gmod-ajax — JBrowse list

[Gmod-ajax] Failed to import the fasta file. Procedure

[<cho...@qq...>]

After installing jbrowse1 software, I want to import a fasta file, I follow the instructions, but nothing is displayed.Please help me, thank you.

[Gmod-ajax] About the use of programs under jbrowse/bin

[yun w. <wan...@gm...>]

I would like to know what is the role of these files under the jbrowse/bin
directory?

[image: 屏幕截图 2023-05-01 111322.png]

Now I have some xxx.maf data, how can I create an index file for it？

Re: [Gmod-ajax] can not opening local gz file

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

You may want to use a different file server (apache2, or nginx, or python
RangeHTTPServer, or npx serve, etc) to serve your static files as the
Django server doesn't support range requests and adds some gzip headers
like Content-Encpding: gzip which jbrowse does not want.

I tried the Django server here and ran into many of the same issues you did
so made a small write up in the readme
https://github.com/cmdcolin/django-jbrowse2-nonworking-example

-Colin

On Wed, Apr 19, 2023, 12:45 AM lpsong--- via Gmod-ajax <
gmo...@li...> wrote:

> I have embedded Jbrowse into a django framework site and am using the
> example given by doc. I have this problem, I get error when opening local
> gz file, the information is'index.ts:144 GET
> http://8.218.176.27:7000/static/Jbrowse/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz
> net::ERR_CONTENT_DECODING_FAILED'. How can I fix it please?
>
> ------------------------------
> 宋利璞
> 中国科学院 监督与审计局
> 北京市西城区三里河路52号（100864）
> 电话：010-68597127
> 手机：15210675921
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] can not opening local gz file

[<lp...@ca...>]

I have embedded Jbrowse into a django framework site and am using the example given by doc. I have this problem, I get error when opening local gz file, the information is'index.ts:144 GET http://8.218.176.27:7000/static/Jbrowse/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz net::ERR_CONTENT_DECODING_FAILED'. How can I fix it please?



宋利璞
中国科学院 监督与审计局
北京市西城区三里河路52号（100864）
电话：010-68597127
手机：15210675921

Re: [Gmod-ajax] [apollo] Importing itemRgb column of bed files

[Antonin T. <ant...@gm...>]

Hi Colin,

Thanks for the advice, the BEDTabix track upload worked great!

Antonin


Le vendredi 14 avril 2023 à 19:46:59 UTC+2, Colin a écrit :

Hi Antonin
I would use BEDTabix because the BED handling of flatfile-to-json doesn't 
load the itemRgb info correctly as far as I can tell, but with BEDTabix, 
it's fairly easy.

Example config for a BEDTabix track

{
  "label": "My track",
  "urlTemplate": "file.bed.gz",
  "storeClass": "JBrowse/Store/SeqFeature/BEDTabix",
  "style": { "color": "function(feature){return feature.get('itemrgb')}" }
}

-Colin



On Thu, Apr 13, 2023 at 11:03 AM Nathan Dunn <ndu...@gmail.com> wrote:


This is more of a JBrowse 1 question. 

Nathan 


On Apr 13, 2023, at 8:49 AM, Antonin Thiébaut <antonin.t...@gmail.com> 
wrote:

Hello all,

I was wondering whether there is a way to import the itemRgb column of a 
bed file. I would like to use it to color the features.

I am currently using the following command in Apollo v2.6.2 to create the 
bed tracks:
perl -w bin/flatfile-to-json.pl --bed path/to/bed --trackLabel putative_orf 
--key "PCCR bacteria" --out data/bacteria/ --config '{ "category": "Coding 
Potential" }' --trackType CanvasFeatures

This successfully imports the file and there is no display problem on the 
browser, however I have the feeling it only imports the data of the first 
few columns of the file (I checked in the tracks directory that is created 
during the import). Can it be caused by an improper formatting or my file? 
Or am I missing an option in the command, is there another script to do 
this?

Thank you in advance,

*Antonin*

-- 
To unsubscribe from this group and stop receiving emails from it, send an 
email to apollo+un...@lbl.gov.


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To unsubscribe from this group and stop receiving emails from it, send an 
email to apollo+un...@lbl.gov.

Re: [Gmod-ajax] [apollo] Importing itemRgb column of bed files

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

Hi Antonin
I would use BEDTabix because the BED handling of flatfile-to-json doesn't
load the itemRgb info correctly as far as I can tell, but with BEDTabix,
it's fairly easy.

