[DAS] DAS setup questions
James Freeman
jfreeman@variagenics.com
Fri, 12 Apr 2002 11:46:23 -0400
Hi Graeme,
This problem is one I have faced before, my choice was to get an LDAS
server for annotations and use the Dazzle engine to serve an internal
Ensembl reference server, which worked fine. I still suggest an LDAS
annotation server, at least to get to the demo and then to debug your
Dazzle annotation server at your leisure. However, you mentioned before
that you set up a Tomcat 4.0 server for Dazzle, I would strongly suggest
Resin:
http://www.caucho.com/
It is better and free to academics, but worth the money.
I suggest that you set up an internal Ensembl reference server using
Dazzle under Resin, which is really easy at this point, then point your
internal Dazzle annotation server to your internal Dazzle reference
server and check the logs, I also suggest Resin because the error log
file for Resin is quite detailed. You can't debug the external Ensembl
website because you can't see the error logs and to be fair the
developers at Ensembl have other things they are working full time on
and can't spend alot of time looking at vague bug reports, however they
are quite responsive when you give them a repeatable provable error. I
completely internal Ensembl service gives you all of the software and
all of the information needed to start testing and debugging. It is
pretty easy to do as well.
Good luck,
Jim
Graeme Campbell wrote:
>
> Thanks for your suggestions Jim.
>
> I've had no problem uploading data directly to ensembl so far, but I'm
> still not able to serve up the same data via the sample Dazzle web app.
> For example, if I upload the first line from the sample upload file
> http://dev.ensembl.org/das/example.das, I can easily view it by browsing
> the region between 1 and 10000 on chromosome 1. I just can't figure out
> how to fit the same data into the sample database and webapp structure
> to serve the information from there.
>
> >From the Ensembl DAS setup document, the schema provided to work with
> the EnsemblGenericSeqFeatureSource bridge/adapter looks like this:
>
> CREATE TABLE my_feature (
> contig_id varchar(40) NOT NULL default '',
> start int(10) NOT NULL default '0',
> end int(10) NOT NULL default '0',
> strand int(2) NOT NULL default '0',
> id varchar(40) NOT NULL default '',
> score double(16,4) NOT NULL default '0.0000',
> gff_feature varchar(40) default NULL,
> gff_source varchar(40) default NULL,
> name varchar(40) default NULL,
> hstart int(11) NOT NULL default '0',
> hend int(11) NOT NULL default '0',
> hid varchar(40) NOT NULL default '',
> evalue varchar(40) default NULL,
> perc_id int(10) default NULL,
> phase int(11) NOT NULL default '0',
> end_phase int(11) NOT NULL default '0',
> KEY id_contig (contig_id),
> KEY id_pos (id,start,end)
> ) TYPE=MyISAM;
>
> The sample data looks like this:
>
> | contig_id | start | end | strand | id |
> +----------------------+-----------+-----------+--------+------------+
> | AC000041.2.1.45436 | 1 | 57 | -1 | Alu |
> | AC000041.2.1.45436 | 325 | 628 | -1 | AluSg |
> | AC000041.2.1.45436 | 1299 | 1350 | 1 | Alu |
> | AC000041.2.1.45436 | 1354 | 1661 | 1 | AluJb |
> | AC000041.2.1.45436 | 2164 | 2451 | -1 | AluSg |
>
> After inserting the sample data into the database I am unable to view it
> online after my das source has been added. I'm assuming that these
> annotations should appear if I browse to the AC000041 contig. Am I
> wrong about this?
>
> Maybe the problem is in my configuration file. I'll post it here minus
> internal info (as I've seen other people do) and if someone could point
> out any mistakes I've made, I'd really appreciate it.
