
Welcome to the ARB Sequence Analysis Suite


System Requirements
-------------------

  Operating System: Linux or OSX
  Harddrive:        200 MB for arb (+some GB for databases)
  Memory:           much

  Notes:

      The resources required for ARB to run smoothly depend on the
      size of the database(s) you intend to work with. Large
      databases, especially the SSU databases provided by the
      SILVA project, require large amounts of fast memory.

  Please refer to http://bugs.arb-home.de/wiki/SystemRequirements
  for details on memory usage.


Choose ARB version:
-------------------

Currently there are two arb versions available:
 * the frequently updated PRODUCTION version (recommended)
 * the last stable public RELEASE version


Installation using Package Managers:
----------------------------------

  OSX:

    Please refer to
        https://github.com/arb-project/homebrew-arb

  Linux:

    We generally recommend installation from Pre-Compiled Binary (see below)!

       Some arb versions are distributed via apt or launchpad.
       These versions are modified (to fit better into linux systems),
       but they are not supported nor tested by us.


Installation from Pre-Compiled Binaries:
----------------------------------------

  1) Download "arb_install.sh" and the arb-*.tgz matching your distribution

      * for production version from http://download.arb-home.de/production/latest/
      * for release    version from http://download.arb-home.de/release/latest/

     We currently only provide a few precompiled versions:

          arb-*.debian#-amd64.tgz
          arb-*.ubuntu#-amd64.tgz

          (here '*' stands for the version or revision number, e.g. '6.0.6' or 'r17491'
           and  '#' stands for the OS version number)

     Note:
        * all versions are compiled without OPENGL

  2) Install using "arb_install.sh"

      Open a terminal, change to the directory where you have saved the
      files needed for installation:

         'arb_install.sh'                // install script
         'arb_README.txt'                // this file
         'arb-*.tgz'                     // your chosen ARB version

      and type

          bash arb_install.sh

      (to install arb for all users call the script as root or via sudo)

      Answer all questions asked by the script.

      Notes:
         - The script will ask about a pt_server directory. This is a
           directory where arb will store big index files.
           You should enter a different path as you do not want to
           recreate those files after an ARB update.
         - Normally pressing enter will be a good choice.
         - You can rerun the script as often as needed.
           It can be used to reconfigure an existing arb installation.

      Change your ".cshrc" or ".profile" files or create an 'arb' alias.

         To do so, follow the instructions printed when installation
         does succeed.

  3) Install library dependencies.

     ARB needs:
        gnuplot, gv, openmotif, xfig, transfig, xterm, libtiff, libX11, libXaw,
        libXext, libxml2, libXpm, libXt, lynx, time, libxslt, glib2, readline

     On Centos, dependencies should be satisfied by running:

        sudo yum install gnuplot openmotif xfig transfig xterm libXpm \
           libtiff libX11 libXaw libXext libxml2 libXpml libXt lynx \
           time libxslt readline glib2

     On Ubuntu use the package installation script delivered together with arb:

        SH/arb_installubuntu4arb.sh

     If any of the packages is not available on your system, it might just
     have a slightly differing name. Try using  "yum search" or
     "apt-cache search" to search for packages matching the base name
     (e.g. "yum search libxpm") and pick the one that's available. The only
     known issue is that you must not use "lesstif" instead of
     motif/openmotif (if you do, the GUI will be corrupted).

   4) prepare alias / PATH for arb

      During step 2) above, the script should have advised you howto
      change your login script or howto create an alias.

          Then go to a directory with a demo database (e.g. 'demo.arb' in the
          arb installation directory) and start 'ARB' by typing

              arb


      Alternatively:

          You can now run ARB simply by entering "./bin/arb" from the folder
          where you installed ARB into. For convenience, put a symlink to
          that file into any folder that is in your PATH so that you can
          just type "arb" to run it.


    5) install some more fonts

       apt-get install \
               x11-xfs-utils gsfonts-x11 \
               xfonts-terminus xfonts-terminus-dos xfonts-terminus-oblique


Compiling ARB from source
-------------------------

  * See arb_INSTALL.txt for information about how to compile
    arb from source.


Additional information
----------------------

  * See arb_INSTALL.txt for additional software needed and/or useful
   together with ARB.


PT_server
---------

  To Install 'ARB' you have to know that some modules use a so
  called 'pt_server' (prefix tree server).

  ARB needs a writeable directory to store the pt_server files.
  Those files are needed for fast database search
  (by probe_design, probe_match and the automatic aligner)
  and need a lot of disc space (up to several 100 mega bytes,
  e.g. 4000 16S RNA sequences require about 40 MB).
  This files are not created now. They can be build by any user via
      <ARB/Probes/PT_SERVER Admin/Build server>
  You may define a special directory as the pt_server files location.
  This prevents any loss of data installing a new version of
  ARB.
  To minimize the use of resources in a workstation cluster
  only one pt_server for each database is started on a user defined
  host. The first user starts the pt_server, and all other users
  can connect to it.


The Database
------------

  In the current release a small dataset (demo.arb) is provided.
  This database contains a selection of artificial and real-life
  sequences.

  The intention of providing this small dataset first is to give
  you the opportunity to get familiar with the program and to
  test the performance of your computer system as well as the
  stability of ARB on your system.


Bugs
----

  ARB is running properly and stably on our systems. However, it
  may be that there are bugs never detected by us or never
  appearing on our systems. Please don't hesitate to inform us
  about any bugs. A detailed description of the steps performed
  before the problem was evident and of the number and types of
  modules running at the same time would be extremely helpful to
  our computer scientists.

  Please report bugs into our bug tracker at
         http://bugs.arb-home.de/


Support
-------

  Please send any comments, bug reports or questions to

         arb@arb-home.de


Copyright Notice
----------------

   Please see the file

         arb_LICENSE.txt

  in the ARB installation directory.


Disclaimer
----------

  THE AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED OR IMPLIED
  FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT
  NOT LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF
  FITNESS FOR A PARTICULAR PURPOSE.


Have fun!

