gmod-ajax — JBrowse list

Re: [Gmod-ajax] A question for JBrowse1

[<fa...@ca...>]

Thanks very much.   We have tested view->trackPadding, yes, it works now!  




fa...@ca...
 
From: Colin
Date: 2022-03-26 00:15
To: Scott Cain
CC: Ian Holmes; fa...@ca...; gmod-ajax
Subject: Re: [Gmod-ajax] A question for JBrowse1
>However, we met a problem on setting the distance between each tracks. 

You can try setting view->trackPadding (see   https://jbrowse.org/docs/global_options.html)


Basically, editing jbrowse.conf to have

[GENERAL]
view.trackPadding=0

-Colin


On Thu, Mar 24, 2022 at 3:08 PM Scott Cain <sc...@sc...> wrote:
Hi Wei,

While I agree with Ian's suggestion that you try JBrowse 2, if there is a reason you want to stick with JBrowse 1 for the moment, note that there is at least an option to add a little bit of space between tracks so that the labels don't overlap the features by adding "trackLabels = no-block" to the "[GENERAL]" section of the jbrowse.conf file for the entire site.

Scott


On Thu, Mar 24, 2022 at 1:48 PM Ian Holmes <ihh...@gm...> wrote:
Dear Wei,

Thanks for your interest in JBrowse. I'm glad it's been helpful to you!

JBrowse1, which is now in maintenance mode only, does not allow adjustment of the vertical height of tracks.
Active development of JBrowse is now focused on JBrowse2, whose "Linear Genome Browser" component reproduces most of the functionality of JBrowse1, while fixing a lot of the limitations. For example, it is easy to adjust the height of tracks in JBrowse2. There are also many new features, such as the ability to view synteny between genomes.
Furthermore, JBrowse2 should be straightforward to install on any website where you already have JBrowse1 installed.
We would be very interested in hearing feedback on your experience with JBrowse2, as we are actively encouraging new users to try JBrowse2, and would like to try and make the experience as easy as possible for you.

I have CC'd the JBrowse mailing list on this reply; you can also often get quicker responses by engaging with the software development team directly in the various ways described on the contact page on the JBrowse website.

Thanks & best wishes,
Ian

On Thu, Mar 24, 2022 at 4:00 AM fa...@ca... <fa...@ca...> wrote:
Dear Prof. Holmes,
      We are trying to build a genome website for our sequenced species, and found JBrowse1 an excellent tool to use.   However, we met a problem on setting the distance between each tracks.  Is there a way to set the distance of drawing among any neiboring tracks? 
     Thanks for your great work.  I am looking forward to hearing from you! 

Wei Fan
Agriculture genomics Institute at Shenzhen, China


fa...@ca...
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott at scottcain dot net
GMOD Project Manager (http://gmod.org/)                            216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] A question for JBrowse1

[Colin <col...@gm...>]

>However, we met a problem on setting the distance between each tracks.

You can try setting view->trackPadding (see
https://jbrowse.org/docs/global_options.html)


Basically, editing jbrowse.conf to have

[GENERAL]
view.trackPadding=0

-Colin


On Thu, Mar 24, 2022 at 3:08 PM Scott Cain <sc...@sc...> wrote:

> Hi Wei,
>
> While I agree with Ian's suggestion that you try JBrowse 2, if there is a
> reason you want to stick with JBrowse 1 for the moment, note that there is
> at least an option to add a little bit of space between tracks so that the
> labels don't overlap the features by adding "trackLabels = no-block" to the
> "[GENERAL]" section of the jbrowse.conf file for the entire site.
>
> Scott
>
>
> On Thu, Mar 24, 2022 at 1:48 PM Ian Holmes <ihh...@gm...> wrote:
>
>> Dear Wei,
>>
>> Thanks for your interest in JBrowse. I'm glad it's been helpful to you!
>>
>> JBrowse1, which is now in maintenance mode only, does not allow
>> adjustment of the vertical height of tracks.
>> Active development of JBrowse is now focused on JBrowse2
>> <https://jbrowse.org/jb2/>, whose "Linear Genome Browser" component
>> reproduces most of the functionality of JBrowse1, while fixing a lot of the
>> limitations. For example, it is easy to adjust the height of tracks in
>> JBrowse2. There are also many new features, such as the ability to view
>> synteny between genomes.
>> Furthermore, JBrowse2 should be straightforward to install on any website
>> where you already have JBrowse1 installed.
>> We would be very interested in hearing feedback on your experience with
>> JBrowse2, as we are actively encouraging new users to try JBrowse2, and
>> would like to try and make the experience as easy as possible for you.
>>
>> I have CC'd the JBrowse mailing list on this reply; you can also often
>> get quicker responses by engaging with the software development team
>> directly in the various ways described on the contact page
>> <https://jbrowse.org/jb2/contact/> on the JBrowse website.
>>
>> Thanks & best wishes,
>> Ian
>>
>> On Thu, Mar 24, 2022 at 4:00 AM fa...@ca... <fa...@ca...> wrote:
>>
>>> Dear Prof. Holmes,
>>>       We are trying to build a genome website for our sequenced species,
>>> and found JBrowse1 an excellent tool to use.   However, we met a problem on
>>> setting the distance between each tracks.  Is there a way to set the
>>> distance of drawing among any neiboring tracks?
>>>      Thanks for your great work.  I am looking forward to hearing from
>>> you!
>>>
>>> Wei Fan
>>> Agriculture genomics Institute at Shenzhen, China
>>> ------------------------------
>>> fa...@ca...
>>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
> GMOD Project Manager (http://gmod.org/)
> 216-392-3087
> WormBase Developer (http://wormbase.org/)
> Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
> VirusSeq Project Manager (https://virusseq-dataportal.ca/)
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] A question for JBrowse1

[<fa...@ca...>]

Thanks a lot.  We will try JBrowse2.

Best regards
Wei Fan


fa...@ca...
 
From: Scott Cain
Date: 2022-03-25 05:08
To: Ian Holmes
CC: fa...@ca...; gmod-ajax
Subject: Re: [Gmod-ajax] A question for JBrowse1
Hi Wei,

While I agree with Ian's suggestion that you try JBrowse 2, if there is a reason you want to stick with JBrowse 1 for the moment, note that there is at least an option to add a little bit of space between tracks so that the labels don't overlap the features by adding "trackLabels = no-block" to the "[GENERAL]" section of the jbrowse.conf file for the entire site.

Scott


On Thu, Mar 24, 2022 at 1:48 PM Ian Holmes <ihh...@gm...> wrote:
Dear Wei,

Thanks for your interest in JBrowse. I'm glad it's been helpful to you!

JBrowse1, which is now in maintenance mode only, does not allow adjustment of the vertical height of tracks.
Active development of JBrowse is now focused on JBrowse2, whose "Linear Genome Browser" component reproduces most of the functionality of JBrowse1, while fixing a lot of the limitations. For example, it is easy to adjust the height of tracks in JBrowse2. There are also many new features, such as the ability to view synteny between genomes.
Furthermore, JBrowse2 should be straightforward to install on any website where you already have JBrowse1 installed.
We would be very interested in hearing feedback on your experience with JBrowse2, as we are actively encouraging new users to try JBrowse2, and would like to try and make the experience as easy as possible for you.

I have CC'd the JBrowse mailing list on this reply; you can also often get quicker responses by engaging with the software development team directly in the various ways described on the contact page on the JBrowse website.

Thanks & best wishes,
Ian

On Thu, Mar 24, 2022 at 4:00 AM fa...@ca... <fa...@ca...> wrote:
Dear Prof. Holmes,
      We are trying to build a genome website for our sequenced species, and found JBrowse1 an excellent tool to use.   However, we met a problem on setting the distance between each tracks.  Is there a way to set the distance of drawing among any neiboring tracks? 
     Thanks for your great work.  I am looking forward to hearing from you! 

Wei Fan
Agriculture genomics Institute at Shenzhen, China


fa...@ca...
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott at scottcain dot net
GMOD Project Manager (http://gmod.org/)                            216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)

Re: [Gmod-ajax] A question for JBrowse1

[Scott C. <sc...@sc...>]

Hi Wei,

While I agree with Ian's suggestion that you try JBrowse 2, if there is a
reason you want to stick with JBrowse 1 for the moment, note that there is
at least an option to add a little bit of space between tracks so that the
labels don't overlap the features by adding "trackLabels = no-block" to the
"[GENERAL]" section of the jbrowse.conf file for the entire site.

