[EMBOSS] Problem with showdb and seqret

[Guy Bottu]

Mohd Afiq Hazlami wrote:
> But when
> it comes to 'showdb' tutorial, the program returns this:

Alas, the manual and tutorial are out-of-date. This is an unfortunate chronic 
disease of EMBOSS, even if for the rest EMBOSS is great.

Before you can access 'public' sequences using the
<database name>:<sequence identifier>
syntax you must first define databases in the file
<EMBOSS installation dir>/share/EMBOSS/emboss.default
There is a file emboss.default.template with examples.

To get a quick try using the EMBOSS tutorial data you could put the following in 
emboss.default :

DB test_embl [ type: N comment: 'testset for EMBL' format: embl
             method: emblcd dir: /opt/sw/EMBOSS6/EMBOSS-6.0.1/test/embl
]

Do replace /opt/sw/EMBOSS6/EMBOSS-6.0.1/test/embl by
<EMBOSS download dir>/test/embl
You will note that this directory does contain sequences and indexes.

You can then do
showdb
entret test_embl:Z11115

You can read more about it at 
http://emboss.sourceforge.net/docs/themes/Databases.html

A question for the EMBOSS development team : what is the status of the new 
EMBOSS manual ?

	Regards,
	Guy Bottu,
	Belgian EMBnet Node