[DAS] Dazzle with Ensembl 3.26.1

[Stefano Tine]

Well, I tried forgetting our own DAS service
and just requesting a contigview with one of the
predefined DAS services on (=LINE repeat):

http://localhost/Homo_sapiens/contigview?chr=chr15&vc_start=61218530&vc_end=
61938748

this takes 5 seconds with 1.2.0
this takes 35 seconds with 3.26.1

Since in both cases I am calling an external DAS service (which
I assume uses its own reference data) I would expect them to be 
equally fast (or slow) independent of a potentially screwed up 
install of 3.26.1 here, or am I missing something?

Anyway, I will try reinstalling 3.26.1 data/software from scratch,
since I suppose by now that Dazzle/Tomcat is not the issue here but
Ensembl is.

Thanks

Stefano




-----Original Message-----
From: Tony Cox [mailto:avc@sanger.ac.uk]
Sent: Friday, February 15, 2002 11:54 AM
To: Thomas Down
Cc: Stefano Tine; das@biodas.org
Subject: Re: [DAS] Dazzle with Ensembl 3.26.1


On Fri, 15 Feb 2002, Thomas Down wrote:

+>On Fri, Feb 15, 2002 at 10:21:29AM -0000, Stefano Tine wrote:
+>> 
+>> 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.
+>
+>
+>Hmmm, worrying...
+>
+>How big is your snps.gff file?
+>
+>I'm still not sure I understand what's going on here.  It
+>makes me wonder if maybe an index got lost when you loaded
+>tables into your database (the Java code uses the database
+>in a slightly different way to the Perl, so it's possible that
+>an indexing change could clobber biojava-ensembl, but still
+>leave contigview running normally).

I gave up on GFF-based data sources. I tried them for some repeat data and
after
a certain file size (can't remember what) the data source just bogs down
completely.

Try changing the data to a simple generic feature source. Worked for me.

Tony

+>
+>Anyone else got any ideas about this?
+>
+>    Thomas.
+>_______________________________________________
+>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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