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

[Hilmar Lapp]

This is great to hear that you got it working! Thanks so much Marc and  
everybody else. -hilmar

On Jan 25, 2005, at 2:08 PM, Genevieve DeClerck wrote:

> Thanks a lot for all the help everyone - especially Marc Logghe for  
> #2,3. Summary of what I changed in my conf file and modules to get  
> gbrowse working with biosql:
>
> 1) changed 'biodbname' tag in db_args definition in .conf file to  
> 'namespace'
>
> 2) replaced line 1682 in Bio/Graphics/Browser.pm with:
>
> my $n =  
> $_->display_name.$_->abs_ref.(eval{$_->version}||'').(eval{$_- 
> >class}||'');
>
> 3) entirely replaced sub 'asString' in Bio/DB/Das/BioSQL/Segment.pm  
> with:
>
> sub asString {
>   my $self = shift;
>   my $label = $self->display_name;
>   my $start = $self->start || '';
>   my $stop  = $self->stop  || '';
>   return "$label:$start,$stop";
> }
>
> -Genevieve
>
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>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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