[EMBOSS] Configuring EMBOSS to use getz

[Ran Rubinstein]

Your dbalias parameter is probably wrong. It should be the name of the
databank in SRS. Try to run getz directly with your query and see whether it
works.

-- 
Ran Rubinstein 
Dept. of Molecular Biology 
Faculty of Medicine, Hebrew University, Ein Karem, Jerusalem, Israel
Tel +972-2-6757906 Fax +972-2-6758992

-----Original Message-----
From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk] On
Behalf Of yann-francois.bizouerne at bayercropscience.com
Sent: Wednesday, October 08, 2003 5:33 PM
To: emboss at embnet.org
Subject: [EMBOSS] Configuring EMBOSS to use getz





Hi,

I am trying to use the method "srs".
I am using Emboss  2.7.1 and SRS 7.1.

In my emboss.default file, I have :

   DB Nrl3dGetz [
   methodquery: srs
   format: pir
   type: P
   comment: "NRL 3D using SRS"
   app: getz
   dbalias:NRL3D
   methodall: direct
   file: "*.seq"
   dir: $emboss_data_dir/nrl_3d
   ]

When I execute the command "showdb", I obtain :

   user>showdb
   Displays information on the currently available databases
   # Name        Type ID  Qry All Comment
   # ====        ==== ==  === === =======
   Nrl3dGetz     P    OK  OK  OK  NRL 3D using SRS

So I looks fine. But when I try to find an entry, I just obtain a error.

   user>entret Nrl3dGetz:11ASA -outfile stdout
   Reads and writes (returns) flatfile entries
   error: Unknown set or databank
     No set or library named "Nrl3dGetz"
   Error: Unable to read sequence 'Nrl3dGetz:11ASA'
   Died: entret terminated: Bad value for '-sequence' and no prompt

I have read all the SRS and EMBOSS documentations  related to this
configuration
and I don't know where the problem is.
Do you have any clue ??

Thanks in advance.


Yann-François BIZOUERNE
BioInformatic Team
BAYER CropScience
1, rue Pierre Fontaine
91058 Evry Cedex
FRANCE
Phone:      33-(0) 1-69-47-61-56
FAX:        33-(0) 1-69-47-61-42
E-mail:     yann-francois.bizouerne at bayercropscience.com
Intranet: http://bioinfo.evry.fr.bayercropscience/