[BioSQL-l] Re: [Gmod-gbrowse] Re: gbrowse on top of biosql

[Lincoln Stein]

The adaptor you want is Bio::DB::Das::BioSQL.  Once you install 
GBrowse, do "perldoc Bio::DB::Das::BioSQL" and it will describe the 
parameters you need to pass in the conf file.  Also see 
contrib/conf/06.biosql.conf for an example.

There is also a BIOSQL HOWTO in the pod documentation.  It seems to be 
unecessarily pessimistic, saying that "the biosql adaptor is not 
known to work."

One thing I just noticed, is that there is a typo in the example conf 
file.  It says the adaptor is Bio::DB::BioSQL, but it should be 
Bio::DB::Das::BioSQL.

Lincoln

On Friday 21 January 2005 02:27 pm, Hilmar Lapp wrote:
> It is possible. There were even benchmarks run for gbrowse against
> dbgff, chado, and biosql. Gbrowse will need a special adaptor that
> was written and tested by Simon at CSHL last year. I'm not sure
> whether this was included in the last gbrowse release, but the
> folks at the gbrowse mailing list can probably help you out.
>
> 	-hilmar
>
> On Friday, January 21, 2005, at 11:06  AM, Genevieve Ann DeClerck 
wrote:
> > Hi,
> >
> > I've recently installed biosql v.1.7 and bioperl-db v.1.2 (w/
> > mysql, on OS
> > X) and successfully loaded some sample data (parkin.fasta,
> > parkin.gb). I'm
> > now trying to get this biosql database to work with gbrowse
> > (1.62), but have not been successfully as of yet. From what I've
> > gathered from scanning the BioSQL-l archives and from various
> > google searches, it may not be possible to view a biosql database
> > with gbrowse yet. Is this true?
> >
> > Thanks,
> > Genevieve
> >
> > _______________________________________________
> > BioSQL-l mailing list
> > BioSQL-l at open-bio.org
> > http://open-bio.org/mailman/listinfo/biosql-l

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

NOTE: Please copy Sandra Michelsen <michelse at cshl.edu> on
all emails regarding scheduling and other time-critical topics.
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