[DAS] Dazzle with Ensembl 3.26.1
Stefano Tine
s.tine@oxagen.co.uk
Thu, 14 Feb 2002 17:11:34 -0000
Just in case anybody else is interested (jfreeman?),
below you can see an example of my present dazzlecfg.xml.
I seem to be doing the right things (see recent posts
by Tony/Thomas) but I still have the long delays mentioned
in the original message in this thread.
Any help greatly appreciated
Stefano
-----Original Message-----
From: Stefano Tine
Sent: Tuesday, February 12, 2002 5:18 PM
To: 'Tony Cox'
Subject: RE: [DAS] Dazzle with Ensembl 3.26.1
Hello,
thxs for your reply and offer of help. Here is a simplified (just one DAS
service) dazzlecfg.xml that we are using:
<?xml version="1.0" ?>
<dazzle xmlns="http://www.biojava.org/2000/dazzle">
<resource id="ensembl130_bridge" jclass="ensembl.EnsemblHolder">
<string name="dbURL"
value="jdbc:mysql://ensembl.oxagen.co.uk/homo_sapiens_c
ore_3_26" />
<string name="dbUser" value="root" />
<string name="dbPass" value="***" />
<int name="schemaVersion" value="130" />
</resource>
<datasource id="ensembl130" jclass="ensembl.EnsemblReferenceSource">
<string name="ensemblHolderID" value="ensembl130_bridge" />
<string name="name" value="Ensembl" />
<string name="description" value="The human genome from ensembl" />
<string name="version" value="1.30" />
<string name="stylesheet" value="ensemblbase-style.xml" />
<set name="elideTypes">
<string value="repeat" />
<string value="similarity" />
</set>
</datasource>
<datasource id="testsnps"
jclass="org.biojava.servlets.dazzle.datasource.GFFAnnotationSource">
<string name="name" value="SNPs" />
<string name="description" value="SNPs" />
<string name="version" value="default" />
<string name="fileName" value="snps.gff" />
<string name="mapMaster"
value="http://ensembl.oxagen.co.uk:8080/das/ensembl130" />
<string name="stylesheet" value="snp-style.style" />
</datasource>
</dazzle>
and in Homo_sapiens.ini we have an entry like:
[test_snps]
dsn = testsnps
url = http://ensembl.oxagen.co.uk:8080/das
label = snps
caption = snps
col = contigblue1
linktext =
linkURL =
strand = r
depth = 0
This all works well when using 1.20 everywhere above and our own local
copy of Ensembl 1.2.0. Yes, I know, putting the root password in this
file is not a good idea ;)
But when using this (with our local copy of Ensembl 3.26.1)
it loads very slowly (but it does work) and the ensembl log shows:
Using assembly 0
UNDEF ON ENSEMBL_DAS_PROXY [Homo_sapiens]
Added internal DAS source: snps (Proxy: )
UNDEF ON ENSEMBL_DAS_PROXY [Homo_sapiens]
Using assembly 0
DrawableContainer::new failed to require
Bio::EnsEMBL::GlyphSet::human_trace: Ca
n't locate Bio/EnsEMBL/GlyphSet/human_trace.pm in @INC (@INC contains: ....)
DrawableContainer::new failed to require
Bio::EnsEMBL::GlyphSet::mouse_trace: Ca
n't locate Bio/EnsEMBL/GlyphSet/mouse_trace.pm in @INC (@INC contains:
.....)
DrawableContainer::new failed to require
Bio::EnsEMBL::GlyphSet::human_trace: Ca
n't locate Bio/EnsEMBL/GlyphSet/human_trace.pm in @INC (@INC contains:
.....)
DrawableContainer::new failed to require
Bio::EnsEMBL::GlyphSet::mouse_trace: Ca
n't locate Bio/EnsEMBL/GlyphSet/mouse_trace.pm in @INC (@INC contains:
.....)
Using assembly 0
URL/DSN: http://ensembl.oxagen.co.uk:8080/das/testsnps
Attempt to free unreferenced scalar.
LONG PROCESS PID: 15747 DT: Tue Feb 12 15:19:44 2002 Time:
44
LONG PROCESS REQ:
/Homo_sapiens/contigview?chr=1&highlight=&vc_start=12345678&vc_end=12355678&
bottom=%7Ctest_snps%3Aon
LONG PROCESS IP: UA: Mozilla/4.0 (compatible; MSIE 5.0; Windows NT;
DigExt)
Any suggestion? That ENSEMBL_DAS_PROXY is not defined/customizable anywhere
in Homo_Sapiens.ini or SiteDefs.pm.
