[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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