Scott


On Thu, Mar 24, 2022 at 1:48 PM Ian Holmes <ihh...@gm...> wrote:

> Dear Wei,
>
> Thanks for your interest in JBrowse. I'm glad it's been helpful to you!
>
> JBrowse1, which is now in maintenance mode only, does not allow adjustment
> of the vertical height of tracks.
> Active development of JBrowse is now focused on JBrowse2
> <https://jbrowse.org/jb2/>, whose "Linear Genome Browser" component
> reproduces most of the functionality of JBrowse1, while fixing a lot of the
> limitations. For example, it is easy to adjust the height of tracks in
> JBrowse2. There are also many new features, such as the ability to view
> synteny between genomes.
> Furthermore, JBrowse2 should be straightforward to install on any website
> where you already have JBrowse1 installed.
> We would be very interested in hearing feedback on your experience with
> JBrowse2, as we are actively encouraging new users to try JBrowse2, and
> would like to try and make the experience as easy as possible for you.
>
> I have CC'd the JBrowse mailing list on this reply; you can also often get
> quicker responses by engaging with the software development team directly
> in the various ways described on the contact page
> <https://jbrowse.org/jb2/contact/> on the JBrowse website.
>
> Thanks & best wishes,
> Ian
>
> On Thu, Mar 24, 2022 at 4:00 AM fa...@ca... <fa...@ca...> wrote:
>
>> Dear Prof. Holmes,
>>       We are trying to build a genome website for our sequenced species,
>> and found JBrowse1 an excellent tool to use.   However, we met a problem on
>> setting the distance between each tracks.  Is there a way to set the
>> distance of drawing among any neiboring tracks?
>>      Thanks for your great work.  I am looking forward to hearing from
>> you!
>>
>> Wei Fan
>> Agriculture genomics Institute at Shenzhen, China
>> ------------------------------
>> fa...@ca...
>>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)

Re: [Gmod-ajax] A question for JBrowse1

[Ian H. <ihh...@gm...>]

Dear Wei,

Thanks for your interest in JBrowse. I'm glad it's been helpful to you!

JBrowse1, which is now in maintenance mode only, does not allow adjustment
of the vertical height of tracks.
Active development of JBrowse is now focused on JBrowse2
<https://jbrowse.org/jb2/>, whose "Linear Genome Browser" component
reproduces most of the functionality of JBrowse1, while fixing a lot of the
limitations. For example, it is easy to adjust the height of tracks in
JBrowse2. There are also many new features, such as the ability to view
synteny between genomes.
Furthermore, JBrowse2 should be straightforward to install on any website
where you already have JBrowse1 installed.
We would be very interested in hearing feedback on your experience with
JBrowse2, as we are actively encouraging new users to try JBrowse2, and
would like to try and make the experience as easy as possible for you.

I have CC'd the JBrowse mailing list on this reply; you can also often get
quicker responses by engaging with the software development team directly
in the various ways described on the contact page
<https://jbrowse.org/jb2/contact/> on the JBrowse website.

Thanks & best wishes,
Ian

On Thu, Mar 24, 2022 at 4:00 AM fa...@ca... <fa...@ca...> wrote:

> Dear Prof. Holmes,
>       We are trying to build a genome website for our sequenced species,
> and found JBrowse1 an excellent tool to use.   However, we met a problem on
> setting the distance between each tracks.  Is there a way to set the
> distance of drawing among any neiboring tracks?
>      Thanks for your great work.  I am looking forward to hearing from you!
>
>
> Wei Fan
> Agriculture genomics Institute at Shenzhen, China
> ------------------------------
> fa...@ca...
>

[Gmod-ajax] Announcing BOSC 2022, the 23rd Bioinformatics Open Source Conference

[Scott C. <sc...@sc...>]

BOSC 2022 dates: July 13-14, as part of ISMB 2022

Location: Madison, WI, USA, and virtual

Website: <https://www.open-bio.org/wiki/BOSC_2019>
https://www.open-bio.org/events/bosc/

BOSC announcements mailing list:
<http://lists.open-bio.org/mailman/listinfo/bosc-announce>
https://groups.google.com/forum/#!forum/bosc-announce

Slack channel:
https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew


Twitter: @OBF_BOSC <https://twitter.com/OBF_BOSC>, #BOSC2022

Key Dates

   -

   April 21, 2022: Deadline for submitting talk/poster abstracts
   <https://www.open-bio.org/events/bosc-2022/submit/>
   -

   May 12: Talk/poster acceptance notifications
   -

   May 19: Late poster (and Late-Breaking Lightning Talk) submission
   deadline
   -

   May 26: Late poster / LBLT acceptance notifications
   -

   July 13-14: BOSC 2022 <https://www.open-bio.org/events/bosc-2022/>
   -

   July 15-16: CollaborationFest (CoFest)


About BOSC

The Bioinformatics Open Source Conference promotes and facilitates the open
source development of bioinformatics tools and open science. Since 2000,
BOSC has provided a forum for developers and users to interact and share
research results and ideas in open source bioinformatics and open science.
BOSC’s broad spectrum of topics includes practical techniques for solving
bioinformatics problems; software development practices; standards and
ontologies; approaches that promote open science and sharing of data,
results and software; and ways to grow open source communities while
promoting diversity within them.
As usual, BOSC will include keynote talks, longer and shorter (lightning)
talks from submitted abstracts, posters, Birds of a Feather, and more!

New this year: Joint session with Bio-Ontologies
<https://www.open-bio.org/2022/03/03/bosc-and-bio-ontologies-joint-session/>
!
We are excited to announce that BOSC and Bio-Ontologies
<https://www.bio-ontologies.org.uk/ismb-annual-meeting> will join forces
for part of a day at ISMB 2022. The joint session will feature keynote
speaker Melissa Haendel as well as talks chosen from abstracts submitted to
BOSC or Bio-Ontologies.

Keynote Speakers <https://open-bio.org/events/bosc-2022/bosc-2022-keynotes>

Melissa Haendel is the Chief Research Informatics Officer at University of
Colorado Anschutz Medical Campus, and Director of the Center for Data to
Health (CD2H). With expertise in molecular genetics and developmental
biology as well as translational informatics, Dr. Haendel focuses on open
science and data integration to improve rare-disease diagnosis and
mechanism discovery. She is a leader in ontologies and standards for data
sharing.

Lior Pachter is the Bren professor of computational biology at Caltech. He
is a Fellow of the International Society of Computational Biology
<https://www.iscb.org/iscb-fellows> and has been awarded a National Science
Foundation CAREER award, a Sloan Research Fellowship His research interests
span the mathematical and biological sciences, including algorithms,
combinatorics, comparative genomics, algebraic statistics, molecular
biology and evolution. Dr. Pachter is known as a vociferous advocate of
open and accountable science.

A third keynote speaker will be announced soon!

Abstract submission

We encourage you to submit abstracts
<https://www.open-bio.org/events/bosc-2022/submit/> (due April 21 – sorry,
no extensions) on any topic relevant to open source bioinformatics or open
science. After review, some abstracts will be selected for lightning talks,
longer talks, or posters. Abstracts that are not chosen for talks will
automatically be considered for posters.

Abstract submission will be via ISMB’s EasyChair. Note that ISMB/ECCB
requires a short (200-word) text-only abstract for all submissions (talk or
poster), plus a “long abstract” (PDF, 2 pages max) if you want to be
considered for a talk. A second, later round of submissions will end May
19. Abstracts submitted in the late round will be considered only for
posters and a limited number of “late-breaking lightning talk” slots; they
are not eligible for longer talks.

Registration fee assistance

We realize that the cost of ISMB may be prohibitive for some. If you are
submitting an abstract to BOSC and would have difficulty covering the cost
of registration, you can request a registration fee waiver right on the
abstract submission form (which will not be seen by reviewers). Those who
are not submitting abstracts can apply for an OBF Event Fellowship
<https://www.open-bio.org/event-awards/> (deadline April 1, 2022).

BOSC topics include (but are not limited to):

   -

   Ontologies: Open Source Tools and Approaches (new this year – joint
   session with Bio-Ontologies COSI <http://www.bio-ontologies.org.uk/>)
   -

   Open Science and Reproducible Research
   -

   Open Biomedical Data
   -

   Citizen/Participatory Science
   -

   Standards and Interoperability
   -

   Data Science
   -

   Workflows
   -

   Open Approaches to Translational Bioinformatics
   -

   Open Science for Global Health
   -

   Developer Tools and Libraries
   -

   Inclusion, Outreach and Training
   -

   Bioinformatics Open Source Project Reports (about new or existing
   projects)
   -

   Open and interoperable ontologies (joint session with Bio-Ontologies
   <https://www.open-bio.org/2022/03/03/bosc-and-bio-ontologies-joint-session/>
   )


We look forward to reading your abstract and seeing you (in person or
virtually) at BOSC 2022!

