[Bio-Linux] Fwd: subject: arb does not call GDE anymore.

[Bela Tiwari]

Dear Jack,

Thank you very  much for alerting us to the problems with the latest update of the ARB package. The permissions on the /home/db/pt_server directory were being set by a post install script that was failing. We have fixed this and updated the package. 

I will write to you via our helpdesk about the libstdc++2.10-glibc2.2 package and the issues you have seen with GDE via our helpdesk system in a moment.


best wishes, 

Bela



*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************


>>> NEBC at wpo.nerc.ac.uk 10/10/2006 13:52 >>>
Dear all,

Today I found out that arb (16S phylogeny programme) does not want to call
a GDE window anymore. In practise this means that one can not calculate ML
or PARS trees anymore. This is one of the 'core businesses' of arb, for
which we even run a dedicated computer, so this problem needs to be
addressed.

I think that this problem came up in the latest update, because in August
(I think) I could still produce these trees in the same computer
(Ubuntu+bio-linux) without a problem. And I know that there has been a
bio-linux update recently.

The problem must be in the deb package. I guess it is a wrong permission,
or a wrong link to the GDE part. It used to work before the update, and
other (Suse) computers, that use the same arb version (22-08-2003), work.
If worse comes to worse we will have to reinstall arb from the tar.gz from
the arb homepage, thereby missing out on easy install and updates etc, etc
(a main reason to use bio-linux).

This also brings me to these facts that I ran into:
1) The bio-linux arb package depends on libstdc++2.10-glibc2.2, which must
be installed by hand (is an apt-get package) to make it work. I suggest
that this dependency is included into the deb package.
2) The /home/db/pt_server directory must be made RW for all arb users to
make arb useable, now the arb package makes it only RW by root. I suggest
that this will be solved in the deb package.

Thanks

Regards,
Jack van de Vossenberg
J.vandeVossenberg at science.ru.nl 


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