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From: Dave C. G. H. D. <he...@gm...> - 2010-02-04 17:29:39
|
Hello all, Need a logo that tells people what your web site, database or GMOD component is about? If your resource needs a logo then the GMOD Logo Program (http://gmod.org/wiki/GMOD_Logo_Program) can help. I am pleased to announce the first call for participation in the GMOD Logo Program. This program is for GMOD users and developers that would like have a custom designed logo for their web site, database or GMOD component. The program pairs GMOD community members with students in advanced design classes at colleges and universities. This spring we will be working with a class at Linn-Benton Community College. Participants will meet several times (remotely) over a 3 week period, with the end result being a new logo for your resource. Participation is limited to non-profits, and costs US$75. If you are interested, please see http://gmod.org/wiki/GMOD_Logo_Program for additional details and requirements, and an application form. The program is accepting applications until March 1. Thanks, Dave Clements GMOD Help Desk PS: This program was inspired by ZFIN's success with its logo (see http://zfin.org). ZFIN's excellent logo was created by working with a design class at the University of Oregon. -- Please keep responses on the list! http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas http://gmod.org/wiki/GMOD_Logo_Program http://gmod.org/wiki/GMOD_News Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback |
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From: Dave C. G. H. D. <he...@gm...> - 2010-01-29 22:01:36
|
Hello all, I am pleased to announce that we are now accepting applications for: 2010 GMOD Summer School - Americas 6-9 May 2010 NESCent, Durham, NC, USA http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas This will be a hands-on multi-day course aimed at teaching new GMOD users/administrators how to get GMOD Components up and running. The course will introduce participants to the GMOD project and then focus on installation, configuration and integration of popular GMOD Components. The course will be held May 6-9, at NESCent in Durham, NC. These components will be covered: * Apollo - genome annotation editor * Chado - a modular and extensible database schema * Galaxy - workflow system * GBrowse - the Generic Genome Browser * GBrowse_syn - A generic synteny browser * JBrowse - genome browser * MAKER - genome annotation pipeline * Tripal - web front end for Chado The deadline for applying is the end of Friday, February 22. Admission is competitive and is based on the strength of the application (especially the statement of interest). In 2009 there were over 50 applications for the 25 slots. Any applications received after the deadline will be placed on the waiting list. See the course page for details and an application link: http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas Thanks, Dave Clements GMOD Help Desk PS: We are also investigating holding a GMOD course in the Asia/Pacific region, sometime this fall. Watch the GMOD mailing lists and the GMOD News page/RSS feed for updates. -- Please keep responses on the list! http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas http://gmod.org/wiki/GMOD_News Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback |
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From: Lankerovich, M. <Mic...@sw...> - 2010-01-29 02:45:39
|
Hi. I were going to install JBrowse and ran into a few problems. 1. Download button did not work for me, so I should manually copied all files. 2. When I ran "perl bin/flatfile-to-json.pl -gff=docs/tutorial/data_files/volvox.gff3 I've got an errors: STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:368 STACK: Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree_in_tables /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:687 STACK: Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:666 STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:319 STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:325 STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:222 STACK: Bio::DB::SeqFeature::Store::memory::post_init /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/memory.pm:167 STACK: Bio::DB::SeqFeature::Store::new /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store.pm:376 STACK: bin/flatfile-to-json.pl: To get rid out this error I had to change a library file, which is not good. 3. When I tried to run Index.html, I've got an empty web page. Can somebody help me with my problems, please? Thanks, Michael Lankerovich. |
|
From: James C. <ca...@gm...> - 2010-01-15 16:56:16
|
2010/1/15 Mitch Skinner <mit...@be...>: > Well, the idea was to use bioperl to deal with parsing GFF3 so that we > wouldn't have to write our own GFF3 parser. The problem was in bioperl in > this particular case, but (if you haven't already) you could also see if > your GFF3 validates: > http://dev.wormbase.org/db/validate_gff3/validate_gff3_online > > The bug where some features at the end of the refseq wouldn't show up has > been fixed in bioperl, although it'll be a little while before the fix gets > released. I've attached a patch that you could apply to your bioperl > installation, or you could get this file: > > http://code.open-bio.org/svnweb/index.cgi/bioperl/checkout/bioperl-live/trunk/Bio/DB/SeqFeature/Store/memory.pm?rev=16695 > > and replace the version you currently have installed. Thanks, very much, Mitch. I'll try that out and let you know. To be honest, the parser has given me a lot of hassle with other stuff (line endings and memory use) so I might try out BED and see if that is any better. James |