Example config for a BEDTabix track

{
  "label": "My track",
  "urlTemplate": "file.bed.gz",
  "storeClass": "JBrowse/Store/SeqFeature/BEDTabix",
  "style": { "color": "function(feature){return feature.get('itemrgb')}" }
}

-Colin



On Thu, Apr 13, 2023 at 11:03 AM Nathan Dunn <nd...@gm...> wrote:

>
> This is more of a JBrowse 1 question.
>
> Nathan
>
>
> On Apr 13, 2023, at 8:49 AM, Antonin Thiébaut <
> ant...@gm...> wrote:
>
> Hello all,
>
> I was wondering whether there is a way to import the itemRgb column of a
> bed file. I would like to use it to color the features.
>
> I am currently using the following command in Apollo v2.6.2 to create the
> bed tracks:
> perl -w bin/flatfile-to-json.pl --bed path/to/bed --trackLabel
> putative_orf --key "PCCR bacteria" --out data/bacteria/ --config '{
> "category": "Coding Potential" }' --trackType CanvasFeatures
>
> This successfully imports the file and there is no display problem on the
> browser, however I have the feeling it only imports the data of the first
> few columns of the file (I checked in the tracks directory that is created
> during the import). Can it be caused by an improper formatting or my file?
> Or am I missing an option in the command, is there another script to do
> this?
>
> Thank you in advance,
>
> *Antonin*
>
> --
> 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....
>

[Gmod-ajax] Fwd: Submit your abstract to BOSC 2023 by April 20! 🍐

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

Highlights

   - Submit <https://www.open-bio.org/events/bosc-2023/submit/> your 1-2
   page abstract by April 20 (by the end of the day anywhere in the world).
   (Sorry, no extensions.)
   -

      You can request registration fee assistance right on the submission
      form!
      -

   We have two exciting Keynote Speakers
   <https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/> lined up!
   -

   We are planning a Panel Discussion about Open and Ethical Data Sharing!
   -

   BOSC and Bio-Ontologies
   <https://www.bio-ontologies.org.uk/ismb-annual-meeting/2023-meeting>
   will join forces for a joint session on July 24 or 25.
   - We welcome our first sponsors
   <https://www.open-bio.org/events/sponsors/> (more coming soon):
   GigaScience <https://academic.oup.com/gigascience>, GeneVia
   <https://geneviatechnologies.com/>, and Software Sustainability Institute
   <https://www.software.ac.uk/>!


Keynote speakers
[image: Sara El-Gebali]

Sara El-Gebali
<https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/>
(SciLifeLab-DataCentre-Sweden): “A New Odyssey: Pioneering the Future of
Scientific Progress Through Open Collaboration.”

Joseph M. Yracheta
<https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/> (Native
BioData Consortium): “The Dissonance between Scientific Altruism &
Capitalist Extraction: The Zero Trust and Federated Data Sovereignty
Solution

Abstract submission

We encourage you to submit abstracts
<https://www.open-bio.org/events/bosc-2023/submit/> (due April 20 – sorry,
no extensions) on any topic relevant to open source bioinformatics or open
science (see topic list below). After review, some abstracts will be
selected for lightning talks, longer talks, or posters. A second “late
poster” round of submissions will end May 18.

Abstract submission is via ISMB’s EasyChair (linked from our submission page
<https://www.open-bio.org/events/bosc-2023/submit/>). Note that ISMB
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.

About BOSC

Since 2000, the Bioinformatics Open Source Conference
<https://www.open-bio.org/events/bosc-2021/about/> has provided a forum for
developers and users to interact and share research results and ideas in
open source bioinformatics and open science.
As usual, BOSC 2023 <https://www.open-bio.org/events/bosc-2023/> will
include keynote talks, longer and shorter (lightning) talks from submitted
abstracts, posters, Birds of a Feather, and more! Like last year, BOSC and
Bio-Ontologies
<https://www.bio-ontologies.org.uk/ismb-annual-meeting/2023-meeting> will
join forces for a joint session.

BOSC topics include (but are not limited to):

   -

   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)


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 to be considered for a registration fee
waiver right on the abstract submission form (your request will not be seen
by reviewers). Fee waivers are made possible by our sponsors
<https://www.open-bio.org/events/sponsors/>.

Sponsors

We welcome the first Silver sponsors
<https://www.open-bio.org/events/sponsors/> of BOSC 2023! If you’re
interested in becoming a sponsor, let us know!

[image: Gigascience] <https://academic.oup.com/gigascience>
<https://geneviatechnologies.com/>    <https://www.software.ac.uk/>

------------------------------

Key Dates

   -

   April 20, 2023: Deadline for submitting talk/poster abstracts
   <https://www.open-bio.org/events/bosc-2023/submit/>
   -

   May 11: Talk/poster acceptance notifications
   -

   May 18: Late poster submission deadline
   -

   May 25: Late poster acceptance notifications
   -

   July 24-25: BOSC 2023 <https://www.open-bio.org/events/bosc-2023/> (part
   of ISMB/ECCB 2023 in Lyon, France, and online)
   -

   CollaborationFest
   <https://www.open-bio.org/events/bosc-2023/obf-bosc-collaborationfest-2023/>
   (CoFest) – July 22-23 (Lyon, France, and online)


Join our community!