>
> <?xml version="1.0" ?>
>
> <dazzle xmlns="http://www.biojava.org/2000/dazzle">
> <resource id="ensembl428_bridge" jclass="ensembl.EnsemblHolder">
> <string name="dbURL"
> value="jdbc:mysql://kaka.sanger.ac.uk/homo_sapiens_core_4_28" />
> <string name="dbUser" value="anonymous" />
> <string name="dbPass" value="" />
> <int name="schemaVersion" value="4" />
> </resource>
>
> <datasource id="ensembl428" jclass="ensembl.EnsemblReferenceSource">
> <string name="ensemblHolderID" value="ensembl428_bridge" />
> <string name="name" value="Ensembl 4_28" />
> <string name="description" value="Human Ensembl" />
> <string name="version" value="4.28" />
> <set name="elideTypes">
> <string value="repeat" />
> <string value="similarity" />
> </set>
> <string name="stylesheet" value="ensemblbase-style.xml" />
> </datasource>
>
> <alias id="ensembl140" target="ensembl428" />
>
> <datasource id="MyDataSource"
> jclass="ensembl.EnsemblGenericSeqFeatureSource">
> <string name="ensemblHolderID" value="ensembl428_bridge" />
> <string name="name" value="Ensembl Test Source" />
> <string name="description" value="Test DAS feature source" />
> <string name="version" value="1.00" />
> <string name="mapMaster"
> value="http://servlet.sanger.ac.uk:8080/das/ensembl428/" />
> <string name="dbURL" value="jdbc:mysql://<my server
> name>/ensembl_generic" />
> <string name="dbUser" value="<userid>" />
> <string name="dbPass" value="<password>" />
> <string name="tableName" value="my_feature" />
> <string name="stylesheet" value="generic-style.xml" />
> </datasource>
>
> </dazzle>
>
> Thanks,
>
> Graeme
>
> James Freeman wrote:
> >
> > Dear Graeme,
> >
> > If you are trying to view your annotations on the public ensembl website
> > (http:://www.ensembl.org/), there is an some easy ways to do it,
> > depending on your time constraints.
> >
> > Get your annotations matched to the sequences in:
> >
> > ftp://ftp.ensembl.org/pub/human-4.28/data/fasta/dna/Homo_sapiens.latestgp.fa.gz
> >
> > Once you know where your annotations are relative to the above, you
> > there are two options that I recommend:
> >
> > The fastest by far is to upload your data directly into ensembl:
> >
> > http://www.ensembl.org/Homo_sapiens/helpview?se=1&kw=upload
> >
> > or if you want to set up your own client neutral (i.e. not just Ensembl,
> > but also Omnigene, Geodesic, et al.) das annotation service, try the
> > following:
> >
> > http://www.biodas.org/servers/
> > http://www.ensembl.org/Dev/Lists/das/msg01042.html
> > http://www.ensembl.org/Dev/Lists/das/msg01056.html
> >
> > If you are trying to create an internal version of the distributed
> > Ensembl website, follow the instructions on the website and I suggest a
> > Dazzle reference server and an LDAS annotation server, each of which are
> > excellent at their particular jobs.
> >
> > Good luck,
> >
> > Jim Freeman
> > Senior Scientist
> > Variagenics, Inc.
> >
> > Graeme Campbell wrote:
> > >
> > > Hi there,
> > >
> > > I have been attempting to set up a sample DAS installation using the
> > > document "Setting up a Ensembl DAS Server"
> > > (http://www.ensembl.org/Docs/das_server_v1.2.pdf), but have been
> > > stumbling a bit and I was hoping someone could offer some advice.
> > >
> > > I'm confused about the dazzle-webapp-skeleton
> > > (http://www.biojava.org/download/dazzle/dazzle-webapp-skeleton-0.95.tar.gz).
> > > I get a welcome page when I point my browser at localhost:8080/das/.
> > > I'm also able to get back XML (in compressed format) by pointing my
> > > browser at localhost:8080/das/dsn. However, it comes with "test" and
> > > "tss" data sources. What exactly should I be able to do with these
> > > sources once they are installed? Should I be able to connect to my
> > > local das webapp from the Ensembl website and view test annotations
> > > online?
> > >
> > > I've also set up the test database, loaded the sample data, and
> > > configured another sample web-app
> > > (http://www.biojava.org/download/ensembl-das/ensembl-das-webapp-20020214.tar.gz)
> > > as specified in the setup document. From this, I'm able to get back XML
> > > from a DSN request that lists my new datasource, and I'm able to add the
> > > das source to the web-viewer on the ensembl.org site. However, when I
> > > browse the AC000041 contig region, there are no annotations, just a
> > > message saying "No * Ensembl Te.. features in this region." I believe
> > > the test data from the setup document is all in this region though - but
> > > I may be misunderstanding things.
> > >
> > > Any guidance you could give me would be appreciated.
> > >
> > > Thanks,
> > >
> > > Graeme
> > >
> > > --
> > > Graeme Campbell phone: (604) 875-3868
> > > Bioinformatics Core Facility e-mail: graemeca@cmmt.ubc.ca
> > > Centre for Molecular Medicine and Therapeutics
> > > Vancouver, BC. Canada.
> > > _______________________________________________
> > > DAS mailing list
> > > DAS@biodas.org
> > > http://biodas.org/mailman/listinfo/das
>
> --
> Graeme Campbell phone: (604) 875-3868
> Bioinformatics Core Facility e-mail: graemeca@cmmt.ubc.ca
> Centre for Molecular Medicine and Therapeutics
> Vancouver, BC. Canada.
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