[DAS] Ensembl mouse 8.3 DAS server errors

[Thomas Down]

Hi Marco.

On Thu, Oct 31, 2002 at 11:08:46AM +0100, Marco Pontoglio wrote:
> 
> We noted that if Dazzle is configured for Mouse 8.3 with a "bridge" pointing
> to Human 8.30:
> (<string name="dbURL"
> value="jdbc:mysql://gene.vironc.pasteur.fr/homo_sapiens_core_8_30a" />)
> then the display works only for murine chromosomes having a length shorter
> than the corresponding human one.

The mouse assembly data is stored in a slightly... strange way
in the database, and currently biojava-ensembl doesn't try to
automatically detect this.

>   <resource id="mouse83_bridge" jclass="ensembl.EnsemblHolder">
>     <string name="dbURL"
> value="jdbc:mysql://our_local_host.domain.fr/mus_musculus_core_8_3c" />
>     <string name="dbUser" value="mysql" />
>     <string name="dbPass" value="" />
>     <int name="schemaVersion" value="8" />
>   </resource>

You should be able to fix the problem by adding an extra option
into the mouse_bridge section:

      <boolean name="evilDenormalizationHack" value="true" />


Let me know if you still have trouble when this is in place,

     Thomas (off to check that this does actually get mentioned
             in the installation documents).