[DAS] Dazzle with Ensembl 3.26.1
jfreeman
jfreeman@variagenics.com
Thu, 14 Feb 2002 11:55:38 -0500
Thank you!
Tony Cox wrote:
>
> On Thu, 14 Feb 2002, jfreeman wrote:
>
> <!-- Human 326 Core data -->
> <datasource id="ensembl326" jclass="ensembl.EnsemblReferenceSource">
> <string name="ensemblHolderID" value="ensembl326_bridge" />
> <string name="name" value="Ensembl 3_26" />
> <string name="description" value="The human genome from Ensembl" />
> <string name="version" value="3.26" />
> <set name="elideTypes">
> <string value="repeat" />
> <string value="similarity" />
> </set>
> <string name="stylesheet" value="ensemblbase-style.xml" />
> </datasource>
> <alias id="ensembl130" target="ensembl326" />
>
> regards
>
> Tony
>
> +>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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> +>> +>_______________________________________________
> +>> +>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
> +>> ******************************************************
> +>>
> +>> _______________________________________________
> +>> DAS mailing list
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> +>> http://biodas.org/mailman/listinfo/das
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> +>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
> ******************************************************