[DAS] Dazzle with Ensembl 3.26.1

[jfreeman]

Hi Tony or to whom it may concern, on:

http://www.biojava.org/dazzle/ensembldas.html

You have an example dazzlecfg.xml file for a reference server shown here
below:

<datasource id="ensembl110" jclass="ensembl.EnsemblReferenceSource">
             <string name="ensemblHolderID" value="ensembl110_bridge" />

             <string name="name" value="Ensembl 1.10" />
             <string name="description" value="The human genome from
Ensembl" />
             <string name="version" value="1.10" />

             <string name="stylesheet" value="ensemblbase-style.xml" />

             <set name="elideTypes">
               <string value="repeat" />
               <string value="similarity" />
             </set
           </datasource>

Do you have the same example for ensembl-3.26.1?

Thank you very much,

Jim Freeman

Tony Cox wrote:
> 
> On Mon, 11 Feb 2002, Stefano Tine wrote:
> 
> I presume you are using the mose recent dazzle available? - this has fixes
> for changes in the way Ensembl names chromosomes internally (simply
> "N" rather than "chrN"). Can you send me your dazzlcfg.xml file please? I'll see
> if I can see what the problem is. Is there any error message coming out of
> dazzle.
> 
> By way of comment, Tomcat 3.3 is commonly accepted to be pretty grim. We use
> either 3.2 or 4.0 for the public facing services.
> 
> regards
> 
> Tony
> 
> +>
> +>Hi, thanks for your reply.
> +>
> +>Well, we have Dazzle 0.94 + Tomcat 3.3
> +>and all works ok with 1.2.0 but when I change
> +>dazzlecfg.xml to point to 3.26 rather than 1.2
> +>then Ensembl 3.26 takes a long time to load our
> +>DAS services.
> +>
> +>In the error_log for Ensembl 3.26.1 I see:
> +>
> +>
> +>UNDEF ON ENSEMBL_DAS_PROXY [Homo_sapiens]
> +>Added internal DAS source: test1 (Proxy:)
> +>UNDEF ON ENSEMBL_DAS_PROXY [Homo_sapiens]
> +>UNDEF ON ENSEMBL_DAS_PROXY [Homo_sapiens]
> +>Added internal DAS source: test2 (Proxy: )
> +>UNDEF ON ENSEMBL_DAS_PROXY [Homo_sapiens]
> +>then errors that can't find human_trace.pm and mouse_trace.pm (twice)
> +>URL/DSN:  ... /8080/das/test1
> +>(long wait)
> +>URL/DSN:  ... /8080/das/test2
> +>(long wait)
> +>LONG PROCESS  PID:      11512      DT: Mon Feb 11 17:58:22 2002      Time:
> +>61
> +>
> +>
> +>This same page loads in a few secs with Ensembl 1.2.0 (and
> +>dazzlecfg.xml pointing to 1.20).
> +>
> +>So maybe Dazzle is ok but ExternalDAS.pm is doing
> +>something weird (like looking for a Proxy and hanging
> +>there)? Not a question for the DAS list, I guess, but on the
> +>Ensembl list I asked this time ago and got no reply ;-)
> +>
> +>What am I doing wrong? Thanks a lot in advance
> +>
> +>Stefano
> +>
> +>
> +>-----Original Message-----
> +>From: Tony Cox [mailto:avc@sanger.ac.uk]
> +>Sent: Monday, February 11, 2002 1:38 PM
> +>To: Stefano Tine
> +>Cc: das@biodas.org
> +>Subject: Re: [DAS] Dazzle with Ensembl 3.26.1
> +>
> +>
> +>On Mon, 11 Feb 2002, Stefano Tine wrote:
> +>
> +>+>
> +>+>Hello,
> +>+>  just wondering if there is any plan to update
> +>+>Dazzle for use of the Ensembl 3.26.1 schema in the
> +>+>near future.
> +>
> +>the Sanger DAS server uses the latest dazzle which supports 3_26_1
> +>
> +>Tony
> +>
> +>
> +>+>
> +>+>Thanks
> +>+> Stefano
> +>+>_______________________________________________
> +>+>DAS mailing list
> +>+>DAS@biodas.org
> +>+>http://biodas.org/mailman/listinfo/das
> +>+>
> +>
> +>******************************************************
> +>Tony Cox                      Email:avc@sanger.ac.uk
> +>Sanger Institute              WWW:www.sanger.ac.uk
> +>Wellcome Trust Genome Campus  Webmaster
> +>Hinxton                               Tel: +44 1223 834244
> +>Cambs. CB10 1SA                       Fax: +44 1223 494919
> +>******************************************************
> +>
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> +>
> 
> ******************************************************
> Tony Cox                        Email:avc@sanger.ac.uk
> Sanger Institute                WWW:www.sanger.ac.uk
> Wellcome Trust Genome Campus    Webmaster
> Hinxton                         Tel: +44 1223 834244
> Cambs. CB10 1SA                 Fax: +44 1223 494919
> ******************************************************
> 
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