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From: Mitch S. <mit...@be...> - 2010-01-15 16:03:25
|
On 01/13/2010 01:49 AM, James Casbon wrote: > > I think you are right that it may be a problem with bioperl, but I am > fairly certain I am on 1.61, although this is confusing: > $ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"' > 1.006001 > Yeah, that's 1.6.1; I think it's formatted that way so that textual comparisons of version strings give the right answer (e.g., when comparing 1.6.2 to 1.6.12). > Is there any way to load data that doesn't go via bioperl? My > experience getting GFF3 to parse has not been joyful. > Well, the idea was to use bioperl to deal with parsing GFF3 so that we wouldn't have to write our own GFF3 parser. The problem was in bioperl in this particular case, but (if you haven't already) you could also see if your GFF3 validates: http://dev.wormbase.org/db/validate_gff3/validate_gff3_online The bug where some features at the end of the refseq wouldn't show up has been fixed in bioperl, although it'll be a little while before the fix gets released. I've attached a patch that you could apply to your bioperl installation, or you could get this file: http://code.open-bio.org/svnweb/index.cgi/bioperl/checkout/bioperl-live/trunk/Bio/DB/SeqFeature/Store/memory.pm?rev=16695 and replace the version you currently have installed. That said, you can also use BED, or a database (although the database would have to be one that has a bioperl Bio::DB::(whatever) interface, like chado, Bio::DB::SeqFeature::Store, or Bio::DB::GFF). I've been thinking about writing something to import data into JBrowse that doesn't use bioperl, but some of the interfaces in the JBrowse code have to be reworked a bit before that can happen. Regards, Mitch |
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From: Christopher F. <cjf...@gm...> - 2010-01-15 06:36:11
|
<html><body class="ApplePlainTextBody" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Mitch,<br><br>I went ahead and committed that fix (r16695), seems to pass all SeqFeature::Store tests using mem, BDB, mysql. thanks for the patch!<br><br>chris<br><br>On Jan 14, 2010, at 4:10 PM, Mitch Skinner wrote:<br><br><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Some people haven't been getting all of the features in their GFF3 into JBrowse, and a nice test case that James Casbon posted to the list helped me track it down.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Here's an example of the behavior I was seeing with BioPerl 1.6.1 (using Devel::REPL):<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">==============<br></blockquote><blockquote type="cite">$ use Bio::DB::SeqFeature::Store<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">$ my $db = Bio::DB::SeqFeature::Store->new(-adaptor=>"memory", -dsn=>"casbon.gff3")<br></blockquote><blockquote type="cite">$Bio_DB_SeqFeature_Store_memory1 = Bio::DB::SeqFeature::Store::memory=HASH(0xa27ceec);<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">$ $db->features(-seq_id=>"CYP2C8")<br></blockquote><blockquote type="cite">$ARRAY1 = [<br></blockquote><blockquote type="cite"> Feature:src(41),<br></blockquote><blockquote type="cite"> region(CYP2C8),<br></blockquote><blockquote type="cite"> Feature:src(37),<br></blockquote><blockquote type="cite"> Feature:src(39),<br></blockquote><blockquote type="cite"> Feature:src(42),<br></blockquote><blockquote type="cite"> Feature:src(40),<br></blockquote><blockquote type="cite"> Feature:src(38)<br></blockquote><blockquote type="cite"> ];<br></blockquote><blockquote type="cite">==============<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I expected to also see the features with IDs 43 and 44 (the gff3 file is attached).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I think there's a problem in the filter_by_location method. If start and end parameters aren't passed to the method, it sets default start and end values that lead it to examine all of the bins in its index. But the end value that it creates is at the beginning of the last bin, and I think it should be at the end of the last bin instead. The attached patch changes it to be at the end of the last bin.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Regards,<br></blockquote><blockquote type="cite">Mitch<br></blockquote><blockquote type="cite"><casbon.gff3><bdsfsm-filter_by_location.patch>_______________________________________________<br></blockquote><blockquote type="cite">Bioperl-l mailing list<br></blockquote><blockquote type="cite">Bio...@li...<br></blockquote><blockquote type="cite">http://lists.open-bio.org/mailman/listinfo/bioperl-l<br></blockquote><br></body></html> |
|
From: Mitch S. <mit...@be...> - 2010-01-14 22:26:25
|
Hi,
Some people haven't been getting all of the features in their GFF3 into
JBrowse, and a nice test case that James Casbon posted to the list
helped me track it down.
Here's an example of the behavior I was seeing with BioPerl 1.6.1 (using
Devel::REPL):
==============
$ use Bio::DB::SeqFeature::Store
$ my $db = Bio::DB::SeqFeature::Store->new(-adaptor=>"memory",
-dsn=>"casbon.gff3")
$Bio_DB_SeqFeature_Store_memory1 =
Bio::DB::SeqFeature::Store::memory=HASH(0xa27ceec);
$ $db->features(-seq_id=>"CYP2C8")
$ARRAY1 = [
Feature:src(41),
region(CYP2C8),
Feature:src(37),
Feature:src(39),
Feature:src(42),
Feature:src(40),
Feature:src(38)
];
==============
I expected to also see the features with IDs 43 and 44 (the gff3 file is
attached).
