[DAS] (no subject)
Tony Cox
avc@sanger.ac.uk
Fri, 18 Oct 2002 13:37:25 +0100 (BST)
On Fri, 18 Oct 2002, Sidd Nakade wrote:
Go to
http://biojava.org/dazzle/
and get Dazzle plus the installation info. This will expose your Ensembl
installation as a DAS server.
regards
Tony
+>
+>Hello,
+> Can any one help me to setup configure a DAS server in Ensembl . We have a mirror of ensembl in our lab and we want to setup a DAS server with this.
+>your help wil be highly appreciated.
+>Regards
+>Sidd
+>
+> das-request@biodas.org wrote:Send DAS mailing list submissions to
+>das@biodas.org
+>
+>To subscribe or unsubscribe via the World Wide Web, visit
+>http://biodas.org/mailman/listinfo/das
+>or, via email, send a message with subject or body 'help' to
+>das-request@biodas.org
+>
+>You can reach the person managing the list at
+>das-admin@biodas.org
+>
+>When replying, please edit your Subject line so it is more specific
+>than "Re: Contents of DAS digest..."
+>
+>
+>Today's Topics:
+>
+>1. Re: Link Command (Lincoln Stein)
+>2. Re: Link Command (Dave Wall)
+>
+>--__--__--
+>
+>Message: 1
+>From: Lincoln Stein
+>Reply-To: lstein@cshl.org
+>Organization: Home
+>To: "Dave Wall" , das@biodas.org
+>Subject: Re: [DAS] Link Command
+>Date: Tue, 1 Oct 2002 07:32:22 -0400
+>
+>You're not going crazy. It's just that all the servers to date have chosen to
+>implement the client-side form of link (where the link information is
+>returned gratis with every feature record) rather than implement server-side
+>link. The servers should be returning an empty record, are they?
+>
+>Lincoln
+>
+>On Friday 27 September 2002 11:46 am, Dave Wall wrote:
+>> Geoff and I are stumped. What I am looking for is a working example of the
+>> link command. I have other commands working but I cannot get the link
+>> command to return an annotation. I have tried a couple different severs
+>> (Geoff tried others) but no success yet. An example is
+>>
+>> http://genome.ucsc.edu/cgi-bin/das/hg12/link?field=feature;id=GC.chr18.6000
+>>0
+>>
+>> It may be that my syntax is wrong, or maybe my whole approach is wrong. Am
+>> I going to the wrong server? Is my use of the link command incorrect?
+>> Thanks for any help!
+>>
+>> David Wall
+>> 553-5329
+>> IBM Life Sciences
+>>
+>> ----- Forwarded by Dave Wall/Rochester/IBM on 09/27/2002 10:38 AM -----
+>>
+>> Geoff Purdy
+>> > Wall/Rochester/IBM@IBMUS cience.com> cc:
+>> Subject: RE: [DAS]
+>> Getting Started With DAS 09/27/2002 09:36 AM
+>>
+>>
+>>
+>>
+>>
+>> Well, I'm out of ideas. There is evidence that "link" works on the Sanger
+>> DAS server as the pop-up menus are populated with additional information.
+>> However, I've been unable to access that information using a script.
+>>
+>> I suggest posting your question on the biodas list. The collective
+>> expertise on the list is orders of magnitude greater than my own.
+>>
+>> I don't know of any alternatives to "link" for accessing annotation
+>> details.
+>> The reason I quoted "link" is that command names appear in italics in the
+>> DAS documentation and italics isn't available in a plain text message.
+>>
+>> > -----Original Message-----
+>> > From: Dave Wall [mailto:dawall@us.ibm.com]
+>> > Sent: Thursday, September 26, 2002 5:29 PM
+>> > To: Geoff Purdy
+>> > Subject: RE: [DAS] Getting Started With DAS
+>> >
+>> >
+>> >
+>> > Thanks for looking into it. If I read between the lines a little it
+>>
+>> almost
+>>
+>> > sounds as if there is another way to get the annotation. You tried
+>>
+>> three
+>>
+>> > servers and none of them delivered the data via the link command. Is
+>>
+>> there
+>>
+>> > another way to do it?
+>> >
+>> > David Wall
+>> > 553-5329
+>> > IBM Life Sciences
+>>
+>> Dave,
+>> You raise a good point here. I notice that if I use the link command on
+>> three different das servers, I see three different behaviors.
+>>
+>> Last I saw, the UCSC DAS server was Jim Kent's C implementation of the DAS
+>> specification. As you pointed out, the link command gives no output (in
+>> the
+>> handful of cases I've tried).
+>>
+>> I also tried a similar query on the Sanger Center DAS server (a Java
+>> implementation, I believe). This server gives the following message if a
+>> feature doesn't have associated annotations:
+>> No extra information about this object
+>>
+>field: feature
+>id: 18/p11.32
+>
+>>
+>> Finally, I tried CSHL's wormbase DAS server (a perl implementation by
+>> Lincoln Stein). This doesn't seem to implement the link command at all.