   - BOSC announcements mailing list:
   <http://lists.open-bio.org/mailman/listinfo/bosc-announce>
   https://groups.google.com/forum/#!forum/bosc-announce
   - Slack:
   https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew

   - Twitter: @OBF_BOSC <https://twitter.com/OBF_BOSC>, #BOSC2023
   - Mastodon: https://genomic.social/@BOSC
   -

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


------------------------------

We look forward to reading your abstract and seeing you (in person or
virtually) at BOSC 2023!

Sincerely,

BOSC 2023 Organizing Committee (Nomi Harris, Karsten Hokamp, Hervé Ménager,
Monica Munoz-Torres, Deepak Unni, Jason Williams, Chris Fields, Jessica
Maia, Radhika Khetani)



-- 
------------------------------------------------------------------------
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/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)

Re: [Gmod-ajax] [apollo] Importing itemRgb column of bed files

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

This is more of a JBrowse 1 question. 

Nathan	


> On Apr 13, 2023, at 8:49 AM, Antonin Thiébaut <ant...@gm...> wrote:
> 
> Hello all,
> 
> I was wondering whether there is a way to import the itemRgb column of a bed file. I would like to use it to color the features.
> 
> I am currently using the following command in Apollo v2.6.2 to create the bed tracks:
> perl -w bin/flatfile-to-json.pl --bed path/to/bed --trackLabel putative_orf --key "PCCR bacteria" --out data/bacteria/ --config '{ "category": "Coding Potential" }' --trackType CanvasFeatures
> 
> This successfully imports the file and there is no display problem on the browser, however I have the feeling it only imports the data of the first few columns of the file (I checked in the tracks directory that is created during the import). Can it be caused by an improper formatting or my file? Or am I missing an option in the command, is there another script to do this?
> 
> Thank you in advance,
> 
> Antonin
> 
> -- 
> To unsubscribe from this group and stop receiving emails from it, send an email to apo...@lb... <mailto:apo...@lb...>.

Re: [Gmod-ajax] GSOC project proposal draft

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

Hi Assel,
That is great to hear, it is one of the more challenging projects and it is
great to hear you are willing to try it!

You can email col...@gm... and I can circulate with the team if
interested

-Colin

On Thu, Mar 16, 2023 at 10:31 AM Assel Abzalova <abz...@gm...>
wrote:

> Dear JBrowse development team,
>
> I am writing to express my interest in developing new features for JBrowse
> 2, specifically a method to compare multiple genomes at once using data
> from PAF files or other synteny pipelines.
>
> I have prepared a draft proposal outlining a clear plan to achieve the
> expected results within the allocated project time of 350 hours. Would it
> be possible for me to send the proposal to you for review and feedback?
>
> Thank you for considering my application. I look forward to hearing from
> you and the opportunity to work with you on this project.
>
> Best regards,
> Assel
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] GSOC project proposal draft

[Assel A. <abz...@gm...>]

Dear JBrowse development team,

I am writing to express my interest in developing new features for JBrowse
2, specifically a method to compare multiple genomes at once using data
from PAF files or other synteny pipelines.

I have prepared a draft proposal outlining a clear plan to achieve the
expected results within the allocated project time of 350 hours. Would it
be possible for me to send the proposal to you for review and feedback?

Thank you for considering my application. I look forward to hearing from
you and the opportunity to work with you on this project.

Best regards,
Assel

[Gmod-ajax] bionano data

[Ying S. <yy...@sa...>]

Hi Colin,

Thanks for offering to test the plugin, I have prepared some data on our sftp:

you could access the data using the following detail:
sftp yy...@sf...<mailto:yy...@sf...>
password:Foo5pho6

all relevant data is here:
/teamsoranzo/Yumi/bionano
Reference fasta: sSteFas4.HiC.hap1.20221121.decontaminated.fa
Reference cmap: sSteFas4_Saphyr_DLE1_3719009_r.cmap
Query cmap: sSteFas4_Saphyr_DLE1_3719009_q.cmap
Alignment xmap: sSteFas4_Saphyr_DLE1_3719009.xmap

Thanks you
Yumi
From: Colin <col...@gm...>
Date: Thursday, 19 May 2022 at 19:31
To: Ying Sims <yy...@sa...>
Cc: "gmo...@li..." <gmo...@li...>
Subject: Re: [Gmod-ajax] hic track on jb2 [EXT]

Hi Ying,
I think some of this dialog is continued in various other places (github/gitter) but to answer