I think there's a problem in the filter_by_location method. If start
and end parameters aren't passed to the method, it sets default start
and end values that lead it to examine all of the bins in its index.
But the end value that it creates is at the beginning of the last bin,
and I think it should be at the end of the last bin instead. The
attached patch changes it to be at the end of the last bin.
Regards,
Mitch
|
|
From: James C. <ca...@gm...> - 2010-01-13 09:49:49
|
2010/1/12 Mitch Skinner <mit...@be...>: > On 01/12/2010 02:29 AM, James Casbon wrote: >> >> Changing the sequence-region pragma to be a larger region fixes the >> problem: >> ##sequence-region CYP2C8 1 46725 >> >> What is going on here? Why do I not get all the features I declared? >> > > Thanks for providing such a nice clean test case. > > This sounds like it might be related to an issue in > Bio::DB::SeqFeature::Store::memory that was fixed last year after bioperl > 1.6 was released. The fix is in bioperl 1.6.1, though--what version are you > using? > > Also, JBrowse used to need the sequence-region line, but in the current code > it's no longer required. So one work-around if you can't upgrade bioperl > would be to leave out the sequence-region line, I think. I think you are right that it may be a problem with bioperl, but I am fairly certain I am on 1.61, although this is confusing: $ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"' 1.006001 Is there any way to load data that doesn't go via bioperl? My experience getting GFF3 to parse has not been joyful. cheers, James |
|
From: Mitch S. <mit...@be...> - 2010-01-12 18:10:14
|
On 01/12/2010 02:29 AM, James Casbon wrote: > Changing the sequence-region pragma to be a larger region fixes the problem: > ##sequence-region CYP2C8 1 46725 > > What is going on here? Why do I not get all the features I declared? > Thanks for providing such a nice clean test case. This sounds like it might be related to an issue in Bio::DB::SeqFeature::Store::memory that was fixed last year after bioperl 1.6 was released. The fix is in bioperl 1.6.1, though--what version are you using? Also, JBrowse used to need the sequence-region line, but in the current code it's no longer required. So one work-around if you can't upgrade bioperl would be to leave out the sequence-region line, I think. Regards, Mitch |
|
From: James C. <ca...@gm...> - 2010-01-12 10:29:09
|
I have the following file: """ ##gff-version 3 ##sequence-region CYP2C8 1 36725 CYP2C8 src Feature 4100 4291 . - . ID=37 CYP2C8 src Feature 6125 6213 . - . ID=38 CYP2C8 src Feature 8093 8330 . - . ID=39 CYP2C8 src Feature 11013 11204 . - . ID=40 CYP2C8 src Feature 23538 23764 . - . ID=41 CYP2C8 src Feature 20003 20213 . - . ID=42 CYP2C8 src Feature 32411 32944 . - . ID=43 CYP2C8 src Feature 34400 35725 . - . ID=44 """ Running "flatfile-to-json.pl --gff /tmp/e.gff --tracklabel 'feature' --cssclass feature --out browsers/human-gene-test --type Feature" produces the following track: "featureNCList":[[4099,4291,-1,"37"],[6124,6213,-1,"38"],[8092,8330,-1,"39"],[11012,11204,-1,"40"],[23537,23764,-1,"41"]] You can see that everything above 30,000 bases is ignored. Changing the sequence-region pragma to be a larger region fixes the problem: ##sequence-region CYP2C8 1 46725 What is going on here? Why do I not get all the features I declared? thanks, James |
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From: Alessandra <ale...@gm...> - 2010-01-10 23:17:09
|
Hi all, I'm Alessandra and I run GBrowse.org. GBrowse.org is a resource for using and setting up GBrowse genome browsers. The site provides one location where biologists and bioinformaticians can find: 1. Genome browser web sites for any organism that has them. If a species has a genome browser anywhere on the web, then we aim to link to it. 2. Links to sequence and annotation files that are available online. 3. Links to genome browser configuration files, when available 4. An FTP site containing genome annotation and configuration files for each annotated genome that does not have its own web site. GBrowse.org emphasizes the GBrowse genome browser in its organization, but also links to sites that use other browser packages such as UCSC, Ensembl, and JBrowse. Also, we are currently conducting a survey seeking input on future project direction. Please take a few minutes now to provide your feedback. Survey link: http://gbrowse.org/survey/index.php?sid=64264&lang=en GBrowse.org introdution link: http://gmod.org/wiki/August_2009_GMOD_Meeting#GBrowse.org Thank you for your help, Alessandra Bilardi. http://gbrowse.org/ CRIBI Genomics, University of Padua http://genomics.cribi.unipd.it/ |
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From: Dave C. G. H. D. <he...@gm...> - 2010-01-06 18:49:37
|
Hello all,
GMOD will once again have a strong presence at the Plant and Animal
Genome Conference (PAG 2010), being held January 9-13 in San Diego.
