[DAS] trouble attaching das source

Sean O'Keeffe seanok at gsf.de
Mon May 17 11:53:33 EDT 2004


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>




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