On Thu, Nov 23, 2006 at 09:29:15AM +0300, Maxim Jankov wrote: > Fortunately, I don't want to download all these gigabytes, and better > configure emboss to work with all that db's online. But the bad thing is > that I'm completely stuck in all that manuals and just begging for help of > someone who done configuration like that and can provide me with ready or > easy-to-understand config files.
Dear Maxim,
I can provide you just like that with some remote databank definitions we
use at the BEN site. Put in your file .../share/EMBOSS/emboss.default :
DB NCBI_NUC [ type: N method: entrez format: genbank
comment: 'nonredundant nuc. acid db at NCBI (by GI number)'
]
DB NCBI_PROT [ type: P method: entrez format: genbank
comment: 'nonredundant protein db at NCBI (by GI number)'
]
DB EBI_EMBL [ type: N methodquery: external format: embl comment: 'EMBL at EBI'
app: '/opt/sw/EBIWS/WSDbfetchClient.pl fetchData embl:%s'
]
DB EBI_EMBLSVA [ type: N methodquery: external format: embl
comment: 'EMBL Sequence Version Archive at EBI (by SV)'
app: '/opt/sw/EBIWS/WSDbfetchClient.pl fetchData emblsva:%s'
]
DB EBI_EMBLCDS [ type: N methodquery: external format: embl
comment: 'EMBL Coding Sequences at EBI (by ProteinID)'
app: '/opt/sw/EBIWS/WSDbfetchClient.pl fetchData emblcds:%s'
]
Note : EMBOSS does have a databank access method "dbfetch", but I never
managed to get it working (can someone who did tell me how ?). Instead I
use the script WSDbfetchClient.pl (see attachment). To make it work you
will need to install in your Perl the module SOAP-Lite (version 0.60 and
not higher !). You will have to adapt the "app" parameter here above and
the "shebang line" of the script.
Regards,
Guy Bottu,
Belgian EMBnet Node
WSDbfetchClient.pl
Description: Perl program
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