[DAS] Couldn't instantiate datasource ensembl1834_bridge

[Thomas Down]

On 17 Feb 2004, at 11:30, Steven Van Vooren wrote:

> Dear DAS-list,
>
> I want to serve textual annotations (from a text mining process) on  
> clones on the human genome, and visualise these in the Ensembl genome  
> browser web site (by entering the url to my own DAS source). For this,  
> I am trying to install and configure a DAS server. I understand that  
> all I need is an "annotation server" and that I should use the ensembl  
> DAS servlet.sanger.ac.uk:8080/das as "reference server" somehow.
>
> However, from the documentation at  
> http://www.ensembl.org/Docs/das_server_v1.2.pdf and the docs on  
> http://www.biojava.org/dazzle/ I gather that I should configure  
> kaka.sanger.ac.uk as a data source for the reference server.

Both approaches ought to work.  Running your own reference server might  
be faster (and is definitely a good idea if you have your own local  
copy of the ensembl core databases).

Incidentally, the Sanger public mysql server formerly known as kaka has  
now become ensembldb.ensembl.org, and you should use that name instead.  
  Not sure if kaka still works.

> Anyhow, after adapting the example configuration XML according to the  
> pdf documentation, I get the following error message:
>
> [11:52:47.156] DazzleServerMain: init
> [11:52:47.172] org.biojava.servlets.dazzle.DazzleServlet: Error  
> initializing installation
> [11:52:47.172]  
> org.biojava.servlets.dazzle.datasource.DataSourceException: Couldn't  
> instantiate datasource ensembl1834_bridge
> [11:52:47.172]  at  
> org.biojava.servlets.dazzle.datasource.BasicDazzleInstallation.initReso 
> urce(BasicDazzleInstallation.java:138)
> ...
>
> I'm using most recent Resin and mySQL versions. As compiling the 0.99  
> version from the CVS repository failed, I am using the Dazzle  
> "dazzle-webapp-skeleton-0.95" (downloaded from  
> http://www.biojava.org/download/dazzle/). I have pasted my  
> configuration file below.

Why did compilation fail?  Which version of BioJava were you using?   
The Dazzle CVS should now be fixed to work with current  CVS  
biojava-live, but it's always possible that I didn't check the changes  
right, or that CVS is doing something strange.

The skeleton you've downloaded is very old.  You can grab something  
more current from:

       http://www.derkholm.net/thomasd/das/

(I'm currently having trouble updating the biojava.org site -- I'll  
move it over there later on).

Hope this helps,

      Thomas.