[DAS] Dazzle with Ensembl 3.26.1

[Stefano Tine]

Thanks for the quick release.

I have now:

Dazzle 0.95
Tomcat 4.0.2
Ensembl 3.26.1 (with human_trace.pm and mouse_trace.pm
still desaparecidos)

and.. I still have the long loading times even with the
simple (one DAS service) dazzlecfg.xml listed below :-((

31" just for a random call such as
/Homo_sapiens/contigview?chr=5&highlight=&vc_start=82457556&vc_end=82557555

with one SNP-type DAS service on. This only takes a couple seconds
when using 1.2.0 schema and Ensembl 1.2.0 distribution.

Cheers,

Stefano

<?xml version="1.0" ?>
<dazzle xmlns="http://www.biojava.org/2000/dazzle">
  <resource id="ensembl130_bridge" jclass="ensembl.EnsemblHolder">
    <string name="dbURL"
value="jdbc:mysql://ensembl.oxagen.co.uk/homo_sapiens_core_3_26" />
    <string name="dbUser" value="root" />
    <string name="dbPass" value="***" />
    <int name="schemaVersion" value="130" />
  </resource>
  <datasource id="ensembl130" jclass="ensembl.EnsemblReferenceSource">
    <string name="ensemblHolderID" value="ensembl130_bridge" />
    <string name="name" value="Ensembl" />
    <string name="description" value="The human genome from ensembl" />
    <string name="version" value="1.30" />
    <string name="stylesheet" value="ensemblbase-style.xml" />
    <set name="elideTypes">
      <string value="repeat" />
      <string value="similarity" />
    </set>
  </datasource>
  <datasource id="testsnps" 
jclass="org.biojava.servlets.dazzle.datasource.GFFAnnotationSource">
    <string name="name" value="SNPs" />
    <string name="description" value="SNPs" />
    <string name="version" value="default" />
    <string name="fileName" value="snps.gff" />
    <string name="mapMaster" 
value="http://ensembl.oxagen.co.uk:8080/das/ensembl130" />
    <string name="stylesheet" value="snp-style.style" />
  </datasource>
</dazzle>


-----Original Message-----
From: Thomas Down [mailto:td2@sanger.ac.uk]
Sent: Thursday, February 14, 2002 7:57 PM
To: Stefano Tine
Cc: 'Thomas Down'; das@biodas.org
Subject: Re: [DAS] Dazzle with Ensembl 3.26.1


On Thu, Feb 14, 2002 at 06:10:45PM -0000, Stefano Tine wrote:
> 
> Dazzle 0.94
> Tomcat 3.3
> Ensembl 3.26.1 (but human_trace.pm and mouse_trace.pm
> are missing/not distributed, this was downloaded a couple
> days after 3.26.1 was released)
> 
> Looking forward to the new package

It's up now, in:
   
    http://www.biojava.org/download/ensembl-das/

Grab:

    ensembl-das-webapp-20020214.tar.gz


You should be able to use exactly the same configuration
as with any other recent version.  The only changes are:

   - For the ensembl bridge, schemaVersion settings of less
     that 80 are now treated as `official' versions.  The only
     one current recognized is version 3.  For connecting to
     older databases, old style versions in the range 80-130
     are still supported.
 
   - You can create datasource aliases, as in the example Tony
     posted earlier.   

> (or I will try upgrading Tomcat as last resource)

I really would try getting rid of Tomcat 3.3.  We've had a /lot/
of reported problems with that container, which always seem to
go away when users either upgrade or downgrade.  I really don't
know what's causing this (maybee some very subtle ClassLoader
bug?), but I know it's bad news...

Good luck!

    Thomas.
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