There will be over 45 talks, workshops, demonstrations and posters
about GMOD Components and projects that use them.
This includes a session and a poster on JBrowse:
Using The JBrowse Genome Browser With Large Amounts Of Data
Session: Monday, Jan 11, 1:10-1:30, California Room
Poster: P919, Monday, Jan 11, 3:00-4:30
Both will be presented by Mitch Skinner.
See the PAG 2010 page on the wiki for a full listing and a flier
showing highlights:
http://gmod.org/wiki/PAG_2010
Thanks,
Dave C.
--
Please keep responses on the list!
http://gmod.org/wiki/January_2010_GMOD_Meeting
http://gmod.org/wiki/GMOD_News
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback
|
|
From: Mitch S. <mit...@be...> - 2009-12-22 23:48:25
|
Hi, sorry this isn't documented better.
The jbrowse scripts get data from a data source and put a subset of that
data into JSON-formatted files that the client can consume.
In those JSON files, each feature has a set of attributes, and each of
those attributes has a name. The required attributes are named "start",
"end", and "strand"; there are also some optional attributes named
"type", "phase", "subfeatures", and "label" that you can optionally
include in the JSON by setting a config setting or using a command line
parameter.
These names are what you can put in curly brackets in a urlTemplate.
You can use the extraData config setting to include more attributes in
the JSON. extraData is a set of name: callback pairs. The bioperl
feature object is passed to the callback (which should be a perl sub);
whatever the callback returns is included in the JSON in the slot with
the given name. Then you can use that name in curly brackets in a
urlTemplate and whatever was in that slot for the given feature will be
substituted into the urlTemplate.
In the example from the Dmel demo config:
"urlTemplate": "http://flybase.org/cgi-bin/fbidq.html?{load_id}",
"extraData": {"load_id": "sub {shift->attributes(\"load_id\");}"}
"load_id" is something the Bio::DB::SeqFeature::Store code generates.
That code needs to guarantee unique IDs in its database, so it generates
its own IDs. If the GFF file that the data came from originally had an
ID attribute, it goes into the "load_id" attribute. And you can get the
attribute from the bioperl object with ->attributes("load_id")
Any piece of information that you could pull out of the bioperl object
can be extracted by the callback and included in the JSON, and you can
name it whatever you want as long as it's not a name that's already
reserved (maybe JBrowse should do something like GFF3 and reserve
capitalized names or something).
Giles is right; if it's "ID" in the GFF3 named attribute column, it'll
be "load_id" on the bioperl object because of the way
Bio::DB::SeqFeature::Store works. Upper-case attributes may get renamed
or otherwise moved around because the GFF3 parser treats them specially,
but if it's a lower-case attribute then it shouldn't get mangled, I
think. Unless it's "load_id", in which case I guess it gets replaced by
the bioperl code?
HTH,
Mitch
On 12/22/2009 09:01 AM, Fox, Richard wrote:
>
> Hi,
>
> Apologies if this as already been answered but I'm not able to get the
> urlTemplate functionality working using the extraData approach that's
> given in the Dmel.json example. It's not clear from the just the
> Dmel.json file what "load_id" is referring to. I assumed it was
> referring to something in the GFF file but the obvious failed to work,
> namely (in the last field):
>
> Name=myname;load_id=my_load_id_for_use_in_urlTemplate
>
> Does anyone know how to place data into a GFF file for use in the
> urlTemplate?
>
> Thanks for the help!
>
> Richard
>
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and easy
> Join now and get one step closer to millions of Verizon customers
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>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
|
|
From: <gv...@sa...> - 2009-12-22 23:31:31
|
Hi Richard,
Sorry I should have been more specific, I think the ID attribute needs to
be in the GFF file. Like this:
BB chado gene 1 1920 . + .
ID=BB0001;Name=BB0001
In my JSON config I have :
...
"TRACK DEFAULTS": {
"class": "feature",
"autocomplete": "all",
"type" : "true",
"phase" : "true",
"extraData": {"load_id": "sub {shift->attributes(\"load_id\");}"},
"urlTemplate": "/gene/{load_id}"
},
...
I think the load_id variable is populated from the GFF's ID attribute
inside column 9.
Regards,
Giles
> Thanks so much Giles,
>
>
>
> This is what I've tried:
>
>
>
> contig_103 example contig 1 1350
> . . . Name=contig_103
>
> contig_103 AUGUSTUS gene 127 1350
> 0.67 + .