We have Dazzle 0.94, which I believe is the latest
version from Thomas Down. I had problems making Tomcat 4+ work with it
(the older version of Dazzle + Ensembl 1.2.0, actually) so we are still
using
Tomcat 3.3, will upgrade asap. Note that for our MySQL Ensembl databases
I used the ..._3_26 naming convention.
Thanks!
Stefano
-----Original Message-----
From: Tony Cox [mailto:avc@sanger.ac.uk]
Sent: Tuesday, February 12, 2002 9:56 AM
To: Stefano Tine
Cc: das@biodas.org
Subject: RE: [DAS] Dazzle with Ensembl 3.26.1
On Mon, 11 Feb 2002, Stefano Tine wrote:
I presume you are using the mose recent dazzle available? - this has fixes
for changes in the way Ensembl names chromosomes internally (simply
"N" rather than "chrN"). Can you send me your dazzlcfg.xml file please? I'll
see
if I can see what the problem is. Is there any error message coming out of
dazzle.
By way of comment, Tomcat 3.3 is commonly accepted to be pretty grim. We use
either 3.2 or 4.0 for the public facing services.
regards
Tony
+>
+>Hi, thanks for your reply.
+>
+>Well, we have Dazzle 0.94 + Tomcat 3.3
+>and all works ok with 1.2.0 but when I change
+>dazzlecfg.xml to point to 3.26 rather than 1.2
+>then Ensembl 3.26 takes a long time to load our
+>DAS services.
+>
+>In the error_log for Ensembl 3.26.1 I see:
+>
+>
+>UNDEF ON ENSEMBL_DAS_PROXY [Homo_sapiens]
+>Added internal DAS source: test1 (Proxy:)
+>UNDEF ON ENSEMBL_DAS_PROXY [Homo_sapiens]
+>UNDEF ON ENSEMBL_DAS_PROXY [Homo_sapiens]
+>Added internal DAS source: test2 (Proxy: )
+>UNDEF ON ENSEMBL_DAS_PROXY [Homo_sapiens]
+>then errors that can't find human_trace.pm and mouse_trace.pm (twice)
+>URL/DSN: ... /8080/das/test1
+>(long wait)
+>URL/DSN: ... /8080/das/test2
+>(long wait)
+>LONG PROCESS PID: 11512 DT: Mon Feb 11 17:58:22 2002 Time:
+>61
+>
+>
+>This same page loads in a few secs with Ensembl 1.2.0 (and
+>dazzlecfg.xml pointing to 1.20).
+>
+>So maybe Dazzle is ok but ExternalDAS.pm is doing
+>something weird (like looking for a Proxy and hanging
+>there)? Not a question for the DAS list, I guess, but on the
+>Ensembl list I asked this time ago and got no reply ;-)
+>
+>What am I doing wrong? Thanks a lot in advance
+>
+>Stefano
+>
+>
+>-----Original Message-----
+>From: Tony Cox [mailto:avc@sanger.ac.uk]
+>Sent: Monday, February 11, 2002 1:38 PM
+>To: Stefano Tine
+>Cc: das@biodas.org
+>Subject: Re: [DAS] Dazzle with Ensembl 3.26.1
+>
+>
+>On Mon, 11 Feb 2002, Stefano Tine wrote:
+>
+>+>
+>+>Hello,
+>+> just wondering if there is any plan to update
+>+>Dazzle for use of the Ensembl 3.26.1 schema in the
+>+>near future.
+>
+>the Sanger DAS server uses the latest dazzle which supports 3_26_1
+>
+>Tony
+>
+>
+>+>
+>+>Thanks
+>+> Stefano
+>+>_______________________________________________
+>+>DAS mailing list
+>+>DAS@biodas.org
+>+>http://biodas.org/mailman/listinfo/das
+>+>
+>
+>******************************************************
+>Tony Cox Email:avc@sanger.ac.uk
+>Sanger Institute WWW:www.sanger.ac.uk
+>Wellcome Trust Genome Campus Webmaster
+>Hinxton Tel: +44 1223 834244
+>Cambs. CB10 1SA Fax: +44 1223 494919
+>******************************************************
+>
+>_______________________________________________
+>DAS mailing list
+>DAS@biodas.org
+>http://biodas.org/mailman/listinfo/das
+>_______________________________________________
+>DAS mailing list
+>DAS@biodas.org
+>http://biodas.org/mailman/listinfo/das
+>
******************************************************
Tony Cox Email:avc@sanger.ac.uk
Sanger Institute WWW:www.sanger.ac.uk
Wellcome Trust Genome Campus Webmaster
Hinxton Tel: +44 1223 834244
Cambs. CB10 1SA Fax: +44 1223 494919
******************************************************
_______________________________________________
DAS mailing list
DAS@biodas.org
http://biodas.org/mailman/listinfo/das