Sincerely,

BOSC 2022 Organizing Committee: Nomi Harris, Karsten Hokamp, Hervé Ménager,
Monica Munoz-Torres, Deepak Unni, Nicole Vasilevsky, Jason Williams


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)

Re: [Gmod-ajax] [apollo] remove 'transcript' track

[Johannes D. <joh...@gm...>]

Thanks Colin,
reloading the file with --type mRNA did indeed filter out the box from
being displayed.
Cheers.

On Wed, 23 Mar 2022 at 01:56, Colin <col...@gm...> wrote:

> The line that produces the "box" features with no exons is
> P9424_ctg_01    AUGUSTUS    gene    220129  221909  .   -   .
> ID=nbisL1-transcript-10667
>
> This has no children and is just a box. If you load your data using --type
> mRNA in flatfile-to-json it would filter out the gene level features. The
> topLevelFeatures may help also
>
> -Colin
>
> On Sun, Mar 20, 2022 at 11:37 AM Nathan Dunn <nd...@gm...> wrote:
>
>>
>> Some quick thoughts:
>>
>> 1 - maybe get rid of the introns.   Not sure if Apollo filters them out
>> or not.
>>
>> 2 - I think having 2 genes in the same track at the same location may be
>> problematic, the latter one looks problematic.
>>
>> 3 - I *think* (if the problem. Persists) you can remove the “gene”
>> annotation OR potentially (and better), you could add the
>> “topLevelFeature”:”mRNA” as this example below.
>>
>> {"storeClass":"JBrowse/Store/SeqFeature/GFF3",
>> "urlTemplate":"raw/824131860720236.gff", "label":"824131860720236",
>> "type":"JBrowse/View/Track/HTMLFeatures", "style":{"className":"feature"},
>> "key":"824131860720236", "topLevelFeatures":"mRNA",
>> "apollo":{"source":"upload", "type":"GFF3", "topType":"mRNA"}}
>>
>> Those are my quick guesses.
>>
>> Nathan
>>
>> On Mar 18, 2022, at 6:50 PM, Johannes Debler <joh...@gm...>
>> wrote:
>>
>> Hi Nathan,
>>
>> I think it is something odd that came out of combining braker 1 and 2
>> results. This is one particular gene annotation, have a look at the first
>> and last line, there are two 'gene' annotations for the same location with
>> different IDs.
>> Is there a way to display CDS features only?
>> Cheers,
>> Johannes
>>
>> P9424_ctg_01    AUGUSTUS    gene    220129  221909  1   -   .
>> ID=nbis-gene-289;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
>> P9424_ctg_01    AUGUSTUS    mRNA    220129  221909  1   -   .
>> ID=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;Parent=nbis-gene-289;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
>> P9424_ctg_01    AUGUSTUS    exon    220129  221050  .   -   .
>> ID=exon-29374;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
>> P9424_ctg_01    AUGUSTUS    exon    221100  221660  .   -   .
>> ID=exon-29375;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
>> P9424_ctg_01    AUGUSTUS    exon    221746  221909  .   -   .
>> ID=exon-29376;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
>> P9424_ctg_01    AUGUSTUS    CDS 220129  221050  1   -   1
>> ID=cds-29377;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
>> P9424_ctg_01    AUGUSTUS    CDS 221100  221660  1   -   1
>> ID=cds-29378;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
>> P9424_ctg_01    AUGUSTUS    CDS 221746  221909  1   -   0
>> ID=cds-29379;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
>> P9424_ctg_01    AUGUSTUS    intron  221051  221099  1   -   .
>> ID=intron-18711;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
>> P9424_ctg_01    AUGUSTUS    intron  221661  221745  1   -   .
>> ID=intron-18712;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
>> P9424_ctg_01    AUGUSTUS    start_codon 221907  221909  .   -   0
>> ID=start_codon-10667;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
>> P9424_ctg_01    AUGUSTUS    stop_codon  220129  220131  .   -   0
>> ID=stop_codon-10667;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
>> P9424_ctg_01    AUGUSTUS    gene    220129  221909  .   -   .
>> ID=nbisL1-transcript-10667
>>
>> On Fri, 18 Mar 2022 at 23:12, Nathan Dunn <nd...@gm...> wrote:
>>
>>>
>>> Sometimes it does that if there is a top-level gene.
>>>
>>> Maybe a more of a JBrowse so cross-posting.
>>>
>>> Could you post the GFF3 snippet?
>>>
>>> Nathan
>>>
>>>
>>> On Mar 18, 2022, at 12:58 AM, Johannes Debler <joh...@gm...>
>>> wrote:
>>>
>>> Hi,
>>> I cannot figure out why for some uploaded GFF files Apollo displays the
>>> exon structure only, but for some it also displays a 'transcript' track
>>> (the blue and gray one underneath all the CDS features). I have removed
>>> 'transcript' from the GFF but it still displays it. Any idea how to make
>>> that go away?
>>> Cheers,
>>> Johannes
>>>
>>>
>>> <image.png>
>>>
>>> --
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to apo...@lb....
>>>
>>>
>>>
>> --
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to apo...@lb....
>>
>

Re: [Gmod-ajax] [apollo] remove 'transcript' track

[Colin <col...@gm...>]

The line that produces the "box" features with no exons is
P9424_ctg_01    AUGUSTUS    gene    220129  221909  .   -   .
ID=nbisL1-transcript-10667

This has no children and is just a box. If you load your data using --type
mRNA in flatfile-to-json it would filter out the gene level features. The
topLevelFeatures may help also

-Colin

On Sun, Mar 20, 2022 at 11:37 AM Nathan Dunn <nd...@gm...> wrote:

>
> Some quick thoughts:
>
> 1 - maybe get rid of the introns.   Not sure if Apollo filters them out or
> not.
>
> 2 - I think having 2 genes in the same track at the same location may be
> problematic, the latter one looks problematic.
>
> 3 - I *think* (if the problem. Persists) you can remove the “gene”
> annotation OR potentially (and better), you could add the
> “topLevelFeature”:”mRNA” as this example below.
>
> {"storeClass":"JBrowse/Store/SeqFeature/GFF3",
> "urlTemplate":"raw/824131860720236.gff", "label":"824131860720236",
> "type":"JBrowse/View/Track/HTMLFeatures", "style":{"className":"feature"},
> "key":"824131860720236", "topLevelFeatures":"mRNA",
> "apollo":{"source":"upload", "type":"GFF3", "topType":"mRNA"}}
>
> Those are my quick guesses.
>
> Nathan
>
> On Mar 18, 2022, at 6:50 PM, Johannes Debler <joh...@gm...>
> wrote:
>
> Hi Nathan,
>
> I think it is something odd that came out of combining braker 1 and 2
> results. This is one particular gene annotation, have a look at the first
> and last line, there are two 'gene' annotations for the same location with
> different IDs.
> Is there a way to display CDS features only?
> Cheers,
> Johannes
>
> P9424_ctg_01    AUGUSTUS    gene    220129  221909  1   -   .
> ID=nbis-gene-289;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    mRNA    220129  221909  1   -   .
> ID=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;Parent=nbis-gene-289;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    exon    220129  221050  .   -   .
> ID=exon-29374;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    exon    221100  221660  .   -   .
> ID=exon-29375;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    exon    221746  221909  .   -   .
> ID=exon-29376;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    CDS 220129  221050  1   -   1
> ID=cds-29377;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    CDS 221100  221660  1   -   1
> ID=cds-29378;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    CDS 221746  221909  1   -   0
> ID=cds-29379;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    intron  221051  221099  1   -   .
> ID=intron-18711;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    intron  221661  221745  1   -   .
> ID=intron-18712;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    start_codon 221907  221909  .   -   0
> ID=start_codon-10667;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    stop_codon  220129  220131  .   -   0
> ID=stop_codon-10667;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    gene    220129  221909  .   -   .
> ID=nbisL1-transcript-10667
>
> On Fri, 18 Mar 2022 at 23:12, Nathan Dunn <nd...@gm...> wrote:
>
>>
>> Sometimes it does that if there is a top-level gene.
>>
>> Maybe a more of a JBrowse so cross-posting.
>>
>> Could you post the GFF3 snippet?
>>
>> Nathan
>>
>>
>> On Mar 18, 2022, at 12:58 AM, Johannes Debler <joh...@gm...>
>> wrote:
>>
>> Hi,
>> I cannot figure out why for some uploaded GFF files Apollo displays the
>> exon structure only, but for some it also displays a 'transcript' track
>> (the blue and gray one underneath all the CDS features). I have removed
>> 'transcript' from the GFF but it still displays it. Any idea how to make
>> that go away?
>> Cheers,
>> Johannes
>>
>>
>> <image.png>
>>
>> --
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to apo...@lb....
>>
>>
>>
> --
> To unsubscribe from this group and stop receiving emails from it, send an
> email to apo...@lb....
>

Re: [Gmod-ajax] Trouble installing JBrowse 1 on new webserver

[Hans Vasquez-G. <hva...@un...>]

Thank you Colin.  Uninstalling Node 17.x and installing 14.x fixed the setup problem.