1) JBrowse 1 plugins will not work with JBrowse 2 unfortunately, but as you have done, a request for support is here https://github.com/GMOD/jbrowse-components/issues/2962 [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_jbrowse-2Dcomponents_issues_2962&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=X9VPYUGy4ibZarh9Rup1XaZ62i2u-I0xOZXEy11dXDM&m=2h4i5rjVAcMUOLuJG5ET8RL8r1px37m0nkj5yAy1VdKoa8DBqDWo4DqgwkuPfpJp&s=VE2KzZVtvhWMDUrKzKZ4pJZpopf4Gt2dThdSQ5fbUgw&e=> :)
2) I think you said that this was resolved, now, by making the scaffold names match the FASTA, but let us know if you have any other concerns


-Colin

On Thu, May 19, 2022 at 9:44 AM Ying Sims <yy...@sa...<mailto:yy...@sa...>> wrote:
Hello,

I am a bioinformatician works on the Darwin Tree of life project in Sanger institute (https://www.darwintreeoflife.org/). I am currently investigating jbrowse2 functionality, and think it could potentially replace our dated genome curation platform(gEVAL).  I have a couple of questions/problem would like to have your help.


  1.  I noticed bionano plugin is available, I also noticed the plugin was developed in 2016, would it work in jb2?
  2.  I use jbrowse cli to load the tracks and assembly. Assembly fasta loads fine,  but bed files and hic files are problematic for me. The hic track doesn't show at all. I have changed the scaffold name in the fasta to capitals but still nothing showed. The following is the command I used to load the hic file. The hic can be displayed in juicebox as I have checked.

jbrowse add-track ~/data/bPtePen1_1/bPtePen1_1_arima.hic -l symlink -a bPtePen1_1



and in the json:

"tracks": [

    {

      "type": "HicTrack",

      "trackId": "bPtePen1_1_arima",

      "name": "bPtePen1_1_arima",

      "adapter": {

        "type": "HicAdapter",

        "hicLocation": {

          "uri": "bPtePen1_1_arima.hic",

          "locationType": "UriLocation"

        }

      },

      "assemblyNames": [

        "bPtePen1_1"

      ]



Could you please help





Kind regards

Yumi
-- The Wellcome 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.
_______________________________________________
Gmod-ajax mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax [lists.sourceforge.net]<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dajax&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=X9VPYUGy4ibZarh9Rup1XaZ62i2u-I0xOZXEy11dXDM&m=2h4i5rjVAcMUOLuJG5ET8RL8r1px37m0nkj5yAy1VdKoa8DBqDWo4DqgwkuPfpJp&s=_T5ACLam-8aQRKMlkktsC7WaVci2zsSyX_BZVxiwRbo&e=>



-- 
 The Wellcome 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.

Re: [Gmod-ajax] setup

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

The issue from your setup.log is probably related to a large change to the
BioPerl package library that happened in BioPerl v1.7.3 (
https://github.com/bioperl/bioperl-live/commit/1760fa57142a5570b1e93e4423c621aa5e9f3b3e
)

You can manually install the last working version of BioPerl with

bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2

This is actually the exact command the latest version (v1.16.11) of JBrowse
1 uses in it's setup.sh, but may help with your version (v1.12.3)

See https://github.com/GMOD/jbrowse/blob/master/setup.sh#L153-L156


-Colin

On Mon, Jan 23, 2023 at 10:53 AM Scott Cain <sc...@sc...> wrote:

> Hello,
>
> It looks like you are trying to install a very old version of JBrowse 1;
> is there a reason you don't want to try something newer?
>
> Scott
>
>
> On Mon, Jan 23, 2023 at 9:18 AM 你好 生活 via Gmod-ajax <
> gmo...@li...> wrote:
>
>>
>> _______________________________________________
>> 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/)
> Human Cancer Models Initiative Project Manager (
> https://hcmi-searchable-catalog.nci.nih.gov/)
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] setup

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

Hello,

It looks like you are trying to install a very old version of JBrowse 1; is
there a reason you don't want to try something newer?

Scott


On Mon, Jan 23, 2023 at 9:18 AM 你好 生活 via Gmod-ajax <
gmo...@li...> wrote:

>
> _______________________________________________
> 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/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)

[Gmod-ajax] setup

[<210...@qq...>]

Re: [Gmod-ajax] JBrowse 2 year in review

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

Link to JBrowse workshop (sunday actually!)
https://plan.core-apps.com/pag_2023/event/3cee484866e6d00c5e492240c4d184df

-Colin

On Thu, Jan 5, 2023 at 7:36 PM Colin <col...@gm...> wrote:

