source: branches/profile/arb_README.txt

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1
2Welcome to the ARB 6 Sequence Analysis Suite
3
4
5System Requirements
6-------------------
7
8  Minimal (demo.arb):
9      Operating System: Linux or OSX
10      CPU:              any
11      Memory:           1 GB
12      Hard drive:       200 MB
13
14  Recommended (SILVA SSU NR99 r115):
15      Operating System: Linux (Ubuntu 12.04 or newer)
16                        OSX (10.5.8 or newer)
17      CPU:              >2 GHz multi-core
18      Memory:           16 GB (or more!)
19      Hard drive:       10 GB
20
21  Notes:
22  The resources required for ARB to run smoothly depend on the size of the
23  database(s) you intend to work with. Large databases, especially the SSU
24  databases provided by the SILVA project, require large amounts of fast
25  memory.
26
27
28Installation using Package Managers:
29----------------------------------
30
31  OSX:
32    The recommended approach is to install MacPorts (macports.org) and use
33    the ports command to install arb: "sudo port install arb"
34
35  Debian Linux:
36    ARB is available in Debian Testing in section "non-free". Install ARB
37    using "apt-get install arb" or your preferred GUI front-end to apt-get.
38
39
40Installation from Pre-Compiled Binaries:
41----------------------------------------
42
43  1) Download "arb_install.sh" and the arb-*.tgz matching your distribution
44     from http://download.arb-home.de/release/latest/
45
46     Files:
47     arb-*.centos5-amd64.tgz
48     arb-*.centos6-amd64.tgz
49     arb-*.osx.tgz
50     arb-*.ubuntu1004-amd64.tgz
51     arb-*.ubuntu1204-amd64.tgz
52     arb-*.ubuntu1304-amd64.tgz
53
54     (where '*' stands for the most recent version number, e.g. '6.0.1')
55
56     If your distribution is neither Ubuntu nor Centos, try Centos.
57     If your distributions version is not among the above, try the next older
58     release (e.g. 12.04 if you have 12.10).
59
60     Notes:
61        * All versions are compiled without OPENGL.
62          (if you rely on OPENGL features, either stick with arb_5.5 or
63          compile arb from source)
64        * Debian users need to pick Centos (due to fun with [e]glibc) or better
65          use the package from non-free.
66         
67  2a) 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          sh 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:
94
95      Set the environment variable ARBHOME to the ARB installation directory
96      Append   $ARBHOME/bin   to your PATH.
97      Re-Login to load the changed environment.
98
99      Go to a directory with a demo database eg 'demo.arb'and start 'ARB' with
100       
101         arb
102
103  2b) Install manually
104
105      i)   Create a folder where you want ARB to reside. E.g:
106     
107         mkdir ~/arb-6.0
108
109      ii)  Unpack ARB into this folder. E.g.
110
111         tar -C ~/arb-6.0 -xzf ~/Downloads/arb-6.0.1.ubuntu1304-amd64.tgz
112
113      iii) Install library dependencies.
114 
115      (If you already have an ARB installation and just want to install another
116      version, you can skip this step.)
117
118      ARB needs:
119         gnuplot, gv, openmotif, xfig, transfig, xterm, libtiff, libX11, libXaw,
120         libXext, libxml2, libXpm, libXt, lynx, time, libxslt, glib2, readline
121
122      On Centos, dependencies should be satisfied by running:
123       
124         sudo yum install gnuplot openmotif xfig transfig xterm libXpm \
125            libtiff libX11 libXaw libXext libxml2 libXpml libXt lynx \
126            time libxslt readline glib2
127
128      On Ubuntu 13.04, use:
129
130         sudo apt-get install gnuplot gv libmotif3 xfig transfig \
131           xterm libxpm4 libtiff4 libx11-6 libxaw7 libxext6 libxml2-utils \
132           libxt6 lynx libreadline6
133         
134      If any of the packages is not available on your system, it might just
135      have a slightly differing name. Try using  "yum search" or
136      "apt-cache search" to  search for packages matching the base name
137      (e.g. "yum search libxpm") and pick the one that's available. The only
138      known issue is that you must not use "lesstif" instead of
139      motif/openmotif (if you do, the interface will look broken).
140
141      You can now run ARB simply by entering "./bin/arb" from the folder
142      where you installed ARB. For convenience, put a symlink to the file
143      into any folder that is in your PATH so that you can just type "arb"
144      to run it.
145
146
147Compiling ARB from source
148-------------------------
149
150  * See arb_INSTALL.txt for information about how to compile
151    arb from source.
152
153
154Additional information
155----------------------
156
157  * See arb_INSTALL.txt for additional software needed and/or useful
158   together with ARB.
159
160
161PT_server
162---------
163
164  To Install 'ARB' you have to know that some modules use a so
165  called 'pt_server' (prefix tree server).
166
167  ARB needs a writeable directory to store the pt_server files.
168  Those files are needed for fast database search
169  (by probe_design, probe_match and the automatic aligner)
170  and need a lot of disc space (up to several 100 mega bytes,
171  e.g. 4000 16S RNA sequences require about 40 MB).
172  This files are not created now. They can be build by any user via
173      <ARB_NTREE/Probes/PT_SERVER admin/Build server>
174  You may define a special directory as the pt_server files location.
175  This prevents any loss of data installing a new version of
176  ARB.
177  To minimize the use of ressources in a workstation cluster
178  only one pt_server for each database is started on a user defined
179  host. The first user starts the pt_server, and all other users
180  can connect to it.
181
182
183The Database
184------------
185
186  In the current release a small dataset (demo.arb) is provided.
187  This database contains a selection of artificial and real-life
188  sequences.
189
190  The intention of providing this small dataset first is to give
191  you the opportunity to get familiar with the program and to
192  test the performance of your computer system as well as the
193  stability of ARB on your system.
194
195
196Bugs
197----
198
199  ARB is running properly and stably on our systems. However, it
200  may be that there are bugs never detected by us or never
201  appearing on our systems. Please don't hesitate to inform us
202  about any bugs. A detailed description of the steps performed
203  before the problem was evident and of the number and types of
204  modules running at the same time would be extremely helpful to
205  our computer scientists.
206
207  Please report bugs into our bug tracker at
208         http://bugs.arb-home.de/
209
210
211Support
212-------
213
214  Please send any comments, bug reports or questions to
215
216         arb@arb-home.de
217
218
219Copyright Notice
220----------------
221
222   Please see the file
223
224         arb_LICENSE.txt
225
226  in the ARB installation directory.
227
228
229Disclaimer
230----------
231
232  THE AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED OR IMPLIED
233  FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT
234  NOT LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF
235  FITNESS FOR A PARTICULAR PURPOSE.
236
237
238Have fun!
239
240
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