> Name=Genepred:contig_103:127..1350;ID=foo
>
> contig_103 AUGUSTUS CDS 127 653
> 0.72 + 0
> Name=CDSpred:contig_103:127..653;ID=bar
>
> contig_103 AUGUSTUS CDS 785 1350
> 0.9 + 1
> Name=CDSpred:contig_103:785..1350;ID=bam
>
>
>
> And in the .json file:
>
>
>
> "tracks": [
>
> {
>
> "track": "PredictedCDS",
>
> "key": "Predicted CDS",
>
> "feature": ["CDS:AUGUSTUS"],
>
> "class": "cds",
>
> "phase": 1,
>
> "urlTemplate":
> "http://localhost/cgi-bin/jbrowse/C1wt/feature.cgi?{ID}"
>
> },
>
> {
>
> "track": "PredictedGenes",
>
> "key": "Predicted Genes",
>
> "feature": ["gene:AUGUSTUS"],
>
> "class": "dblhelix",
>
> "subfeatures":true,
>
> "urlTemplate":
> "http://localhost/cgi-bin/jbrowse/C1wt/feature.cgi?{ID}",
>
> "extraData": {"ID": "sub {shift->attributes(\"ID\");}"}
>
> }
>
> ]
>
>
>
> Neither approach seems to work. The first construct (PredictedCDS)
> gives '...feature.cgi?undefined' while the second construct
> (PredictedGenes) gives '...feature.cgi?null'.
>
>
>
> Any ideas? I'm sure I'm missing something basic.
>
>
>
> Best,
>
>
>
> Richard
>
>
>
> From: Giles Velarde [mailto:gv...@sa...
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
|
|
From: Giles V. <gv...@sa...> - 2009-12-22 17:19:17
|
In my GFF files I have an ID field, this seems to work for me. On 22 Dec 2009, at 17:01, Fox, Richard wrote: > Hi, > > Apologies if this as already been answered but I’m not able to get > the urlTemplate functionality working using the extraData approach > that’s given in the Dmel.json example. It’s not clear from the just > the Dmel.json file what “load_id” is referring to. I assumed it was > referring to something in the GFF file but the obvious failed to > work, namely (in the last field): > > Name=myname;load_id=my_load_id_for_use_in_urlTemplate > > Does anyone know how to place data into a GFF file for use in the > urlTemplate? > > Thanks for the help! > > Richard > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE. |
|
From: Fox, R. <Ric...@co...> - 2009-12-22 17:14:30
|
Hi, Apologies if this as already been answered but I'm not able to get the urlTemplate functionality working using the extraData approach that's given in the Dmel.json example. It's not clear from the just the Dmel.json file what "load_id" is referring to. I assumed it was referring to something in the GFF file but the obvious failed to work, namely (in the last field): Name=myname;load_id=my_load_id_for_use_in_urlTemplate Does anyone know how to place data into a GFF file for use in the urlTemplate? Thanks for the help! Richard |
|
From: Mitch S. <mit...@be...> - 2009-12-20 20:56:46
|
On 12/17/2009 01:42 AM, Mariette wrote:
> then I added the div to my page content (still just like it is in the
> index.html page of jbrowse) :
> <div id="GenomeBrowser" style="height: 100%; width: 100%; padding: 0;
> border: 0;"></div>
>
> I can see my page changing but I'm far from having the result I can get
> when using it localy !!
>
Thanks for including some detail about what you were doing. However,
it's tough to know for sure what's going on without being able to see
it; if it's accessible over the internet then it will be easier for me
to see what's going on.
My first guess is that it's a CSS thing; did you include this bit of CSS
from index.html?
<style type="text/css">
html, body { height: 100%; width: 100%; padding: 0; border: 0; }
</style>
that's what makes the "height: 100%" style work cross-browser. Also, if
there are other things on the page (unlike the stock index.html, where
it's just that one "GenomeBrowser" div that takes up the whole viewport)
then you might want to specify a different size and placement for that
div (possibly using units other than percent). You should be able to
specify whatever size and placement you want for that element and
JBrowse should adjust; if not it's a bug and we'll fix it.
> So I was wondering if using it the ?loc and&tracks are important, we
> give to our page some
> arguments and it may be a problem ?
>
They're important for bookmarking; if that's not necessary in your case
you can turn it off by leaving out the "bookmark", "location", and
"tracks" parameters to the Browser constructor.
If you're not using "loc" or "tracks" as url parameters for your
server-side code, though, I don't think there would be a problem, but it
probably depends on the details of your server code. If you are using
parameters with those names in your server-side code, you could always
change the parameter names, either on the JBrowse side or on the
server-code side.