> Hello all,
> We haven't been keeping the mailing list properly updated with all our
> JBrowse 2 releases, but we compiled a "year in review" blogpost covering
> some highlights of JBrowse 2 development this year!
>
> https://jbrowse.org/jb2/blog/2022/12/16/yearinreview/
>
> It's been a big year for our development so check it out :)
>
> Cheers,
> -Colin
>
> PS: Many of our team members will be attending PAG2023 (Scott, Colin,
> Caroline, Garrett, and Rob)! We'll be presenting the JBrowse workshop using
> JBrowse 2 saturday, and mulling about the halls the rest of the time. Hope
> to see you there :)
>

[Gmod-ajax] JBrowse 2 year in review

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

Hello all,
We haven't been keeping the mailing list properly updated with all our
JBrowse 2 releases, but we compiled a "year in review" blogpost covering
some highlights of JBrowse 2 development this year!

https://jbrowse.org/jb2/blog/2022/12/16/yearinreview/

It's been a big year for our development so check it out :)

Cheers,
-Colin

PS: Many of our team members will be attending PAG2023 (Scott, Colin,
Caroline, Garrett, and Rob)! We'll be presenting the JBrowse workshop using
JBrowse 2 saturday, and mulling about the halls the rest of the time. Hope
to see you there :)

[Gmod-ajax] Apollo 2.7.0 released

[Garrett S. <ste...@gm...>]

Apollo 2.7.0 has been released:
https://github.com/GMOD/Apollo/releases/tag/2.7.0

*Features*

   - Add info icon with tooltip describing meaning of fmin and fmax in
   "Partial". @garrettjstevens <https://github.com/garrettjstevens>. 2649
   <https://github.com/GMOD/Apollo/pull/2649>.

*Infrastructure Changes*

   - Upgrade Log4j to 2.19.0. Thanks @cmdcolin <https://github.com/cmdcolin>.
   2654 <https://github.com/GMOD/Apollo/pull/2654>.
      - Due to this change, export of instructor reports is no longer
      available

Full change long for all versions can be found here:
https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md

Docker builds are on docker hub: https://hub.docker.com/r/gmod/apollo

Please review the documentation pages for more details:
http://genomearchitect.readthedocs.io/en/latest/

Note: You can find a guide to upgrading existing Apollo installations here:
https://genomearchitect.readthedocs.io/en/latest/Migration.html

Report issues if found.
Active mailing list (ap...@lb...) and google group
<https://groups.google.com/a/lbl.gov/g/apollo>.

Re: [Gmod-ajax] Jbrowse failing on production environment

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

Hi João
Are you creating a custom build of JBrowse or using the default min e.g.
https://github.com/GMOD/jbrowse/releases/download/1.16.11-release/JBrowse-1.16.11.zip?
if you are using custom, can you try using the default build from the link
above to see? Can also try the "dev" version, which is unminified and a bit
easier to debug sometimes (from
https://github.com/GMOD/jbrowse/archive/1.16.11-release.zip)


Also are you seeing any 404 in the network tab of Chrome devtools, or maybe
any 0 byte chunks or something odd? If you think it is firewall,
downgrading jbrowse has been one option in the past
https://github.com/GMOD/jbrowse/issues/1571

Alternatively, can consider upgrading to jbrowse 2 https://jbrowse.org/jb2
:) that is where most of our effort is directed now

-Colin

On Wed, Nov 30, 2022 at 10:19 AM João Paulo <jpr...@ho...>
wrote:

> Hi,
>
>     I am trying to deploy a website that uses JBrowse 1.16.11. In the
> development machine running a django web server with development settings
> it's running correctl, but on the server (nginx) it's interrupted. The
> initial error (image 1: code_1_error.png). One difference that I spotted
> was an additional undefined after printing values (images 2 and
> 3: undefined_localhost.png and undefined_server.png).
>
>     As a band-aid I added this to the main.bundle.js file:
>
>    19,21c19
>         <         if (t[n] != undefined) {
>         < return t[n].call(e.exports, e, e.exports, i), e.l = !0, e.exports
>         <         }
>     ---
>     >         return t[n].call(e.exports, e, e.exports, i), e.l = !0,
> e.exports
>
>     Which allowed me to jump on this problem but I faced a second problem
> (image 4: second_error_dojo.png).
>
>     I tried to disable the firewall on the server and to do some tweaks on
> the nginx settings but none with a good result. I am not sure about the
> origin of the problem which makes it more complicated to debug and/or solve.
>
>     I hope someone can give me some hints to explore a possible solution.
>
> Thanks,
>
> João
>
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Jbrowse failing on production environment

[João P. <jpr...@ho...>]

Hi,

    I am trying to deploy a website that uses JBrowse 1.16.11. In the development machine running a django web server with development settings it's running correctl, but on the server (nginx) it's interrupted. The initial error (image 1: code_1_error.png). One difference that I spotted was an additional undefined after printing values (images 2 and 3: undefined_localhost.png and undefined_server.png).