+>>
+>> I notice that the "link" command is an annotation server specific command
+>> (not part of reference server specification). I'm unsure which of these
+>> servers purport to be reference, annotation, or both. Another possibility
+>> is that different implementations of DAS may omit implementing portions of
+>> the specification.
+>>
+>> I'll give this a closer look, but I'm beginning to think this might be a
+>> good subject for on-list discussion.
+>>
+>> > -----Original Message-----
+>> > From: Dave Wall [mailto:dawall@us.ibm.com]
+>> > Sent: Thursday, September 26, 2002 4:15 PM
+>> > To: Geoff Purdy
+>> > Subject: RE: [DAS] Getting Started With DAS
+>> >
+>> >
+>> >
+>> > Thanks for offering to help!
+>> >
+>> > I have been having pretty good luck getting a list of data
+>> > sources, types,
+>> > segments, etc., but crash when I trying to get an annotation.
+>> > Here is an
+>> > example for the purpose of verifying URL syntax ...
+>> >
+>> >
+>> > http://genome.cse.ucsc.edu:80/cgi-bin/das/hg12/features?segmen
+>> > t=18:1,100000
+>> >
+>> > In the returned data is
+>> > -
+>> > GC
+>> > Percent
+>> >
+>> > 60001
+>> > 80000
+>> > 0
+>> > 0
+>> >
+>-
+>
+>> > -
+>> >
+>> >
+>> > http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr18:60000-8
+>> > 0000&db=hg12
+>> > ">Link to UCSC Browser
+>> >
+>> >
+>> >
+>> > I then send the following which returns a blank page.
+>> >
+>> > http://genome.cse.ucsc.edu/cgi-bin/das/hg12/link?field=feature
+>> > ;id=GC.chr18.60000
+>> >
+>> > I am probably missing something obvious, but I sure can't
+>> > figure out what
+>> > it is. Thanks again!
+>> >
+>> > David Wall
+>> > 553-5329
+>> > IBM Life Sciences
+>>
+>> _______________________________________________
+>> DAS mailing list
+>> DAS@biodas.org
+>> http://biodas.org/mailman/listinfo/das
+>
+>--
+>Lincoln Stein
+>lstein@cshl.org
+>
+>--__--__--
+>
+>Message: 2
+>Subject: Re: [DAS] Link Command
+>To: lstein@cshl.org, das@biodas.org
+>From: "Dave Wall"
+>Date: Tue, 1 Oct 2002 10:30:23 -0500
+>
+>
+>That makes some sense. The servers are returning an empty record so it
+>sounds like that is what they are supposed to do. That means the
+>information I am looking for is in the results of the 'feature' command(?).
+>
+>Does an example scenario (using the wormbase server) become?
+>http://www.wormbase.org/db/das/dsn. Returns the list of data sources on
+>this server. The only server that is returned is 'elegans'
+>http://www.wormbase.org/db/das/elegans/entry_points. Returns a list of
+>entry points. For the purpose of this discussion I will select
+> Sequence" id=X subparts="yes" orientation="+" stop="17683571" start="1" size="17683571">X
+>
+>http://www.wormbase.org/db/das/elegans/features?segment=X:1,100000.
+>Returns a list of features against this segment. Many feature records
+>are returned (around 300). An example record is:
+>
+>
+>curated exon
+> curated
+> 24479
+> 24819
+> -
+> -
+>
+>0
+>
+>
+>
+> http://www.wormbase.org/db/get?name=Y73B3A.1;class=Sequence">
+>Y73B3A.1
+>
+>
+>
+>
+>I see the "link" which is part of the . Is that the
+>annotation or does this entry not have one since there is no
+>
+>under the feature tag? Actually none of the entries have a
+>
+>parameter under the feature tag. If one exists it is in the
+>section. Am I getting closer?
+>
+>Thanks again!
+>
+>
+>
+>David Wall
+>553-5329
+>IBM Life Sciences
+>
+>
+>
+>
+>Lincoln Stein
+>To: Dave Wall/Rochester/IBM@IBMUS, das@biodas.org
+>cc:
+>10/01/2002 06:32 Subject: Re: [DAS] Link Command
+>AM
+>Please respond to
+>lstein
+>
+>
+>
+>
+>
+>You're not going crazy. It's just that all the servers to date have chosen
+>to
+>implement the client-side form of link (where the link information is
+>returned gratis with every feature record) rather than implement
+>server-side
+>link. The servers should be returning an empty record, are they?
+>
+>Lincoln
+>
+>On Friday 27 September 2002 11:46 am, Dave Wall wrote:
+>> Geoff and I are stumped. What I am looking for is a working example of
+>the
+>> link command. I have other commands working but I cannot get the link
+>> command to return an annotation. I have tried a couple different severs
+>> (Geoff tried others) but no success yet. An example is
+>>
+>>
+>http://genome.ucsc.edu/cgi-bin/das/hg12/link?field=feature;id=GC.chr18.6000
+>>0
+>>
+>> It may be that my syntax is wrong, or maybe my whole approach is wrong.
+>Am
+>> I going to the wrong server? Is my use of the link command incorrect?
