Hello.
I am trying to install the DAS server Dazzle to serve data from a
local copy of Ensembl, but it is not working. Does Dazzle not support
the newest releases of Ensembl? I can get it to work with Ensembl 30
from ensembldb.ensembl.org, but not with the 34 version we have
mirrored.
I have setup three datasources in dazzlecfg.xml: "local" (local
Ensembl 34), "new" (34 from ensembl.org), and "old" (30 from
ensembl.org). The weird part is that datasources "local" and "new"
give me different error messages even though the only difference in
the config file is the host name. Getting the entry_points works for
both of them, and so does getting the features for the first kb of
chromosome 1:
$ curl http://localhost:8090/das/local/features?segment=1:1,1000
gives 3 features of the type "contig", and so does:
$ curl http://localhost:8090/das/new/features?segment=1:1,1000
But when I try to get features for the first 10 kb, I get two
different error messages from the local and remote Ensembl 34 databases:
$ curl http://localhost:8090/das/local/features?segment=1:1,10000
...
javax.servlet.ServletException:
org.biojava.bio.seq.db.ensembl.spi.AdaptorException:
java.sql.SQLException: null, message from server: "Unknown
column 'exon.exon_id' in 'on clause'"
...
$ curl http://localhost:8090/das/new/features?segment=1:1,10000
...
javax.servlet.ServletException:
org.biojava.bio.seq.db.ensembl.spi.AdaptorException:
java.sql.SQLException: Base table or view not found, message from
server: "Table 'homo_sapiens_core_34_35g.gene_description'
doesn't exist"
...
The first error message is really weird, because that column really
does exist:
mysql> desc exon;
+-------------------+------------------+------+-----+---------
+----------------+
| Field | Type | Null | Key | Default |
Extra |
+-------------------+------------------+------+-----+---------
+----------------+
| exon_id | int(10) unsigned | NO | PRI | NULL |
auto_increment |
...
The second error message is caused, because the table
gene_description is missing. Newest Ensembl releases don't seem to
have it anymore and the newest one where I could find it was version
30. That is why I also configured a datasource for that version from
ensembldb.ensembl.org, which seems to work.
So, is Dazzle not compatible with the newest Ensembl releases? Any
ideas why I get different error messages from a local mirror and
ensembldb.ensembl.org?
I'm running J2SE 5.0, Tomcat 5.0.28 and the ensembl-das-webapp-1.4.30
version of Dazzle.
Thanks,
Ilari
--
Ilari Scheinin, BSc.
Biomedicum Bioinformatics Unit
National Public Health Institute
Helsinki, Finland
[EMAIL PROTECTED]
http://www.bioinfo.helsinki.fi/
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