Bests,
-Hans
________________________________
From: Colin <col...@gm...>
Sent: Wednesday, March 16, 2022 8:05 PM
To: Hans Vasquez-Gross <hva...@un...>
Cc: gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] Trouble installing JBrowse 1 on new webserver

Hi there,
You may need node version 14 or less. More recent versions have an issue with the node-sass module

See readme
https://github.com/gmod/jbrowse#readme<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgmod%2Fjbrowse%23readme&data=04%7C01%7Chvasquezgross%40unr.edu%7C0e9863c0b29d4f667f1e08da07c30fa9%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1%7C0%7C637830831629320472%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=%2FElkOKZ%2FfB41LGqhhgSceI%2FzT46RLE%2Bm8He14QfG9To%3D&reserved=0>

Feel free to attach setup log also

-Colin

On Wed, Mar 16, 2022 at 8:21 PM Hans Vasquez-Gross <hva...@un...<mailto:hva...@un...>> wrote:
Hello,

About 1.25 years ago, I installed JBrowse1 for a new position and got it running with some custom plugins. Now that we have a racked webserver, I am trying to transfer those genomes to our new webserver. First step was to setup the latest JBrowse1 installation on the webserver. However, when running the setup.sh script, I am getting errors during the node.js dependencies setup.

Is there a particular version I should be using? I have Node v17.7.1 installed

I would be happy to send the full setup.log as well.

Thank you,
-Hans


--



[signature_998258195]

Hans Vasquez-Gross, Ph.D

Bioinformatics Scientist,
Nevada Bioinformatics Center

https://www.unr.edu/bioinformatics

hva...@un...<mailto:hva...@un...>

_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=04%7C01%7Chvasquezgross%40unr.edu%7C0e9863c0b29d4f667f1e08da07c30fa9%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1%7C0%7C637830831629320472%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=V2UTL1LL6JfMv5Si6ULr4tRsYjyPUBxLq8mWOjSbBxA%3D&reserved=0>

Re: [Gmod-ajax] Jbrowse2 Gridlines

[Colin <col...@gm...>]

Hi there,

There is not currently a way to do this inside the LGV, but if you want you
can use the "Export SVG" feature and this will not have gridlines

I created an issue to track this here
https://github.com/GMOD/jbrowse-components/issues/2837

-Colin

On Mon, Mar 21, 2022 at 12:40 PM MK Huang via Gmod-ajax <
gmo...@li...> wrote:

> Hi,
>
> Could we get rid of these gridlines in the Jbrowse2 web via editing the
> Index.html file or other parameter setting?
>
>
>
> Many thanks!
>
> Best,
> MK
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] [apollo] remove 'transcript' track

[Nathan D. <nd...@gm...>]

Some quick thoughts:

1 - maybe get rid of the introns.   Not sure if Apollo filters them out or not. 

2 - I think having 2 genes in the same track at the same location may be problematic, the latter one looks problematic.

3 - I *think* (if the problem. Persists) you can remove the “gene” annotation OR potentially (and better), you could add the “topLevelFeature”:”mRNA” as this example below. 

{"storeClass":"JBrowse/Store/SeqFeature/GFF3", "urlTemplate":"raw/824131860720236.gff", "label":"824131860720236", "type":"JBrowse/View/Track/HTMLFeatures", "style":{"className":"feature"}, "key":"824131860720236", "topLevelFeatures":"mRNA", "apollo":{"source":"upload", "type":"GFF3", "topType":"mRNA"}}

Those are my quick guesses. 

Nathan

> On Mar 18, 2022, at 6:50 PM, Johannes Debler <joh...@gm...> wrote:
> 
> Hi Nathan,
> 
> I think it is something odd that came out of combining braker 1 and 2 results. This is one particular gene annotation, have a look at the first and last line, there are two 'gene' annotations for the same location with different IDs. 
> Is there a way to display CDS features only?
> Cheers,
> Johannes
> 
> P9424_ctg_01    AUGUSTUS    gene    220129  221909  1   -   .   ID=nbis-gene-289;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    mRNA    220129  221909  1   -   .   ID=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;Parent=nbis-gene-289;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    exon    220129  221050  .   -   .   ID=exon-29374;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    exon    221100  221660  .   -   .   ID=exon-29375;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    exon    221746  221909  .   -   .   ID=exon-29376;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    CDS 220129  221050  1   -   1   ID=cds-29377;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    CDS 221100  221660  1   -   1   ID=cds-29378;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    CDS 221746  221909  1   -   0   ID=cds-29379;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    intron  221051  221099  1   -   .   ID=intron-18711;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    intron  221661  221745  1   -   .   ID=intron-18712;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    start_codon 221907  221909  .   -   0   ID=start_codon-10667;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    stop_codon  220129  220131  .   -   0   ID=stop_codon-10667;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
> P9424_ctg_01    AUGUSTUS    gene    220129  221909  .   -   .   ID=nbisL1-transcript-10667
> 
> On Fri, 18 Mar 2022 at 23:12, Nathan Dunn <nd...@gm... <mailto:nd...@gm...>> wrote:
> 
> Sometimes it does that if there is a top-level gene. 
> 
> Maybe a more of a JBrowse so cross-posting.
> 
> Could you post the GFF3 snippet? 
> 
> Nathan
> 
> 
>> On Mar 18, 2022, at 12:58 AM, Johannes Debler <joh...@gm... <mailto:joh...@gm...>> wrote:
>> 
>> Hi,
>> I cannot figure out why for some uploaded GFF files Apollo displays the exon structure only, but for some it also displays a 'transcript' track (the blue and gray one underneath all the CDS features). I have removed 'transcript' from the GFF but it still displays it. Any idea how to make that go away?
>> Cheers,
>> Johannes
>> 
>> 
>> <image.png>
>> 
>> -- 
>> To unsubscribe from this group and stop receiving emails from it, send an email to apo...@lb... <mailto:apo...@lb...>.
> 

Re: [Gmod-ajax] [apollo] remove 'transcript' track

[Johannes D. <joh...@gm...>]

Hi Nathan,

I think it is something odd that came out of combining braker 1 and 2
results. This is one particular gene annotation, have a look at the first
and last line, there are two 'gene' annotations for the same location with
different IDs.
Is there a way to display CDS features only?
Cheers,
Johannes

P9424_ctg_01    AUGUSTUS    gene    220129  221909  1   -   .
ID=nbis-gene-289;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    mRNA    220129  221909  1   -   .
ID=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;Parent=nbis-gene-289;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    exon    220129  221050  .   -   .
ID=exon-29374;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    exon    221100  221660  .   -   .
ID=exon-29375;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    exon    221746  221909  .   -   .
ID=exon-29376;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    CDS 220129  221050  1   -   1
ID=cds-29377;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    CDS 221100  221660  1   -   1
ID=cds-29378;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    CDS 221746  221909  1   -   0
ID=cds-29379;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    intron  221051  221099  1   -   .
ID=intron-18711;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    intron  221661  221745  1   -   .
ID=intron-18712;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    start_codon 221907  221909  .   -   0
ID=start_codon-10667;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    stop_codon  220129  220131  .   -   0
ID=stop_codon-10667;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    gene    220129  221909  .   -   .
ID=nbisL1-transcript-10667

On Fri, 18 Mar 2022 at 23:12, Nathan Dunn <nd...@gm...> wrote:

>
> Sometimes it does that if there is a top-level gene.
>
> Maybe a more of a JBrowse so cross-posting.
>
> Could you post the GFF3 snippet?
>
> Nathan
>
>
> On Mar 18, 2022, at 12:58 AM, Johannes Debler <joh...@gm...>
> wrote:
>
> Hi,
> I cannot figure out why for some uploaded GFF files Apollo displays the
> exon structure only, but for some it also displays a 'transcript' track
> (the blue and gray one underneath all the CDS features). I have removed
> 'transcript' from the GFF but it still displays it. Any idea how to make
> that go away?
> Cheers,
> Johannes
>
>
> <image.png>
>
> --
> To unsubscribe from this group and stop receiving emails from it, send an
> email to apo...@lb....
>
>
>

Re: [Gmod-ajax] [apollo] remove 'transcript' track

[Nathan D. <nd...@gm...>]

Sometimes it does that if there is a top-level gene. 

