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

[J.vandeVossenberg at science.ru.nl]

Dear Bela,

Thanks for setting the right permissions for the /home/db/pt_server
directory. That was indeed one of the problems, but in fact we had solved
it already.
I have just installed the new arb package, but unfortunately the update
has not solved the tree builing problem. I will describe as accurate as
possible what goes wrong now (and used to work):
In arb, open a database (does not matter which one), select a few species,
click (in the menu) Tree - Build Tree from sequence data - AxML +
FastDNAML (max 150 species), a new window opens. Then: Click FastdnaML in
'Select program to use', click GO. A terminal/text window for GDE should
open, but nothing happens... Same for Tree - Build Tree from sequence data
- Phylip DNAPARS

Unfortunately I do not know enough of arb to be able to deduce what
happens exactly. I started arb in the console, the output is below:

jack at linux:~$ arb
Program ARB starting, please wait
ARB: Loading '.arb_prop/ntree.arb'
ARB: Loading '/usr/local/bioinf/arb/arb/lib/arb_default/ntree.arb' done

Font size 11 not found, using larger 12 pointFont size 10 not found, using
larger 12 pointFont size 14 not found, using smaller 12 pointARB: Loading
'/home/jack/arb/08_May_2006.arb' + Changes-File
/home/jack/arb/08_May_2006.a00
ARB: no FastLoad File '/home/jack/arb/08_May_2006.ARM' found: loading
entire database
ARB: Loading '/home/jack/arb/08_May_2006.arb' done

The path '/home/jack/.arb_prop/inputMasks' is invalid.

  ........[comment: now I start a Phylip DNAPARS tree].........

Font size 13 not found, using smaller 12 pointAction: (/bin/rm -f treefile
infile outfile; arb_convert_aln -GenBank  /tmp/gde24491_0  -phylip infile
;${ARB_XCMD:-cmdtool} sh -c
'LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export
LD_LIBRARY_PATH;  (echo >arb_read_tree_args;arb_echo y |
dnapars;arb_read_tree `/bin/cat arb_read_tree_args` tree_ph_$$ treefile
"PRG=dnapars FILTER=none PKG=phylip")  ;arb_wait' ;/bin/rm -f 
/tmp/gde24491_0 arb_read_tree_args  infile outfile treefile
arb_read_tree_args  )&
Warning: Cannot convert string "nil2" to type FontStruct
X Error of failed request:  BadWindow (invalid Window parameter)
  Major opcode of failed request:  18 (X_ChangeProperty)
  Resource id in failed request:  0x0
  Serial number of failed request:  99
  Current serial number in output stream:  100


> 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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