Longer-term, the plan is for JBrowse to stop using URL query parameters
and use the fragment identifier (the part after the #) instead, which
should remove the possibility of a conflict with server-side code.
> Also, there was something wrong in the Utils.js file, I had to change
> the following function from :
> function $(element) {
> ...
> }
>
> to
> function (element) {
> ...
> }
>
> It may be a problem has well !
> Thanks for giving me some info if I'm doing something wrong or not,
>
>
Giles is right that there can be conflicts between different pieces of
javascript code when you combine them, but this ought to be fixable (or
at least, it should be possible to improve the situation).
In particular, with the $ function, I put that into Util.js to make it
easier to port away from the prototype js library, but that causes
problems for anyone actually wanting to use prototype. Just removing it
from Util.js the way you did would certainly have broken JBrowse, so
that may be part of the problem you're seeing.
But it was straightforward to take all the uses of the $ function in
JBrowse and replace them with the dojo equivalent (dojo.byId), which
I've done and pushed to the master branch:
http://github.com/jbrowse/jbrowse/commit/ed13ddeb11dd28137c6d3c3022fe38e42efdf6d1
which should address the problem you encountered there.
Longer term, the javascript libraries are getting better at co-existing,
and JBrowse should also clean up its namespace usage (by moving
everything into a "jbrowse" object).
Regards,
Mitch
|
|
From: Giles V. <gv...@sa...> - 2009-12-18 00:41:22
|
Hi Jerome,
I don't know about this particular case, but it is very common that JS
libraries like JQuery, Dojo, Mootools and so on can't be used together
on the same page. This is often due to the fact that each library
extends Javascript in a similar, but subtly different way and conflict
with each other. If you are intending to embed Jbrowse on your page,
you're probably better off using the same libraries Jbrowse uses.
Either that, or embed Jbrowse in an iframe.
Regards,
Giles
On 17 Dec 2009, at 16:01, Mariette wrote:
>
> Re HI,
>
> I fugured out that it's a conflict between jquery and dojo. Do you
> have
> a version of jbrowse
> not using dojo ? Do you know if it's possible to mix the both of
> them in
> a same web page.
>
> Jerome
>
>
>
>
> Mariette a écrit :
>> Hi everyone,
>>
>> I'm trying to add jbrowse to our website, which is basicly a
>> detection
>> and annotation
>> platform for non coding RNA. When RNAs are detected, I'd like to show
>> them up using
>> jbrowse, but I got some trouble adding it to our web page !
>> So I added all the javascript and css to our page and then placed the
>> following code (
>> which is the one provided in the index.html) to the javascript
>> section :
>>
>> var queryParams =
>> dojo.queryToObject(window.location.search.slice(1));
>> var bookmarkCallback = function(brwsr) {
>> return window.location.protocol
>> + "//" + window.location.host
>> + window.location.pathname
>> + "?loc=" + brwsr.visibleRegion()
>> + "&tracks=" + brwsr.visibleTracks();
>> }
>>
>> var t = new Browser({
>> containerID: "GenomeBrowser",
>> refSeqs: refSeqs,
>> trackData: trackInfo,
>> defaultTracks: "DNA,gene,mRNA,noncodingRNA",
>> location: queryParams.loc,
>> tracks: queryParams.tracks,
>> bookmark: bookmarkCallback
>> });
>>
>> then I added the div to my page content (still just like it is in the
>> index.html page of jbrowse) :
>> <div id="GenomeBrowser" style="height: 100%; width: 100%; padding: 0;
>> border: 0;"></div>
>>
>> I can see my page changing but I'm far from having the result I can
>> get when using it localy !!
>> So I was wondering if using it the ?loc and &tracks are important, we
>> give to our page some
>> arguments and it may be a problem ?
>>
>> Also, there was something wrong in the Utils.js file, I had to change
>> the following function from :
>> function $(element) {
>> ...
>> }
>>
>> to
>> function (element) {
>> ...
>> }
>>
>> It may be a problem has well !
>> Thanks for giving me some info if I'm doing something wrong or not,
>>
>> Jerome
>>
>
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast
> and easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
|
|
From: Ian H. <ih...@be...> - 2009-12-17 21:49:07
|
Sue, thanks for this bug report & feedback. I'm copying to the gmod- ajax mailing list; when I'm at a terminal I'll add a ticket and we'll try to resolve it as quickly as we can. -Ian (by phone) On Dec 18, 2009, at 6:14 AM, Sue Celniker <cel...@fr...> wrote: > Dear Ian, > > We love jbrowse and have been using it to review our RNA-seq data. > We found a bug today. If we make the window very large (>2000 > pixels wide) (my monitor is 2560 wide) none of the data is > displayed and a java script exception is thrown and displayed in the > error consul. The exception is [Exception... "'RangeError: > stripeWidth too small: 250, 2104' when calling method: etc... > > Sue > > > Susan Celniker, PhD > Berkeley Drosophila Genome Project > Lawrence Berkeley National Laboratory > 1 Cyclotron Rd MS 64-0119 > Berkeley, CA 94720, USA > E-mail: celniker @bdgp.lbl.gov > Telephone: (510) 486-6258 > Fax Number: (510) 486- 6798 |
|
From: Mariette <jma...@to...> - 2009-12-17 16:01:33
|
Re HI,
I fugured out that it's a conflict between jquery and dojo. Do you have
a version of jbrowse
not using dojo ? Do you know if it's possible to mix the both of them in
a same web page.