    As a band-aid I added this to the main.bundle.js file:

   19,21c19
        <         if (t[n] != undefined) {
        < return t[n].call(e.exports, e, e.exports, i), e.l = !0, e.exports
        <         }
    ---
    >         return t[n].call(e.exports, e, e.exports, i), e.l = !0, e.exports

    Which allowed me to jump on this problem but I faced a second problem (image 4: second_error_dojo.png).

    I tried to disable the firewall on the server and to do some tweaks on the nginx settings but none with a good result. I am not sure about the origin of the problem which makes it more complicated to debug and/or solve.

    I hope someone can give me some hints to explore a possible solution.

Thanks,

João


[cid:1825db9e-5667-4aab-9602-8bfa3851f184]

[cid:6e53b1b7-9e50-4013-b6c1-03cad0816da6]

[cid:b5ea2751-1987-4332-8696-75a80e99b13c]

[cid:97efd740-c61c-4f8b-85bc-1aa38e0203be]

Re: [Gmod-ajax] GWAS plugin question

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

Hi,

I found out the reason. I didn't place the "plugin" at the same level with
"assemblies" and "tracks", but outside the chunk. Once I follow the
example, it works!

Thanks for your help!

Ke

On Fri, Nov 18, 2022 at 11:49 AM Colin <col...@gm...> wrote:

> Hi Ke
>
> There is an example of a working config here
> https://github.com/cmdcolin/jbrowse-plugin-gwas/blob/master/distconfig.json
>
> That exact config is running here
> https://jbrowse.org/code/jb2/main/index.html?config=https%3A%2F%2Funpkg.com%2Fjbrowse-plugin-gwas%2Fdist%2Fconfig.json&session=share-iehjT6AoHd&password=lZS7v
>
>
> Your config looks ok but maybe double check it against that example:)
>
>
> -Colin
>
> On Fri, Nov 18, 2022, 9:42 AM Ke Jiang <bio...@gm...> wrote:
>
>> Hi,
>>
>> I'm trying the GWAS plugin and still a bit confused about the setup (or
>> plugins in general). So I tried the following configuration chunk for a BED
>> file with fifth column as a score (Fst here):
>>
>> {
>>   "type": "FeatureTrack",
>>   "trackId": "snpchip_Fst",
>>   "name": "snpchip_Fst",
>>   "category": ["PopGen"],
>>   "assemblyNames": ["Bovine B. taurus v1.2"],
>>   "adapter": {
>>     "type": "BedTabixAdapter",
>>     "bedGzLocation": {
>>       "uri": "data/bovine/ARS/PopGen/Fst.bed.gz"
>>     },
>>     "index": {
>>       "location": {
>>         "uri": "data/bovine/ARS/PopGen/Fst.bed.gz.tbi"
>>       },
>>       "indexType": "TBI"
>>     }
>>   },
>>   "displays": [
>>     {
>>       "displayId": "Fst_display",
>>       "type": "LinearManhattanDisplay"
>>     }
>>   ]
>> }
>>
>> But this track broke the browser and threw an error "Failed to load
>> element...Failed element had snapshot", which is this chunk. Anything
>> advice for this track?
>>
>> Is this because I didn't have the GWAS plugin in the overall
>> configuration? But "BedTabixAdaptor" should already be present, right?
>>
>> Then I tried adding the plugin chunk to the configuration:
>>
>> {
>>   "plugins": [
>>     {
>>       "name": "GWAS",
>>       "url": "
>> https://unpkg.com/jbrowse-plugin-gwas/dist/jbrowse-plugin-gwas.umd.production.min.js
>> "
>>     }
>>   ]
>> }
>>
>> But adding this at the top level of config.json breaks the entire config.
>> Should I add the "plugin" at the same level with "assemblies" and "tracks"?
>>
>> Thanks!
>>
>> Ke
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] GWAS plugin question

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

Hi Ke

There is an example of a working config here
https://github.com/cmdcolin/jbrowse-plugin-gwas/blob/master/distconfig.json

That exact config is running here
https://jbrowse.org/code/jb2/main/index.html?config=https%3A%2F%2Funpkg.com%2Fjbrowse-plugin-gwas%2Fdist%2Fconfig.json&session=share-iehjT6AoHd&password=lZS7v


Your config looks ok but maybe double check it against that example:)


