[DAS] Dazzle with Ensembl 3.26.1
Tony Cox
avc@sanger.ac.uk
Thu, 14 Feb 2002 16:49:26 +0000 (GMT)
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
+>> +>******************************************************
+>> +>
+>> +>_______________________________________________
+>> +>DAS mailing list
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+>> +>http://biodas.org/mailman/listinfo/das
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+>> +>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
******************************************************