Jerome
Mariette a écrit :
> Hi everyone,
>
> I'm trying to add jbrowse to our website, which is basicly a detection
> and annotation
> platform for non coding RNA. When RNAs are detected, I'd like to show
> them up using
> jbrowse, but I got some trouble adding it to our web page !
> So I added all the javascript and css to our page and then placed the
> following code (
> which is the one provided in the index.html) to the javascript section :
>
> var queryParams = dojo.queryToObject(window.location.search.slice(1));
> var bookmarkCallback = function(brwsr) {
> return window.location.protocol
> + "//" + window.location.host
> + window.location.pathname
> + "?loc=" + brwsr.visibleRegion()
> + "&tracks=" + brwsr.visibleTracks();
> }
>
> var t = new Browser({
> containerID: "GenomeBrowser",
> refSeqs: refSeqs,
> trackData: trackInfo,
> defaultTracks: "DNA,gene,mRNA,noncodingRNA",
> location: queryParams.loc,
> tracks: queryParams.tracks,
> bookmark: bookmarkCallback
> });
>
> then I added the div to my page content (still just like it is in the
> index.html page of jbrowse) :
> <div id="GenomeBrowser" style="height: 100%; width: 100%; padding: 0;
> border: 0;"></div>
>
> I can see my page changing but I'm far from having the result I can
> get when using it localy !!
> So I was wondering if using it the ?loc and &tracks are important, we
> give to our page some
> arguments and it may be a problem ?
>
> Also, there was something wrong in the Utils.js file, I had to change
> the following function from :
> function $(element) {
> ...
> }
>
> to
> function (element) {
> ...
> }
>
> It may be a problem has well !
> Thanks for giving me some info if I'm doing something wrong or not,
>
> Jerome
>
|
|
From: Mariette <jma...@to...> - 2009-12-17 09:42:34
|
Hi everyone,
I'm trying to add jbrowse to our website, which is basicly a detection
and annotation
platform for non coding RNA. When RNAs are detected, I'd like to show
them up using
jbrowse, but I got some trouble adding it to our web page !
So I added all the javascript and css to our page and then placed the
following code (
which is the one provided in the index.html) to the javascript section :
var queryParams = dojo.queryToObject(window.location.search.slice(1));
var bookmarkCallback = function(brwsr) {
return window.location.protocol
+ "//" + window.location.host
+ window.location.pathname
+ "?loc=" + brwsr.visibleRegion()
+ "&tracks=" + brwsr.visibleTracks();
}
var t = new Browser({
containerID: "GenomeBrowser",
refSeqs: refSeqs,
trackData: trackInfo,
defaultTracks: "DNA,gene,mRNA,noncodingRNA",
location: queryParams.loc,
tracks: queryParams.tracks,
bookmark: bookmarkCallback
});
then I added the div to my page content (still just like it is in the
index.html page of jbrowse) :
<div id="GenomeBrowser" style="height: 100%; width: 100%; padding: 0;
border: 0;"></div>
I can see my page changing but I'm far from having the result I can get
when using it localy !!
So I was wondering if using it the ?loc and &tracks are important, we
give to our page some
arguments and it may be a problem ?
Also, there was something wrong in the Utils.js file, I had to change
the following function from :
function $(element) {
...
}
to
function (element) {
...
}
It may be a problem has well !
Thanks for giving me some info if I'm doing something wrong or not,
Jerome
|
|
From: Mariette <jma...@to...> - 2009-12-16 17:36:04
|
Hi everyone,
I'm trying to add jbrowse to our website, which is basicly a detection
and annotation
platform for non coding RNA. When RNAs are detected, I'd like to show
them up using
jbrowse, but I got some trouble adding it to our web page !
