[DAS] trouble attaching das source

Tue May 18 12:48:25 EDT 2004

I'm not the best person to confirm this, but as far as I know all three 
servers are being used, for different types of data.

(You might be interested to look at release 1.01 of Dazzle, which 
includes a plugin to serve data from the same Bio::DB::GFF databases 
which LDAS uses)

           Thomas

On 17 May 2004, at 21:50, Hong Xu wrote:

> 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
>>
>> _______________________________________________
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>> http://biodas.org/mailman/listinfo/das
>>
>
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