[DAS] trouble attaching das source

[Hong Xu]

So what's the DAS server Ensembl is using on its site? Is it a modified
version of dazzle, LDAS, or ProServer? I need to find out this before I
update our local Ensembl to the latest release.

thanks,
Hong Xu      +1 919 684 3962
hong.xu at duke.edu  wwwchg.duhs.duke.edu


----- Original Message ----- 
From: "Thomas Down" <td2 at sanger.ac.uk>
To: "Sean O'Keeffe" <seanok at gsf.de>
Cc: <das at biodas.org>
Sent: Monday, May 17, 2004 4:33 PM
Subject: Re: [DAS] trouble attaching das source


> Hi Sean,
>
> I'm afraid the version 20 databases include some major changed to the
> schema.  Updating the old biojava-ensembl and ensembl-das code wasn't
> going to be practical, since a lot of the internal assumptions about
> how assemblies work, etc., have been broken.
>
> I've written some new code which should do the job -- unfortunately I
> haven't had a chance to put together a release yet.  But you can get
> the latest code using Subversion (http://subversion.tigris.org/) from:
>
>      http://www.derkholm.net/svn/repos/biojava-ensembl/trunk/
>
> Or send me an e-mail directly if you'd prefer me to send you a snapshot.
>
> This includes both some new biojava-ensembl bridge code which can
> handle both schema-20+ and old-format database, and a new set of
> ensembl-das plugins which are compatible with dazzle 1.0x:
>
>      http://www.biojava.org/dazzle/
>
> A typical configuration for the new system looks something like:
>
> <dazzle xmlns="http://www.biojava.org/2000/dazzle">
>    <resource id="connection_hsa_core_20_34"
> jclass="org.ensembl.das.DatabaseHolder">
>      <string name="dbURL"
> value="jdbc:mysql://noranti/homo_sapiens_core_20_34b" />
>      <string name="dbUser" value="foo" />
>      <string name="dbPass" value="bar" />
>    </resource>
>
>    <datasource id="hsa2034"
> jclass="org.ensembl.das.EnsemblCoreReference">
>      <string name="name" value="Human assembly" />
>      <string name="description" value="Human genome from Ensembl" />
>      <string name="version" value="20.34" />
>
>      <string name="coreHolder" value="connection_hsa_core_20_34" />
>      <int name="schemaVersion" value="20" />
>
>      <string name="ensemblWebURL"
> value="http://www.ensembl.org/Homo_sapiens/" />
>    </datasource>
> </dazzle>
>
>
> Sorry I've been so slow getting this properly released -- give me a
> shout if you need any help with it,
>
>       Thomas.
>
>
>
> On 17 May 2004, at 16:53, Sean O'Keeffe wrote:
>
> > Hi there,
> > I'm a bioinformatics researcher at the GSF national research institute
> > in munich, germany.
> > I have set-up a das server (dazzle 0.97a) according to instructions on
> > the ensembl site.
> > It seems fine and shows up all the data-sources when I point to the
> > das server.
> > My problem arises when i try to attach the server to the ensembl web
> > site - click on 'manage sources' on the das sources tab in contig
> > view. Nothing happens when i type in our server
> > 'andromeda.gsf.de:7070' and click on "show sources" - after about 5-10
> > seconds it just refreshes and is blank.
> > I had it running fine on a previous ensembl version but this is now
> > version 20 and we've added extra data here also.
> > My dazzle config xml file (part of it) is below:
> > Any help would be great.
> > Thanks, Sean.
> >
> > <?xml version="1.0" ?>
> >
> > <!-- Example configuration file for ensembl-das
> >
> >     Check all paths, database details, and mapMaster URLs before
> >     deploying.
> >
> >     In case of problems, contact Thomas Down <td2 at sanger.ac.uk>
> >
> >  -->
> > <dazzle xmlns="http://www.biojava.org/2000/dazzle">
> >  <resource id="mouse20_32b_bridge" jclass="ensembl.EnsemblHolder">
> >    <string name="dbURL"
> > value="jdbc:mysql://andromeda.gsf.de/mus_musculus_core_20_32b" />
> >    <string name="dbUser" value="hmmmm" />
> >    <string name="dbPass" value="whatever" />
> >    <int name="schemaVersion" value="20" />
> >  </resource>
> >
> >  <datasource id="mouse2032b" jclass="ensembl.EnsemblReferenceSource">
> >    <string name="ensemblHolderID" value="mouse20_32b_bridge" />
> >    <string name="name" value="Ensembl" />
> >    <string name="description" value="The mouse genome from ensembl" />
> >    <string name="version" value="20.32b" />
> >    <string name="stylesheet" value="ensemblbase-style.xml" />
> >    <set name="elideTypes">
> >      <string value="repeat" />
> >      <string value="similarity" />
> >    </set>
> > </datasource>
> >
> >   <datasource id="HNB_TF_mouse"
> > jclass="ensembl.EnsemblGenericSeqFeatureSource">
> >    <string name="ensemblHolderID" value="mouse20_32b_bridge" />
> >    <string name="name" value="Mouse TF binding sites" />
> >    <string name="description" value="Mouse TF binding sites predicted
> > using MatInspector" />
> >    <string name="version" value="1.0" />
> >    <string name="mapMaster"
> > value="http://andromeda.gsf.de:7070/das/mouse2032b/" />
> >    <string name="dbURL"
> > value="jdbc:mysql://andromeda.gsf.de/ensembl_generic/" />
> >    <string name="dbUser" value="user" />
> >    <string name="dbPass" value="***" />
> >    <string name="tableName" value="TF_mouse" />
> >    <string name="stylesheet" value="HNB-style.xml" />
> >  </datasource>
> >
> >
> > _______________________________________________
> > DAS mailing list
> > DAS at biodas.org
> > http://biodas.org/mailman/listinfo/das
>
> _______________________________________________
> DAS mailing list
> DAS at biodas.org
> http://biodas.org/mailman/listinfo/das
>