[EMBOSS] External DB problems

[Peter Rice]

Stefanie Lager wrote:

> Hi,
> 
> In version 2.8.0 of EMBOSS I have problems to access external databases
> (UniProt)using methods URL and SRSWWW. It's not a proxy problem since 
> 
> app: "wget http://www.ebi.ac.uk/cgi-bin/dbfetch?db=UniProt&id=%s" 
> 
> works nice. 
> 
> But I can't get
> 
> DB uniprot [ 
> type: P
> format: embl
> method: url
> url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[uniprot-AllText:%s]"
> ]
> 
> or
> 
> DB uniprot [ 
> type: P
> format: embl
> method: srswww
> url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
> ]
> 
> 
> to work. In both cases it trys for a very long time and then times out
> with the message: 
> 
> "Error: socket connect failed for database 'uniprot'
> socket connect failed for database 'uniprot': Connection timed out"
> 
> Does anyone know what could be wrong?

Firstly, it could still be a proxy problem. Your wget application will not use 
an EMBOSS proxy definition which should be defined as EMBOSS_PROXY as an 
environment variable, or in emboss.default (or your own ~/.embossrc) as 
something like:

SET emboss_proxy "proxy.mydomain.ac.uk:8080"

UniProt in SRS is running a little slowly but should work for you. You shuold 
however define it as:

url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[uniprot-AllText:%s]+-ascii"

(otherwise you will be trting to read HTML output from SRS).

The SRSWWW definition is fine .. well, it works for me.

Hope this helps, let me know if it's not a proxy problem.

Peter Rice