Maybe a more of a JBrowse so cross-posting.

Could you post the GFF3 snippet? 

Nathan


> On Mar 18, 2022, at 12:58 AM, Johannes Debler <joh...@gm...> wrote:
> 
> Hi,
> I cannot figure out why for some uploaded GFF files Apollo displays the exon structure only, but for some it also displays a 'transcript' track (the blue and gray one underneath all the CDS features). I have removed 'transcript' from the GFF but it still displays it. Any idea how to make that go away?
> Cheers,
> Johannes
> 
> 
> <image.png>
> 
> -- 
> To unsubscribe from this group and stop receiving emails from it, send an email to apo...@lb... <mailto:apo...@lb...>.

Re: [Gmod-ajax] Trouble installing JBrowse 1 on new webserver

[Colin <col...@gm...>]

Hi there,
You may need node version 14 or less. More recent versions have an issue
with the node-sass module

See readme
https://github.com/gmod/jbrowse#readme

Feel free to attach setup log also

-Colin

On Wed, Mar 16, 2022 at 8:21 PM Hans Vasquez-Gross <hva...@un...>
wrote:

> Hello,
>
> About 1.25 years ago, I installed JBrowse1 for a new position and got it
> running with some custom plugins. Now that we have a racked webserver, I am
> trying to transfer those genomes to our new webserver. First step was to
> setup the latest JBrowse1 installation on the webserver. However, when
> running the setup.sh script, I am getting errors during the node.js
> dependencies setup.
>
> Is there a particular version I should be using? I have Node v17.7.1
> installed
>
> I would be happy to send the full setup.log as well.
>
> Thank you,
> -Hans
>
> --
>
>
>
> [image: signature_998258195]
>
> *Hans Vasquez-Gross, Ph.D*
>
> Bioinformatics Scientist,
> Nevada Bioinformatics Center
>
> https://www.unr.edu/bioinformatics
>
> hva...@un...
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Trouble installing JBrowse 1 on new webserver

[Hans Vasquez-G. <hva...@un...>]

Hello,

About 1.25 years ago, I installed JBrowse1 for a new position and got it running with some custom plugins. Now that we have a racked webserver, I am trying to transfer those genomes to our new webserver. First step was to setup the latest JBrowse1 installation on the webserver. However, when running the setup.sh script, I am getting errors during the node.js dependencies setup.

Is there a particular version I should be using? I have Node v17.7.1 installed

I would be happy to send the full setup.log as well.

Thank you,
-Hans


--



[signature_998258195]

Hans Vasquez-Gross, Ph.D

Bioinformatics Scientist,
Nevada Bioinformatics Center

https://www.unr.edu/bioinformatics

hva...@un...<mailto:hva...@un...>

[Gmod-ajax] Jbrowse2 Gridlines

[<hm...@qq...>]

Hi,

Could we get rid of these gridlines in the Jbrowse2 web via editing the Index.html file or other parameter setting?




Many thanks!


Best,
MK

[Gmod-ajax] 2022 AgBioData Community Workshop

[Annarita M. <ama...@ar...>]

Dear JBrowse community members,

I am Annarita Marrano, the program coordinator of AgBioData
<https://www.agbiodata.org/>.

AgBioData is a consortium of agricultural biological databases and
associated resources working together to ensure standards and best
practices for the acquisition, display, and retrieval of genomic, genetic,
and breeding data.

We’d like to invite you to join the “2022 AgBioData Community Workshop:
Facilitating crosstalk and network building across Working Groups” on March
15–17 (7-9 AM PT).

Anyone who uses, generates or manages agricultural biological data is
encouraged to attend. Hearing about the issues that you encounter when
searching for, accessing, and reusing data in your research is very
important for developing standards and best practices for FAIR data.
Even if you can’t make it all three days, we hope that you can participate.

As part of our NSF RCN grant <https://www.agbiodata.org/node/472>, we
currently have nine working groups (WGs) focusing on different aspects of
data sharing and management in agriculture (more information about the WGs
here <https://www.agbiodata.org/all-working-groups>). The goals of this
community workshop are:


   -

   providing a forum for the individual WGs to communicate what they are
   working on;

   -

   gathering detailed, impactful community feedback on specific questions
   that the WGs have about data curation, archiving, and management in
   agriculture.



Each day will start with short presentations from selected working groups,
followed by breakout sessions, where WG and non-WG members can meet and
discuss relevant topics, and a brief reporting period at the end.



Register for our community workshop here
<https://us06web.zoom.us/meeting/register/tZYtduqqqjsrGdfRHdV8yKhUNHUQBbAeLIEm>and
for more information on the schedule visit our website
<https://www.agbiodata.org/node/475>.

Please email us with any questions.

Best regards,

Annarita

Re: [Gmod-ajax] JBrowse2 CRAM rendering problem after upgrade to 1.6.4

[Colin <col...@gm...>]

Fix released in 1.6.5 :)

Thanks again for reporting!


-Colin

On Wed, Feb 16, 2022 at 3:45 PM Colin <col...@gm...> wrote:

> Excellent, thank you for reporting the issue! We should have a new version
> out soon
>
>
> -Colin
>
> On Wed, Feb 16, 2022 at 3:02 PM Ke Jiang <bio...@gm...> wrote:
>
>> Hi, Colin,
>>
>> Thanks for the quick response. I saw this error with both Safari and
>> Firefox. Now you mention the rendering issue with the intron lines, I did
>> notice that a while ago. The distinction between BAM and CRAM mentioned in
>> the original email was not accurate. The error not showing up for the BAM
>> tracks was because the coverage was continuous in the WGS data, which
>> happens to be using BAM, while the RNA-Seq data with introns/gaps happens
>> to be CRAM files.
>>
>> Thank you very much for fixing this! Since it was a small glitch for
>> alignment tracks only, I think I'll wait for 1.6.5 to upgrade.
>>
>> Best.
>>
>> Ke
>>
>> On Tue, Feb 15, 2022 at 6:22 PM Colin <col...@gm...> wrote:
>>
>>> Hi Ke,
>>> This is an interesting error. The issue would probably be related to the
>>> new rendering of the "sashimi" style arcs introduced in 1.5.2 (
>>> https://jbrowse.org/jb2/blog/2021/12/20/v1.5.2-release/) but I have not
>>> seen this error.
>>>
>>> Can you tell me what browser you are using?
>>>
>>>
>>> I found what I think is a fix here
>>> https://github.com/GMOD/jbrowse-components/pull/2750 but I would still
>>> like to know more info because there are also some possible rendering
>>> glitches in your screenshot (looks like some "intron" lines are drawn on
>>> top of features). If you have data that reproduces this let me know
>>>
>>>
>>> -Colin
>>>
>>>
>>>
>>> On Tue, Feb 15, 2022 at 2:31 PM Ke Jiang <bio...@gm...> wrote:
>>>
>>>> Hi,
>>>>
>>>> After upgrading to 1.6.4, the CRAM tracks give an error
>>>> ("e.bezierCurveTo is nor function") when rendering coverage plots (the BAM
>>>> tracks are fine), the read alignment rendering part seems to be fine. Here
>>>> is a screenshot and configuration. I'd like to put it here before taking it
>>>> to github issues, maybe there is a simple fix or configuration error on my
>>>> side.
>>>>
>>>> Thanks!
>>>>
>>>> Ke
>>>>
>>>> [image: ScreenShot.png]
>>>>
>>>>
>>>> {
>>>>       "type": "AlignmentsTrack",
>>>>       "trackId": "SRR11185046_reads",
>>>>       "name": "SRR11185046",
>>>>       "category": [
>>>>         "mRNASeq"
>>>>       ],
>>>>       "assemblyNames": [
>>>>         "Porcine S. scrofa v11.1"
>>>>       ],
>>>>       "adapter": {
>>>>         "type": "CramAdapter",
>>>>         "cramLocation": {
>>>>           "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram"
>>>>         },
>>>>         "craiLocation": {
>>>>           "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram.crai"
>>>>         },
>>>>         "sequenceAdapter": {
>>>>           "type": "IndexedFastaAdapter",
>>>>           "fastaLocation": {
>>>>             "uri": "Sscrofa11.1.fa"
>>>>           },
>>>>           "faiLocation": {
>>>>             "uri": "Sscrofa11.1.fa.fai"
>>>>           }
>>>>         }
>>>>       }
>>>>     },
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>

