database access

[David Martin]

On Mon, 23 Apr 2001, Charles wrote:

>
>
> On Tue, 17 Apr 2001 CHOO_Keng_Wah at nyp.gov.sg wrote:
>
> > Deal all,
> >      I've just installed the EMBOSS-1.11.0 on my LINUX Red Hat 7.2 and I
> > couldn't setup a connection to any database.
> >      Can soneone help me?
> >
>
> I'm more or less at the same point than you : i've installed emboss on a
> debian woody (for self-training and satisfying curiosity), and could not
> get the time so sit down in front of the database installation manual,
> which is hard to understand for the unfamiliar reader.

OK.. if you have any suggestions on improving it I will see what I can do.
When I wrote the manual it was because I wasn't clear how things were
supposed to be set up, so I asked a lot of questions and hassled Peter
Rice and Alan to give me the answers.

Would a 'quick guide to setting up the EMBL database' section or similar
help?

>
> I copied the emboss.default file to .embossrc in my home directory, and
> uncommented the examples of genebank accassion by the internet.

The example file isn't the best of examples. A case for better annotation.
I'll add it to my list of 'things to do'.

>
> Well, if you have an unlimited internet access, i think it is the quicker
> way to proceed. However, i dont't even know if www.ca.embnet.org is
> designed to provide sequences to everybody, and i don't
> understand the syntax used.
>

To be perfectly honest neither do I but it seems to work..
the syntax is the various arguments given to the wgetz script in the srs
server.

I notice looking through the admin guide that I have omitted www as a
method for database retrieval. I'll add that in to the next version plus
some notes on OS X and SuSE 7.1.

If anyone else would care to contribute any installation quirks or
workarounds they may have had to do (eg. a list of packages required for
Debian to run EMBOSS and so on..) then I would be grateful for them.

..d


> Hope this helps,
>
> Charles
>