[DAS] LDAS + Ensembl
James Freeman
jfreeman@variagenics.com
Mon, 01 Apr 2002 06:14:32 -0500
When reading:
http://208.193.117.11/cgi-bin/das
as written below instead read:
http://208.193.117.11:8080/cgi-bin/das
and then you will see the "freeman2" server, sorry about the confusion.
Jim Freeman
Senior Scientist
Variagenics, Inc.
James Freeman wrote:
>
> Hi Lincoln and Tony,
>
> I have successfully replicated the freeman ldas testing server created
> by Lincoln, and have viewed it successfully at the url below:
>
> http://www.ensembl.org/Homo_sapiens/contigview?contig=Z96810.1.1.99682
>
> in the "Manage Sources" tab of the DAS drop down list menu add:
> http://208.193.117.11/cgi-bin/das
>
> and use the DSN, "freeman2"
>
> The files freeman2.das and freeman2.conf files, I used to create this
> are the same, modulo local database user and password changes, that
> Lincoln attached in his mail:
>
> http://www.ensembl.org/Dev/Lists/das/msg01042.html
>
> To make this demo file work make sure you follow the "set privileges"
> section at:
>
> 'http://www.biodas.org/servers/LDAS.html#setting up the database'
>
> Thank to Lincoln and Tony for their invaluable help in testing this out
> and making this demo possible.
>
> Warmest Regards,
>
> Jim Freeman
> Senior Scientist
> Variagenics, Inc.
>
> Tony Cox wrote:
> >
> > On Thu, 28 Mar 2002, Lincoln Stein wrote:
> >
> > +>Hi Tony,
> > +>
> > +>You'll need to incorporate the Das2 version into the current online version
> > +>of Ensembl in order for the contigviewer not to crash on new LDAS sources.
> > +>You're planning to do this, right?
> >
> > right.
> >
> > +>
> > +>I'm pretty sure that I incorporated James's changes -- at least there is a
> > +>dsn() call now. Just to be absolutely sure you should do a diff of your
> > +>version against the latest version (should be in CVS and on FTP). Or send me
> > +>a tar file of what you're using now and I'll make sure that we are in synch.
> >
> > righto - thanks
> >
> > Tony
> >
> > +>
> > +>Lincoln
> > +>
> > +>On Thursday 28 March 2002 05:16, Tony Cox wrote:
> > +>> On Wed, 27 Mar 2002 lstein@formaggio.cshl.org wrote:
> > +>>
> > +>> Hi Lincoln,
> > +>>
> > +>> Thanks for tracking this down. I'll make the code fix for now but include
> > +>> the updated Das2 version in the next code release - which should be for the
> > +>> mouse release now that the assembly is all but "blessed".
> > +>>
> > +>> I also noticed the file extension thing after getting burned by it when
> > +>> implementing the data upload scripts. One question: is bz2 a sensible
> > +>> supported default format? - while lots of (linux) clients may be able to
> > +>> produce the files it is not a default install on many unix servers like our
> > +>> Tru64 boxes. If you can use bz2, you can use gz, and I believe the
> > +>> difference in compression to be relatively small. All in the name of
> > +>> simplicity and maintainability. It is up there with automatically assuming
> > +>> that everybodys tar supports the -z option.
> > +>>
> > +>> Did you incorporate the changes that James made here, and sent you, to add
> > +>> back the "sources" call? If we update the Das2 code and this is missing our
> > +>> upload code will break. For that reason I'll roll your changes below into
> > +>> our code ASAP and let you know. I'll check out a new copy of Das2 on our
> > +>> dev server and test it out.
> > +>>
> > +>> thanks
> > +>>
> > +>> Tony
> > +>>
> > +>> PS: yes, we do indeed filter out Component features. We also rely on the
> > +>> feature type IDs containing either "transcript" or "exon" to enable drawing
> > +>> of the "humpy/bumpy" introns, rather than simply boxing the features up
> > +>> (naturally the feature ID has to be the same as well!).
> > +>>
> > +>>
> > +>> +>Hi,
> > +>> +>
> > +>> +>I've tracked down the problem with Jim's features not displaying on
> > +>> +>Ensembl contigview. I've got it fixed and working now with my
> > +>> +>server. To see:
> > +>> +>
> > +>> +> 1) go to http://www.ensembl.org/perl/contigview?contig=Z96810.1.99682
> > +>> +> 2) add the das server http://brie2.cshl.org:8081/db/misc/das
> > +>> +> DSN "freeman"
> > +>> +> 3) zoom way way in -- there are a LOT of features in the test
> > +>> +> file -- at low mag it looks like a solid line (I was
> > +>> +> going crazy trying to debug this "bug")
> > +>> +>
> > +>> +>There were a couple of issues that needed to be fixed. I'll start
> > +>> +>with the most important ones:
> > +>> +>
> > +>> +> 1) SOFTWARE VERSION SKEW (For Tony's attention!)
> > +>> +> The Bio-Das2 library on Ensembl needs to be updated. A few
> > +>> +> weeks ago I added a new tag to the XML and updated Bio-Das2
> > +>> +> to accomodate it -- Thomas updated Dazzle. You need Bio-Das2
> > +>> +> version 0.6 or higher. This is available in the FTP directory
> > +>> +> at www.biodas.org, or via CVS (don't worry; only two lines
> > +>> +> changed).
> > +>> +>
> > +>> +> If Tony can't make this change because of release schedules,
> > +>> +> etc., there's a quick workaround with the LDAS server. See
> > +>> +> below.
> > +>> +>
> > +>> +> 2) LOAD PROBLEMS AT JIM'S END
> > +>> +> The load file must have the suffix .das (or .das.gz, .das.Z,
> > +>> +> .das.bz2 for compressed files). Otherwise the loader assumes
> > +>> +> that it is a GFF-format file. The sample file Jim sent me
> > +>> +> ended in .txt! This is a bit anal so I'm going to eliminate
> > +>> +> this restriction in the next version of the loader.
> > +>> +>
> > +>> +> 3) REDUNDANT DATA IN JIM'S FILE
> > +>> +> The same variations were annotated on multiple coordinate
> > +>> +> systems. I suppose this a reflection of frustration, but it
> > +>> +> isn't necessary. A cleaned up load file that works is
> > +>> +> attached.
> > +>> +>
> > +>> +> 4) CONFIGURATION FILE
> > +>> +> This was basically fine, but Jim might want to exclude
> > +>> +> features of type "Component" from the features dump.
> > +>> +> Otherwise it might show up in the Ensembl display (actually
> > +>> +> it doesn't seem to, probably because Tony filters it out).
> > +>> +> A slightly modified configuration file with the exclude=
> > +>> +> option is attached.
> > +>> +>
> > +>> +>WORKAROUND TO MAKE LDAS WORK WITH ENSEMBL CONTIGVIEW (AS OF 3/27/02):
> > +>> +>
> > +>> +> 1) find the CGI script named "das"
> > +>> +> 2) find the subroutine named error_segment() and comment it out
> > +>> +> 3) replace the subroutine with a dummy error_segment() that does
> > +>> +> nothing:
> > +>> +>
> > +>> +> sub error_segment { }
> > +>> +>
> > +>> +>Sorry for the delay in figuring all this out,
> > +>> +>
> > +>> +>Lincoln
> > +>> +>
> > +>> +>--
> > +>> +>
> > +>> +>
> > +>>
> > +>> ******************************************************
> > +>> 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
> > +>> ******************************************************
> > +>>
> > +>> _______________________________________________
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> > +>
> >
> > ******************************************************
> > 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
> > ******************************************************
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