-Colin

On Fri, Nov 18, 2022, 9:42 AM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> I'm trying the GWAS plugin and still a bit confused about the setup (or
> plugins in general). So I tried the following configuration chunk for a BED
> file with fifth column as a score (Fst here):
>
> {
>   "type": "FeatureTrack",
>   "trackId": "snpchip_Fst",
>   "name": "snpchip_Fst",
>   "category": ["PopGen"],
>   "assemblyNames": ["Bovine B. taurus v1.2"],
>   "adapter": {
>     "type": "BedTabixAdapter",
>     "bedGzLocation": {
>       "uri": "data/bovine/ARS/PopGen/Fst.bed.gz"
>     },
>     "index": {
>       "location": {
>         "uri": "data/bovine/ARS/PopGen/Fst.bed.gz.tbi"
>       },
>       "indexType": "TBI"
>     }
>   },
>   "displays": [
>     {
>       "displayId": "Fst_display",
>       "type": "LinearManhattanDisplay"
>     }
>   ]
> }
>
> But this track broke the browser and threw an error "Failed to load
> element...Failed element had snapshot", which is this chunk. Anything
> advice for this track?
>
> Is this because I didn't have the GWAS plugin in the overall
> configuration? But "BedTabixAdaptor" should already be present, right?
>
> Then I tried adding the plugin chunk to the configuration:
>
> {
>   "plugins": [
>     {
>       "name": "GWAS",
>       "url": "
> https://unpkg.com/jbrowse-plugin-gwas/dist/jbrowse-plugin-gwas.umd.production.min.js
> "
>     }
>   ]
> }
>
> But adding this at the top level of config.json breaks the entire config.
> Should I add the "plugin" at the same level with "assemblies" and "tracks"?
>
> Thanks!
>
> Ke
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] GWAS plugin question

[Garrett S. <ste...@gm...>]

Having the "plugins" at the top level like that looks right, how does it
break the config? Here's an example config you can reference:
https://github.com/cmdcolin/jbrowse-plugin-gwas/blob/master/distconfig.json

Also, here's a link to a working example you can try that uses the above
config:
https://jbrowse.org/code/jb2/main/index.html?config=https%3A%2F%2Funpkg.com%2Fjbrowse-plugin-gwas%2Fdist%2Fconfig.json&session=share-iehjT6AoHd&password=lZS7v

Best,
Garrett

On Fri, Nov 18, 2022 at 9:42 AM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> I'm trying the GWAS plugin and still a bit confused about the setup (or
> plugins in general). So I tried the following configuration chunk for a BED
> file with fifth column as a score (Fst here):
>
> {
>   "type": "FeatureTrack",
>   "trackId": "snpchip_Fst",
>   "name": "snpchip_Fst",
>   "category": ["PopGen"],
>   "assemblyNames": ["Bovine B. taurus v1.2"],
>   "adapter": {
>     "type": "BedTabixAdapter",
>     "bedGzLocation": {
>       "uri": "data/bovine/ARS/PopGen/Fst.bed.gz"
>     },
>     "index": {
>       "location": {
>         "uri": "data/bovine/ARS/PopGen/Fst.bed.gz.tbi"
>       },
>       "indexType": "TBI"
>     }
>   },
>   "displays": [
>     {
>       "displayId": "Fst_display",
>       "type": "LinearManhattanDisplay"
>     }
>   ]
> }
>
> But this track broke the browser and threw an error "Failed to load
> element...Failed element had snapshot", which is this chunk. Anything
> advice for this track?
>
> Is this because I didn't have the GWAS plugin in the overall
> configuration? But "BedTabixAdaptor" should already be present, right?
>
> Then I tried adding the plugin chunk to the configuration:
>
> {
>   "plugins": [
>     {
>       "name": "GWAS",
>       "url": "
> https://unpkg.com/jbrowse-plugin-gwas/dist/jbrowse-plugin-gwas.umd.production.min.js
> "
>     }
>   ]
> }
>
> But adding this at the top level of config.json breaks the entire config.
> Should I add the "plugin" at the same level with "assemblies" and "tracks"?
>
> Thanks!
>
> Ke
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] GWAS plugin question

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

Hi,

I'm trying the GWAS plugin and still a bit confused about the setup (or
plugins in general). So I tried the following configuration chunk for a BED
file with fifth column as a score (Fst here):

{
  "type": "FeatureTrack",
  "trackId": "snpchip_Fst",
  "name": "snpchip_Fst",
  "category": ["PopGen"],
  "assemblyNames": ["Bovine B. taurus v1.2"],
  "adapter": {
    "type": "BedTabixAdapter",
    "bedGzLocation": {
      "uri": "data/bovine/ARS/PopGen/Fst.bed.gz"
    },
    "index": {
      "location": {
        "uri": "data/bovine/ARS/PopGen/Fst.bed.gz.tbi"
      },
      "indexType": "TBI"
    }
  },
  "displays": [
    {
      "displayId": "Fst_display",
      "type": "LinearManhattanDisplay"
    }
  ]
}

But this track broke the browser and threw an error "Failed to load
element...Failed element had snapshot", which is this chunk. Anything
advice for this track?

Is this because I didn't have the GWAS plugin in the overall configuration?
But "BedTabixAdaptor" should already be present, right?

