[DAS] Dazzle with Ensembl 3.26.1

[Tony Cox]

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
+>

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Tony Cox			Email:avc@sanger.ac.uk
Sanger Institute		WWW:www.sanger.ac.uk
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