+>> Thanks for any help!
+>>
+>> David Wall
+>> 553-5329
+>> IBM Life Sciences
+>>
+>> ----- Forwarded by Dave Wall/Rochester/IBM on 09/27/2002 10:38 AM -----
+>>
+>> Geoff Purdy
+>> > Wall/Rochester/IBM@IBMUS cience.com> cc:
+>> Subject: RE: [DAS]
+>> Getting Started With DAS 09/27/2002 09:36 AM
+>>
+>>
+>>
+>>
+>>
+>> Well, I'm out of ideas. There is evidence that "link" works on the
+>Sanger
+>> DAS server as the pop-up menus are populated with additional information.
+>> However, I've been unable to access that information using a script.
+>>
+>> I suggest posting your question on the biodas list. The collective
+>> expertise on the list is orders of magnitude greater than my own.
+>>
+>> I don't know of any alternatives to "link" for accessing annotation
+>> details.
+>> The reason I quoted "link" is that command names appear in italics in the
+>> DAS documentation and italics isn't available in a plain text message.
+>>
+>> > -----Original Message-----
+>> > From: Dave Wall [mailto:dawall@us.ibm.com]
+>> > Sent: Thursday, September 26, 2002 5:29 PM
+>> > To: Geoff Purdy
+>> > Subject: RE: [DAS] Getting Started With DAS
+>> >
+>> >
+>> >
+>> > Thanks for looking into it. If I read between the lines a little it
+>>
+>> almost
+>>
+>> > sounds as if there is another way to get the annotation. You tried
+>>
+>> three
+>>
+>> > servers and none of them delivered the data via the link command. Is
+>>
+>> there
+>>
+>> > another way to do it?
+>> >
+>> > David Wall
+>> > 553-5329
+>> > IBM Life Sciences
+>>
+>> Dave,
+>> You raise a good point here. I notice that if I use the link command on
+>> three different das servers, I see three different behaviors.
+>>
+>> Last I saw, the UCSC DAS server was Jim Kent's C implementation of the
+>DAS
+>> specification. As you pointed out, the link command gives no output (in
+>> the
+>> handful of cases I've tried).
+>>
+>> I also tried a similar query on the Sanger Center DAS server (a Java
+>> implementation, I believe). This server gives the following message if a
+>> feature doesn't have associated annotations:
+>> No extra information about this object
+>>
+>field: feature
+>id: 18/p11.32
+>
+>>
+>> Finally, I tried CSHL's wormbase DAS server (a perl implementation by
+>> Lincoln Stein). This doesn't seem to implement the link command at all.
+>>
+>> I notice that the "link" command is an annotation server specific command
+>> (not part of reference server specification). I'm unsure which of these
+>> servers purport to be reference, annotation, or both. Another
+>possibility
+>> is that different implementations of DAS may omit implementing portions
+>of
+>> the specification.
+>>
+>> I'll give this a closer look, but I'm beginning to think this might be a
+>> good subject for on-list discussion.
+>>
+>> > -----Original Message-----
+>> > From: Dave Wall [mailto:dawall@us.ibm.com]
+>> > Sent: Thursday, September 26, 2002 4:15 PM
+>> > To: Geoff Purdy
+>> > Subject: RE: [DAS] Getting Started With DAS
+>> >
+>> >
+>> >
+>> > Thanks for offering to help!
+>> >
+>> > I have been having pretty good luck getting a list of data
+>> > sources, types,
+>> > segments, etc., but crash when I trying to get an annotation.
+>> > Here is an
+>> > example for the purpose of verifying URL syntax ...
+>> >
+>> >
+>> > http://genome.cse.ucsc.edu:80/cgi-bin/das/hg12/features?segmen
+>> > t=18:1,100000
+>> >
+>> > In the returned data is
+>> > -
+>> > GC
+>> > Percent
+>> >
+>> > 60001
+>> > 80000
+>> > 0
+>> > 0
+>> >
+>-
+>
+>> > -
+>> >
+>> >
+>> > http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr18:60000-8
+>> > 0000&db=hg12
+>> > ">Link to UCSC Browser
+>> >
+>> >
+>> >
+>> > I then send the following which returns a blank page.
+>> >
+>> > http://genome.cse.ucsc.edu/cgi-bin/das/hg12/link?field=feature
+>> > ;id=GC.chr18.60000
+>> >
+>> > I am probably missing something obvious, but I sure can't
+>> > figure out what
+>> > it is. Thanks again!
+>> >
+>> > David Wall
+>> > 553-5329
+>> > IBM Life Sciences
+>>
+>> _______________________________________________
+>> DAS mailing list
+>> DAS@biodas.org
+>> http://biodas.org/mailman/listinfo/das
+>
+>--
+>Lincoln Stein
+>lstein@cshl.org
+>
+>
+>
+>
+>
+>
+>
+>--__--__--
+>
+>_______________________________________________
+>DAS mailing list
+>DAS@biodas.org
+>http://biodas.org/mailman/listinfo/das
+>
+>
+>End of DAS Digest
+>
+>
+>---------------------------------
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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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