Then I tried adding the plugin chunk to the configuration:

{
  "plugins": [
    {
      "name": "GWAS",
      "url": "
https://unpkg.com/jbrowse-plugin-gwas/dist/jbrowse-plugin-gwas.umd.production.min.js
"
    }
  ]
}

But adding this at the top level of config.json breaks the entire config.
Should I add the "plugin" at the same level with "assemblies" and "tracks"?

Thanks!

Ke

Re: [Gmod-ajax] Regarding workshop on-line resource of the chickpea and related Cicer genomes

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

Hi Sonal
Currently there is no "built in" way to retrieve such a list of genes from
inside JBrowse 2 (we have had a number of requests for a feature like this
recently, so might be in the cards though!)

One way to do this a little but outside jbrowse could be using the "tabix"
command line program. I got the URL for the GFF track at the legumeinfo
instance by looking at the "About track" menu inside jbrowse (screenshot
attached), and then made this command


tabix
https://data.legumeinfo.org/Cicer/arietinum/annotations/CDCFrontier.gnm3.ann1.NPD7/cicar.CDCFrontier.gnm3.ann1.NPD7.gene_models_main.gff3.gz
cicar.CDCFrontier.gnm3.chr3:2,405,579-2,425,579

- or, just (coarsely) filter gene lines from the GFF

tabix
https://data.legumeinfo.org/Cicer/arietinum/annotations/CDCFrontier.gnm3.ann1.NPD7/cicar.CDCFrontier.gnm3.ann1.NPD7.gene_models_main.gff3.gz
cicar.CDCFrontier.gnm3.chr3:2,405,579-2,425,579|grep gene


Not sure if Andrew (Andrew Farmer ?) is on this mailing list but happy to
see that JBrowse was included in the legumeinfo workshops :)

Let me know if this helps
-Colin

On Mon, Nov 14, 2022 at 4:30 PM Sonal Channale <son...@gm...> wrote:

> Dear Andrew,
>
> Greetings from Australia!
>
> I am Sonal Channale, a recent PhD graduate from University of Southern
> Queensland, Australia. I attended the online workshop on JBrowse early this
> month and it was indeed great to learn about it. I am working on
> chickpea-root-lesion nematode (*Pratylenchus thornei*) interaction and
> currently assessing the candidate genes in chickpea using genome-wide
> association study. I am trying my hands on JBrowse  and I have a few
> queries regarding the same. I would be really grateful if you can please
> help me or advise me to make best use of JBrowse. Here is, in brief what I
> would like to do using JBrowse and steps followed for the same:
>
> The SNP positions were obtained from GWAS and would like to enlist the
> genes flanking SNP positions (+/-10Kb).
>
> 1. I used the below link:
> https://cicer.legumeinfo.org/tools/jbrowse2/?session=local-ac4IbvVnj
> 2. Eg; As per the SNP position the range was edited as :
> cicar.CDCFrontier.gnm3.chr3:2,405,579..2,425,579
> 3. I was able to see a number of genes within the above range. I would
> like to save the list of genes and would like to search for their possible
> role in chickpea-*P. thornei* interaction with available literature.
>
> Based on the above steps, is there any way to save the list of genes as
> per the specified range. I have multiple associations from the study and
> would like to know what best can be done to save the list of genes within
> specified range.
> Please let me know in this regard.
>
> Thank you and kind regards,
> Sonal Channale.
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Regarding workshop on-line resource of the chickpea and related Cicer genomes

[Sonal C. <son...@gm...>]

Dear Andrew,

Greetings from Australia!

I am Sonal Channale, a recent PhD graduate from University of Southern
Queensland, Australia. I attended the online workshop on JBrowse early this
month and it was indeed great to learn about it. I am working on
chickpea-root-lesion nematode (*Pratylenchus thornei*) interaction and
currently assessing the candidate genes in chickpea using genome-wide
association study. I am trying my hands on JBrowse  and I have a few
queries regarding the same. I would be really grateful if you can please
help me or advise me to make best use of JBrowse. Here is, in brief what I
would like to do using JBrowse and steps followed for the same:

The SNP positions were obtained from GWAS and would like to enlist the
genes flanking SNP positions (+/-10Kb).

1. I used the below link:
https://cicer.legumeinfo.org/tools/jbrowse2/?session=local-ac4IbvVnj
2. Eg; As per the SNP position the range was edited as :
cicar.CDCFrontier.gnm3.chr3:2,405,579..2,425,579
3. I was able to see a number of genes within the above range. I would like
to save the list of genes and would like to search for their possible role
in chickpea-*P. thornei* interaction with available literature.

Based on the above steps, is there any way to save the list of genes as per
the specified range. I have multiple associations from the study and would
like to know what best can be done to save the list of genes within
specified range.
Please let me know in this regard.

Thank you and kind regards,
Sonal Channale.