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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.
- The internal copy of RAxML is also replaced by the Debian
packaged version. Due to the fact that RAxML is using SSE and
thus is only available on the architectures
amd64 i386 kfreebsd-i386 kfreebsd-amd64
as a consequence also ARB is only build on these architectures
This is most probably no restriction because ARB used on these
architectures only anyway.
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
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