So I added all the javascript and css to our page and then placed the
following code (
which is the one provided in the index.html) to the javascript section :
var queryParams = dojo.queryToObject(window.location.search.slice(1));
var bookmarkCallback = function(brwsr) {
return window.location.protocol
+ "//" + window.location.host
+ window.location.pathname
+ "?loc=" + brwsr.visibleRegion()
+ "&tracks=" + brwsr.visibleTracks();
}
var t = new Browser({
containerID: "GenomeBrowser",
refSeqs: refSeqs,
trackData: trackInfo,
defaultTracks: "DNA,gene,mRNA,noncodingRNA",
location: queryParams.loc,
tracks: queryParams.tracks,
bookmark: bookmarkCallback
});
then I added the div to my page content (still just like it is in the
index.html page of jbrowse) :
<div id="GenomeBrowser" style="height: 100%; width: 100%; padding: 0;
border: 0;"></div>
I can see my page changing but I'm far from having the result I can get
when using it localy !!
So I was wondering if using it the ?loc and &tracks are important, we
give to our page some
arguments and it may be a problem ?
Also, there was something wrong in the Utils.js file, I had to change
the following function from :
function $(element) {
...
}
to
function (element) {
...
}
It may be a problem has well !
Thanks for giving me some info if I'm doing something wrong or not,
Jerome
|
|
From: Mitch S. <mit...@be...> - 2009-11-20 17:20:18
|
On 11/19/2009 11:13 PM, Martin A. Hansen wrote: > Yup, that is exactly where I downloaded from - and the tarball was > funny. Now I use a clone from GIT and there is no trouble. Hmmm, I haven't been able to reproduce this, so I'm not sure where to go from here. If anyone else encounters this please let me know. > How do you determine current version? Is there a version/revision number? We haven't started tagging versions yet, but tarball downloads and git clones do come with mechanisms that allow you to identify the current commit. If you get a tarball, the tarball name has the first part of the commit hash in it. In the example below, "020db6d" identifies the version. If you have a git clone, you can do a "git rev-parse HEAD" to get the hash of the current head commit. Mitch $ wget http://github.com/jbrowse/jbrowse/tarball/master --2009-11-20 09:10:15-- http://github.com/jbrowse/jbrowse/tarball/master Resolving github.com... 207.97.227.239 Connecting to github.com|207.97.227.239|:80... connected. HTTP request sent, awaiting response... 302 Found Location: http://waitdownload.github.com/jbrowse-jbrowse-020db6d.tar.gz [following] --2009-11-20 09:10:16-- http://waitdownload.github.com/jbrowse-jbrowse-020db6d.tar.gz Resolving waitdownload.github.com... 207.97.227.241 Connecting to waitdownload.github.com|207.97.227.241|:80... connected. HTTP request sent, awaiting response... 302 Moved Temporarily Location: http://download.github.com/jbrowse-jbrowse-020db6d.tar.gz [following] --2009-11-20 09:10:17-- http://download.github.com/jbrowse-jbrowse-020db6d.tar.gz Resolving download.github.com... 207.97.227.240 Connecting to download.github.com|207.97.227.240|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 509686 (498K) [application/octet-stream] Saving to: `jbrowse-jbrowse-020db6d.tar.gz' 100%[======================================>] 509,686 236K/s in 2.1s 2009-11-20 09:10:21 (236 KB/s) - `jbrowse-jbrowse-020db6d.tar.gz' saved [509686/509686] $ ls jbrowse-jbrowse-020db6d.tar.gz |
|
From: Mitch S. <mit...@be...> - 2009-11-20 16:57:25
|
On 11/20/2009 03:48 AM, Martin A. Hansen wrote: > I was reading about lazy loading: > http://biowiki.org/view/JBrowse/LazyFeatureLoading > > How to handle long features that would result in uneven large chunks > and possible overloading? > > 1. One could disallow long features. > 2. or break them into smaller features with a hidden "link" between > them? > > If there's a large real feature, the generated fake features can be within it. For example, suppose you have the following four real features: A: [10, 100) B: [20, 30) C: [40, 50) D: [50, 60) And suppose you want to split this set of features into chunks that each contain two features. JBrowse will generate two fake features: F1: [10, 101) F2: [40,61) And the NCList tree will look something like: F1: (A B *F2) F2: (C D) Where *F2 is a URL pointing to the F2 chunk. I hope that makes sense, maybe I'll add another diagram to that wiki page to try and make it clearer. The one failure case that I know about (with the current code) is when there are lots of features with the exact same boundaries. I think that could be addressed by making the NCList.pm code aware of the fake features (currently, NCList.pm doesn't know anything about the fake features; those are all created and handled by the code that calls NCList.pm). Mitch |
|
From: Martin A. H. <ma...@ma...> - 2009-11-20 11:49:09
|
Hey Mitch, I was reading about lazy loading: http://biowiki.org/view/JBrowse/LazyFeatureLoading How to handle long features that would result in uneven large chunks and possible overloading? 1. One could disallow long features. 2. or break them into smaller features with a hidden "link" between them? Martin |
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