Re: [Gmod-ajax] JBrowse2 CRAM rendering problem after upgrade to 1.6.4

[Colin <col...@gm...>]

Excellent, thank you for reporting the issue! We should have a new version
out soon


-Colin

On Wed, Feb 16, 2022 at 3:02 PM Ke Jiang <bio...@gm...> wrote:

> Hi, Colin,
>
> Thanks for the quick response. I saw this error with both Safari and
> Firefox. Now you mention the rendering issue with the intron lines, I did
> notice that a while ago. The distinction between BAM and CRAM mentioned in
> the original email was not accurate. The error not showing up for the BAM
> tracks was because the coverage was continuous in the WGS data, which
> happens to be using BAM, while the RNA-Seq data with introns/gaps happens
> to be CRAM files.
>
> Thank you very much for fixing this! Since it was a small glitch for
> alignment tracks only, I think I'll wait for 1.6.5 to upgrade.
>
> Best.
>
> Ke
>
> On Tue, Feb 15, 2022 at 6:22 PM Colin <col...@gm...> wrote:
>
>> Hi Ke,
>> This is an interesting error. The issue would probably be related to the
>> new rendering of the "sashimi" style arcs introduced in 1.5.2 (
>> https://jbrowse.org/jb2/blog/2021/12/20/v1.5.2-release/) but I have not
>> seen this error.
>>
>> Can you tell me what browser you are using?
>>
>>
>> I found what I think is a fix here
>> https://github.com/GMOD/jbrowse-components/pull/2750 but I would still
>> like to know more info because there are also some possible rendering
>> glitches in your screenshot (looks like some "intron" lines are drawn on
>> top of features). If you have data that reproduces this let me know
>>
>>
>> -Colin
>>
>>
>>
>> On Tue, Feb 15, 2022 at 2:31 PM Ke Jiang <bio...@gm...> wrote:
>>
>>> Hi,
>>>
>>> After upgrading to 1.6.4, the CRAM tracks give an error
>>> ("e.bezierCurveTo is nor function") when rendering coverage plots (the BAM
>>> tracks are fine), the read alignment rendering part seems to be fine. Here
>>> is a screenshot and configuration. I'd like to put it here before taking it
>>> to github issues, maybe there is a simple fix or configuration error on my
>>> side.
>>>
>>> Thanks!
>>>
>>> Ke
>>>
>>> [image: ScreenShot.png]
>>>
>>>
>>> {
>>>       "type": "AlignmentsTrack",
>>>       "trackId": "SRR11185046_reads",
>>>       "name": "SRR11185046",
>>>       "category": [
>>>         "mRNASeq"
>>>       ],
>>>       "assemblyNames": [
>>>         "Porcine S. scrofa v11.1"
>>>       ],
>>>       "adapter": {
>>>         "type": "CramAdapter",
>>>         "cramLocation": {
>>>           "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram"
>>>         },
>>>         "craiLocation": {
>>>           "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram.crai"
>>>         },
>>>         "sequenceAdapter": {
>>>           "type": "IndexedFastaAdapter",
>>>           "fastaLocation": {
>>>             "uri": "Sscrofa11.1.fa"
>>>           },
>>>           "faiLocation": {
>>>             "uri": "Sscrofa11.1.fa.fai"
>>>           }
>>>         }
>>>       }
>>>     },
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>

Re: [Gmod-ajax] JBrowse2 CRAM rendering problem after upgrade to 1.6.4

[Ke J. <bio...@gm...>]

Hi, Colin,

Thanks for the quick response. I saw this error with both Safari and
Firefox. Now you mention the rendering issue with the intron lines, I did
notice that a while ago. The distinction between BAM and CRAM mentioned in
the original email was not accurate. The error not showing up for the BAM
tracks was because the coverage was continuous in the WGS data, which
happens to be using BAM, while the RNA-Seq data with introns/gaps happens
to be CRAM files.

Thank you very much for fixing this! Since it was a small glitch for
alignment tracks only, I think I'll wait for 1.6.5 to upgrade.

Best.

Ke

On Tue, Feb 15, 2022 at 6:22 PM Colin <col...@gm...> wrote:

> Hi Ke,
> This is an interesting error. The issue would probably be related to the
> new rendering of the "sashimi" style arcs introduced in 1.5.2 (
> https://jbrowse.org/jb2/blog/2021/12/20/v1.5.2-release/) but I have not
> seen this error.
>
> Can you tell me what browser you are using?
>
>
> I found what I think is a fix here
> https://github.com/GMOD/jbrowse-components/pull/2750 but I would still
> like to know more info because there are also some possible rendering
> glitches in your screenshot (looks like some "intron" lines are drawn on
> top of features). If you have data that reproduces this let me know
>
>
> -Colin
>
>
>
> On Tue, Feb 15, 2022 at 2:31 PM Ke Jiang <bio...@gm...> wrote:
>
>> Hi,
>>
>> After upgrading to 1.6.4, the CRAM tracks give an error ("e.bezierCurveTo
>> is nor function") when rendering coverage plots (the BAM tracks are fine),
>> the read alignment rendering part seems to be fine. Here is a screenshot
>> and configuration. I'd like to put it here before taking it to github
>> issues, maybe there is a simple fix or configuration error on my side.
>>
>> Thanks!
>>
>> Ke
>>
>> [image: ScreenShot.png]
>>
>>
>> {
>>       "type": "AlignmentsTrack",
>>       "trackId": "SRR11185046_reads",
>>       "name": "SRR11185046",
>>       "category": [
>>         "mRNASeq"
>>       ],
>>       "assemblyNames": [
>>         "Porcine S. scrofa v11.1"
>>       ],
>>       "adapter": {
>>         "type": "CramAdapter",
>>         "cramLocation": {
>>           "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram"
>>         },
>>         "craiLocation": {
>>           "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram.crai"
>>         },
>>         "sequenceAdapter": {
>>           "type": "IndexedFastaAdapter",
>>           "fastaLocation": {
>>             "uri": "Sscrofa11.1.fa"
>>           },
>>           "faiLocation": {
>>             "uri": "Sscrofa11.1.fa.fai"
>>           }
>>         }
>>       }
>>     },
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] JBrowse2 CRAM rendering problem after upgrade to 1.6.4

[Colin <col...@gm...>]

Hi Ke,
This is an interesting error. The issue would probably be related to the
new rendering of the "sashimi" style arcs introduced in 1.5.2 (
https://jbrowse.org/jb2/blog/2021/12/20/v1.5.2-release/) but I have not
seen this error.

Can you tell me what browser you are using?


I found what I think is a fix here
https://github.com/GMOD/jbrowse-components/pull/2750 but I would still like
to know more info because there are also some possible rendering glitches
in your screenshot (looks like some "intron" lines are drawn on top of
features). If you have data that reproduces this let me know


-Colin



On Tue, Feb 15, 2022 at 2:31 PM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> After upgrading to 1.6.4, the CRAM tracks give an error ("e.bezierCurveTo
> is nor function") when rendering coverage plots (the BAM tracks are fine),
> the read alignment rendering part seems to be fine. Here is a screenshot
> and configuration. I'd like to put it here before taking it to github
> issues, maybe there is a simple fix or configuration error on my side.
>
> Thanks!
>
> Ke
>
> [image: ScreenShot.png]
>
>
> {
>       "type": "AlignmentsTrack",
>       "trackId": "SRR11185046_reads",
>       "name": "SRR11185046",
>       "category": [
>         "mRNASeq"
>       ],
>       "assemblyNames": [
>         "Porcine S. scrofa v11.1"
>       ],
>       "adapter": {
>         "type": "CramAdapter",
>         "cramLocation": {
>           "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram"
>         },
>         "craiLocation": {
>           "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram.crai"
>         },
>         "sequenceAdapter": {
>           "type": "IndexedFastaAdapter",
>           "fastaLocation": {
>             "uri": "Sscrofa11.1.fa"
>           },
>           "faiLocation": {
>             "uri": "Sscrofa11.1.fa.fai"
>           }
>         }
>       }
>     },
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse2 CRAM rendering problem after upgrade to 1.6.4

[Ke J. <bio...@gm...>]

Hi,

After upgrading to 1.6.4, the CRAM tracks give an error ("e.bezierCurveTo
is nor function") when rendering coverage plots (the BAM tracks are fine),
the read alignment rendering part seems to be fine. Here is a screenshot
and configuration. I'd like to put it here before taking it to github
issues, maybe there is a simple fix or configuration error on my side.

Thanks!

