Note:
65        * all versions are compiled without OPENGL
66
67  2) Install using "arb_install.sh"
68
69      Open a terminal, change to the directory where you have saved the
70      files needed for installation:
71
72         'arb_install.sh'                // install script
73         'arb_README.txt'                // this file
74         'arb-*.tgz'                     // your chosen ARB version
75
76      and type
77
78          bash arb_install.sh
79
80      (to install arb for all users call the script as root or via sudo)
81
82      Answer all questions asked by the script.
83
84      Notes:
85         - The script will ask about a pt_server directory. This is a
86           directory where arb will store big index files.
87           You should enter a different path as you do not want to
88           recreate those files after an ARB update.
89         - Normally pressing enter will be a good choice.
90         - You can rerun the script many times, it can be used to
91           change an existing installation.
92
93      Change your ".cshrc" or ".profile" files or create an 'arb' alias.
94
95         To do so, follow the instructions printed when installation
96         did succeed.
97
98  3) Install library dependencies.
99
100     (If you already have an ARB installation and just want to install another
101     version, you can skip this step.)
102
103     ARB needs:
104        gnuplot, gv, openmotif, xfig, transfig, xterm, libtiff, libX11, libXaw,
105        libXext, libxml2, libXpm, libXt, lynx, time, libxslt, glib2, readline
106
107     On Centos, dependencies should be satisfied by running:
108
109        sudo yum install gnuplot openmotif xfig transfig xterm libXpm \
110           libtiff libX11 libXaw libXext libxml2 libXpml libXt lynx \
111           time libxslt readline glib2
112
113     On Ubuntu use the package installation script delivered together with arb:
114
115        SH/arb_installubuntu4arb.sh
116
117     If any of the packages is not available on your system, it might just
118     have a slightly differing name. Try using  "yum search" or
119     "apt-cache search" to  search for packages matching the base name
120     (e.g. "yum search libxpm") and pick the one that's available. The only
121     known issue is that you must not use "lesstif" instead of
122     motif/openmotif (if you do, the GUI will be corrupt).
123
124   4) prepare alias / PATH for arb
125
126      While using 2) above, the script should have advised you howto
127      change your login script or howto create an alias.
128
129          Then go to a directory with a demo database (e.g. 'demo.arb' in the
130          arb installation directory) and start 'ARB' by typing
131
132              arb
133
134
135      Alternatively:
136
137          You can now run ARB simply by entering "./bin/arb" from the folder
138          where you installed ARB into. For convenience, put a symlink to
139          that file into any folder that is in your PATH so that you can
140          just type "arb" to run it.
141
142
143    5) install some more fonts
144
145       apt-get install \
146               x11-xfs-utils gsfonts-x11 \
147               xfonts-terminus xfonts-terminus-dos xfonts-terminus-oblique
148
149
150Compiling ARB from source
151-------------------------
152
153  * See arb_INSTALL.txt for information about how to compile
154    arb from source.
155
156
157Additional information
158----------------------
159
160  * See arb_INSTALL.txt for additional software needed and/or useful
161   together with ARB.
162
163
164PT_server
165---------
166
167  To Install 'ARB' you have to know that some modules use a so
168  called 'pt_server' (prefix tree server).
169
170  ARB needs a writeable directory to store the pt_server files.
171  Those files are needed for fast database search
172  (by probe_design, probe_match and the automatic aligner)
173  and need a lot of disc space (up to several 100 mega bytes,
174  e.g. 4000 16S RNA sequences require about 40 MB).
175  This files are not created now. They can be build by any user via
176      <ARB_NTREE/Probes/PT_SERVER admin/Build server>
177  You may define a special directory as the pt_server files location.
178  This prevents any loss of data installing a new version of
179  ARB.
180  To minimize the use of resources in a workstation cluster
181  only one pt_server for each database is started on a user defined
182  host. The first user starts the pt_server, and all other users
183  can connect to it.
184
185
186The Database
187------------
188
189  In the current release a small dataset (demo.arb) is provided.
190  This database contains a selection of artificial and real-life
191  sequences.
192
193  The intention of providing this small dataset first is to give
194  you the opportunity to get familiar with the program and to
195  test the performance of your computer system as well as the
196  stability of ARB on your system.
197
198
199Bugs
200----
201
202  ARB is running properly and stably on our systems. However, it
203  may be that there are bugs never detected by us or never
204  appearing on our systems. Please don't hesitate to inform us
205  about any bugs. A detailed description of the steps performed
206  before the problem was evident and of the number and types of
207  modules running at the same time would be extremely helpful to
208  our computer scientists.
209
210  Please report bugs into our bug tracker at
211         http://bugs.arb-home.de/
212
213
214Support
215-------
216
217  Please send any comments, bug reports or questions to
218
219         arb@arb-home.de
220
221
222Copyright Notice
223----------------
224
225   Please see the file
226
227         arb_LICENSE.txt
228
229  in the ARB installation directory.
230
231
232Disclaimer
233----------
234
235  THE AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED OR IMPLIED
236  FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT
237  NOT LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF
238  FITNESS FOR A PARTICULAR PURPOSE.
239
240
241Have fun!
242
243
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