Arb for DEBIAN
--------------

Known bugs of arb are listed in the bug-tracker at
    http://bugs.arb-home.de/

Dependencies
------------

 - Arb comes with its own version of Phylip.  Because Phylip has
   its Debian package this is not build into arb package.  Instead
   I replaced links to the appropriate locations.
 - Arb has its own version of FastDNAml which has also a separate
   Debian package.  Here also symlinks to the Debian packaged
   version are used.
 - Arb makes also use of a patched Version of ReadSeq.  The Arb
   version is identical with the latest C version (ReadSeq 2 is
   written from scratch in Java).  The Arb-Verion is missing some
   patches, but has additional patches which make it incompatible
   with the Debian packaged version.  I try to clarify this issue.
 - Arb has its own Version of tree-puzzle 5.0 which is completely
   identical with the Debian version.  Just not compile it and
   set the appropriate links.
 - Arb contains a patched version of phyml which is lagging behind
   upstream releases of phyml.  The latest version of phyml is
   available as Debian package as well and it is in the list of
   Suggested packages of Arb to enable you to compare the results.

Comments regarding the packaging
--------------------------------

Config file:

  Under Debian GNU/Linux all configuration file have to be stored under /etc.
  Thus the config file is symlinked from /usr/lib/arb/lib/arb_tcp.dat to
  /etc/arb/arb_tcp.dat.

User group arb:

  It has shown that arb users need to add their own PT_SERVER databases.
  To enable users to create such database files and insert this file into
  the config file a script arb-add-pt-server was written  (see
  "man arb-add-pt-server").
  
Dynamic libraries:

  The dynamic libraries which are builded by the upstream Arb Makefile
  are moved from ${ARBHOME} to /usr/lib.  Strangely enough these libraries
  issue a warninig of
  
      dpkg-shlibdeps: warning: format of libA*.so not recognized

  which results in a lintian error
  
      E: libarb: sharedobject-in-library-directory-not-actually-a-shlib usr/lib/libA*.so

  This was reportet upstream and is topic of further investigations.

Potentially separate package

  Formerly arb_ntree was separated in an extra package which makes no
  real sense because it is the main Arb application.  The only target
  for splitting would be  PT-Server (binary bin/arb_pt_server - needs
  libraries+(arb_)gene_probe)

 -- Andreas Tille <tille@debian.org>  Thu, 27 Jun 2013 14:52:57 +0200