Ke

[image: ScreenShot.png]


{
      "type": "AlignmentsTrack",
      "trackId": "SRR11185046_reads",
      "name": "SRR11185046",
      "category": [
        "mRNASeq"
      ],
      "assemblyNames": [
        "Porcine S. scrofa v11.1"
      ],
      "adapter": {
        "type": "CramAdapter",
        "cramLocation": {
          "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram"
        },
        "craiLocation": {
          "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram.crai"
        },
        "sequenceAdapter": {
          "type": "IndexedFastaAdapter",
          "fastaLocation": {
            "uri": "Sscrofa11.1.fa"
          },
          "faiLocation": {
            "uri": "Sscrofa11.1.fa.fai"
          }
        }
      }
    },

Re: [Gmod-ajax] JBrowse2

[Ke J. <bio...@gm...>]

Great! It works. Thank you for the help!

I missed two things in my previous example: 1. before "&sessionTracks",
"&tracks=url_track" is also needed to turn the track on first; 2. proper
HTML encoding is needed in the url, for example, spaces by %20 and quotes
by %22.

For a test in case someone is also trying this:

The following is the one did not work:

http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&sessionTracks=[{
<http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&sessionTracks=[%7B>"type":"FeatureTrack","trackId":"url_track","name":"URL
track","assemblyNames":["Porcine S. scrofa
v11.1"],"adapter":{"type":"FromConfigAdapter","features":[{"uniqueId":"one","refName":"1","start":6100,"end":6200,"name":"dynamic_test"}]}}]

The following is the url that works:

http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&tracks=url_track&sessionTracks=[{%22type%22:%22FeatureTrack%22,%22trackId%22:%22url_track%22,%22name%22:%22URL%20track%22,%22assemblyNames%22:[%22Porcine%20S.%20scrofa%20v11.1%22],%22adapter%22:{%22type%22:%22FromConfigAdapter%22,%22features%22:[{%22uniqueId%22:%22one%22,%22refName%22:%221%22,%22start%22:6400,%22end%22:6500,%22name%22:%22dynamic_test%22}]}}]





On Mon, Feb 7, 2022 at 4:48 PM Colin <col...@gm...> wrote:

> Hi Ke
>
> Basically &sessionTracks= added this to your session, and then you have to
> turn the track on with &tracks= referring to the trackId from your
> sessionTrack
>
> Example URL
>
>
> https://jbrowse.org/code/jb2/v1.6.4/?config=test_data/volvox/config.json&loc=ctgA:0-500&assembly=volvox&tracks=url_track&sessionTracks=[{%22type%22:%22FeatureTrack%22,%22trackId%22:%22url_track%22,%22name%22:%22URL%20track%22,%22assemblyNames%22:[%22volvox%22],%22adapter%22:{%22type%22:%22FromConfigAdapter%22,%22features%22:[{%22uniqueId%22:%22one%22,%22refName%22:%22ctgA%22,%22start%22:100,%22end%22:200,%22name%22:%22URL%20Feature%22}]}}]
> <https://jbrowse.org/code/jb2/v1.6.4/?config=test_data/volvox/config.json&loc=ctgA:0-500&assembly=volvox&tracks=url_track&sessionTracks=[%7B%22type%22:%22FeatureTrack%22,%22trackId%22:%22url_track%22,%22name%22:%22URL%20track%22,%22assemblyNames%22:[%22volvox%22],%22adapter%22:%7B%22type%22:%22FromConfigAdapter%22,%22features%22:[%7B%22uniqueId%22:%22one%22,%22refName%22:%22ctgA%22,%22start%22:100,%22end%22:200,%22name%22:%22URL%20Feature%22%7D]%7D%7D]>
>
>
> -Colin
>
> On Mon, Feb 7, 2022 at 2:20 PM Ke Jiang <bio...@gm...> wrote:
>
>> Hi,
>>
>> It was great to see this feature! I was looking forward to it from the
>> start of JBrowse2. Thanks to all the developers behind this! The URL works
>> well but the &sessionTracks didn't quite work for me so far, here is an
>> example:
>>
>>
>> http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&sessionTracks=[{
>> <http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&sessionTracks=[%7B>"type":"FeatureTrack","trackId":"url_track","name":"URL
>> track","assemblyNames":["Porcine S. scrofa
>> v11.1"],"adapter":{"type":"FromConfigAdapter","features":[{"uniqueId":"one","refName":"1","start":6100,"end":6200,"name":"Boris"}]}}]
>>
>> The url works properly up to the "sessionTracks" part, but there was no
>> dynamic track loaded or shown. Anyone have any advice? Do I need to code
>> the spaces in the configuration with "%20", too?
>>
>> Thanks!
>>
>> Ke
>>
>> On Fri, Feb 4, 2022 at 11:45 AM han...@ge... <
>> han...@ge...> wrote:
>>
>>> Hi Colin,
>>>     This is helpful for me. Thanks
>>>
>>> Best
>>>
>>> ------------------------------
>>> Hang Yang, Ph.D.
>>>
>>> Institute of Genetics and Developmental Biology
>>> Chinese Academy of Sciences
>>> No.1 West Beichen Road, Chaoyang District
>>> Beijing, China 100101
>>>
>>>
>>> *From:* Colin <col...@gm...>
>>> *Date:* 2022-02-03 05:25
>>> *To:* han...@ge...
>>> *CC:* gmod-ajax <gmo...@li...>
>>> *Subject:* Re: [Gmod-ajax] JBrowse2
>>> Hi there
>>> JBrowse 1.6.4 merged this finally. Docs here
>>> https://jbrowse.org/jb2/docs/urlparams/
>>>
>>> Let me know if that helps:)
>>> -Colin
>>>
>>> On Tue, Jan 11, 2022 at 11:02 AM Colin <col...@gm...> wrote:
>>>
>>>> Hello,
>>>> This feature has been implemented on a work-in-progress branch. It is
>>>> planned to be released in an upcoming version soon
>>>>
>>>> https://github.com/GMOD/jbrowse-components/pull/2165
>>>>
>>>>
>>>> If you want to try to preview the feature before the official release
>>>> you can use the CLI command to test out the branch (it is otherwise up to
>>>> date with other latest release features)
>>>>
>>>>     jbrowse create --branch nav_with_urlbar2 jbrowse2
>>>>
>>>> This will download the code from that branch to a folder named
>>>> jbrowse2, and then you can use URLs like
>>>>
>>>>
>>>> http://yoursite.com/jbrowse2/?loc=chr1:1-100&assembly=hg19&tracks=track_id1,track_id2
>>>>
>>>>
>>>> -Colin
>>>>
>>>> On Tue, Jan 11, 2022 at 10:12 AM han...@ge... <
>>>> han...@ge...> wrote:
>>>>
>>>>> Dear JBrowse developers,
>>>>>     I am a user of the JBrowse. It's really a useful tool.
>>>>>     I have a question about how to use URL query API in JBrowse2
>>>>>  e.g. specifying ?loc=1:1..100.
>>>>>     Thanks, Look forward to your reply.
>>>>>
>>>>> Best
>>>>>
>>>>> ------------------------------
>>>>> Hang Yang, Ph.D.
>>>>>
>>>>> Institute of Genetics and Developmental Biology
>>>>> Chinese Academy of Sciences
>>>>> No.1 West Beichen Road, Chaoyang District
>>>>> Beijing, China 100101
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>
>>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>

Re: [Gmod-ajax] JBrowse2

[Colin <col...@gm...>]

Can try to elaborate a bit but doc example here
https://jbrowse.org/jb2/docs/urlparams/#sessiontracks

Glad it is already getting interest :)


-Colin

On Mon, Feb 7, 2022 at 3:47 PM Colin <col...@gm...> wrote:

> Hi Ke
>
> Basically &sessionTracks= added this to your session, and then you have to
> turn the track on with &tracks= referring to the trackId from your
> sessionTrack
>
> Example URL
>
>
> https://jbrowse.org/code/jb2/v1.6.4/?config=test_data/volvox/config.json&loc=ctgA:0-500&assembly=volvox&tracks=url_track&sessionTracks=[{%22type%22:%22FeatureTrack%22,%22trackId%22:%22url_track%22,%22name%22:%22URL%20track%22,%22assemblyNames%22:[%22volvox%22],%22adapter%22:{%22type%22:%22FromConfigAdapter%22,%22features%22:[{%22uniqueId%22:%22one%22,%22refName%22:%22ctgA%22,%22start%22:100,%22end%22:200,%22name%22:%22URL%20Feature%22}]}}]
> <https://jbrowse.org/code/jb2/v1.6.4/?config=test_data/volvox/config.json&loc=ctgA:0-500&assembly=volvox&tracks=url_track&sessionTracks=[%7B%22type%22:%22FeatureTrack%22,%22trackId%22:%22url_track%22,%22name%22:%22URL%20track%22,%22assemblyNames%22:[%22volvox%22],%22adapter%22:%7B%22type%22:%22FromConfigAdapter%22,%22features%22:[%7B%22uniqueId%22:%22one%22,%22refName%22:%22ctgA%22,%22start%22:100,%22end%22:200,%22name%22:%22URL%20Feature%22%7D]%7D%7D]>
>
>
> -Colin
>
> On Mon, Feb 7, 2022 at 2:20 PM Ke Jiang <bio...@gm...> wrote:
>
>> Hi,
>>
>> It was great to see this feature! I was looking forward to it from the
>> start of JBrowse2. Thanks to all the developers behind this! The URL works
>> well but the &sessionTracks didn't quite work for me so far, here is an
>> example:
>>
>>
>> http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&sessionTracks=[{
>> <http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&sessionTracks=[%7B>"type":"FeatureTrack","trackId":"url_track","name":"URL
>> track","assemblyNames":["Porcine S. scrofa
>> v11.1"],"adapter":{"type":"FromConfigAdapter","features":[{"uniqueId":"one","refName":"1","start":6100,"end":6200,"name":"Boris"}]}}]
>>
>> The url works properly up to the "sessionTracks" part, but there was no
>> dynamic track loaded or shown. Anyone have any advice? Do I need to code
>> the spaces in the configuration with "%20", too?
>>
>> Thanks!
>>
>> Ke
>>
>> On Fri, Feb 4, 2022 at 11:45 AM han...@ge... <
>> han...@ge...> wrote:
>>
>>> Hi Colin,
>>>     This is helpful for me. Thanks
>>>
>>> Best
>>>
>>> ------------------------------
>>> Hang Yang, Ph.D.
>>>
>>> Institute of Genetics and Developmental Biology
>>> Chinese Academy of Sciences
>>> No.1 West Beichen Road, Chaoyang District
>>> Beijing, China 100101
>>>
>>>
>>> *From:* Colin <col...@gm...>
>>> *Date:* 2022-02-03 05:25
>>> *To:* han...@ge...
>>> *CC:* gmod-ajax <gmo...@li...>
>>> *Subject:* Re: [Gmod-ajax] JBrowse2
>>> Hi there
>>> JBrowse 1.6.4 merged this finally. Docs here
>>> https://jbrowse.org/jb2/docs/urlparams/
>>>
>>> Let me know if that helps:)
>>> -Colin
>>>
>>> On Tue, Jan 11, 2022 at 11:02 AM Colin <col...@gm...> wrote:
>>>
>>>> Hello,
>>>> This feature has been implemented on a work-in-progress branch. It is
>>>> planned to be released in an upcoming version soon
>>>>
>>>> https://github.com/GMOD/jbrowse-components/pull/2165
>>>>
>>>>
>>>> If you want to try to preview the feature before the official release
>>>> you can use the CLI command to test out the branch (it is otherwise up to
>>>> date with other latest release features)
>>>>
>>>>     jbrowse create --branch nav_with_urlbar2 jbrowse2
>>>>
>>>> This will download the code from that branch to a folder named
>>>> jbrowse2, and then you can use URLs like
>>>>
>>>>
>>>> http://yoursite.com/jbrowse2/?loc=chr1:1-100&assembly=hg19&tracks=track_id1,track_id2
>>>>
>>>>
>>>> -Colin
>>>>
>>>> On Tue, Jan 11, 2022 at 10:12 AM han...@ge... <
>>>> han...@ge...> wrote:
>>>>
>>>>> Dear JBrowse developers,
>>>>>     I am a user of the JBrowse. It's really a useful tool.
>>>>>     I have a question about how to use URL query API in JBrowse2
>>>>>  e.g. specifying ?loc=1:1..100.
>>>>>     Thanks, Look forward to your reply.
>>>>>
>>>>> Best
>>>>>
>>>>> ------------------------------
>>>>> Hang Yang, Ph.D.
>>>>>
>>>>> Institute of Genetics and Developmental Biology
>>>>> Chinese Academy of Sciences
>>>>> No.1 West Beichen Road, Chaoyang District
>>>>> Beijing, China 100101
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>
>>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>

Re: [Gmod-ajax] JBrowse2

[Colin <col...@gm...>]

Hi Ke

Basically &sessionTracks= added this to your session, and then you have to
turn the track on with &tracks= referring to the trackId from your
sessionTrack

Example URL

https://jbrowse.org/code/jb2/v1.6.4/?config=test_data/volvox/config.json&loc=ctgA:0-500&assembly=volvox&tracks=url_track&sessionTracks=[{%22type%22:%22FeatureTrack%22,%22trackId%22:%22url_track%22,%22name%22:%22URL%20track%22,%22assemblyNames%22:[%22volvox%22],%22adapter%22:{%22type%22:%22FromConfigAdapter%22,%22features%22:[{%22uniqueId%22:%22one%22,%22refName%22:%22ctgA%22,%22start%22:100,%22end%22:200,%22name%22:%22URL%20Feature%22}]}}]


-Colin

On Mon, Feb 7, 2022 at 2:20 PM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> It was great to see this feature! I was looking forward to it from the
> start of JBrowse2. Thanks to all the developers behind this! The URL works
> well but the &sessionTracks didn't quite work for me so far, here is an
> example:
>
>
> http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&sessionTracks=[{
> <http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&sessionTracks=[%7B>"type":"FeatureTrack","trackId":"url_track","name":"URL
> track","assemblyNames":["Porcine S. scrofa
> v11.1"],"adapter":{"type":"FromConfigAdapter","features":[{"uniqueId":"one","refName":"1","start":6100,"end":6200,"name":"Boris"}]}}]
>
> The url works properly up to the "sessionTracks" part, but there was no
> dynamic track loaded or shown. Anyone have any advice? Do I need to code
> the spaces in the configuration with "%20", too?
>
> Thanks!
>
> Ke
>
> On Fri, Feb 4, 2022 at 11:45 AM han...@ge... <
> han...@ge...> wrote:
>
>> Hi Colin,
>>     This is helpful for me. Thanks
>>
>> Best
>>
>> ------------------------------
>> Hang Yang, Ph.D.
>>
>> Institute of Genetics and Developmental Biology
>> Chinese Academy of Sciences
>> No.1 West Beichen Road, Chaoyang District
>> Beijing, China 100101
>>
>>
>> *From:* Colin <col...@gm...>
>> *Date:* 2022-02-03 05:25
>> *To:* han...@ge...
>> *CC:* gmod-ajax <gmo...@li...>
>> *Subject:* Re: [Gmod-ajax] JBrowse2
>> Hi there
>> JBrowse 1.6.4 merged this finally. Docs here
>> https://jbrowse.org/jb2/docs/urlparams/
>>
>> Let me know if that helps:)
>> -Colin
>>
>> On Tue, Jan 11, 2022 at 11:02 AM Colin <col...@gm...> wrote:
>>
>>> Hello,
>>> This feature has been implemented on a work-in-progress branch. It is
>>> planned to be released in an upcoming version soon
>>>
>>> https://github.com/GMOD/jbrowse-components/pull/2165
>>>
>>>
>>> If you want to try to preview the feature before the official release
>>> you can use the CLI command to test out the branch (it is otherwise up to
>>> date with other latest release features)
>>>
>>>     jbrowse create --branch nav_with_urlbar2 jbrowse2
>>>
>>> This will download the code from that branch to a folder named jbrowse2,
>>> and then you can use URLs like
>>>
>>>
>>> http://yoursite.com/jbrowse2/?loc=chr1:1-100&assembly=hg19&tracks=track_id1,track_id2
>>>
>>>
>>> -Colin
>>>
>>> On Tue, Jan 11, 2022 at 10:12 AM han...@ge... <
>>> han...@ge...> wrote:
>>>
>>>> Dear JBrowse developers,
>>>>     I am a user of the JBrowse. It's really a useful tool.
>>>>     I have a question about how to use URL query API in JBrowse2
>>>>  e.g. specifying ?loc=1:1..100.
>>>>     Thanks, Look forward to your reply.
>>>>
>>>> Best
>>>>
>>>> ------------------------------
>>>> Hang Yang, Ph.D.
>>>>
>>>> Institute of Genetics and Developmental Biology
>>>> Chinese Academy of Sciences
>>>> No.1 West Beichen Road, Chaoyang District
>>>> Beijing, China 100101
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>