gmod-ajax — JBrowse list

Re: [Gmod-ajax] Setting up the directory in Mac

[Rahnama, M. <Mos...@uk...>]

Thanks Nathan. Its working now.


Another question:

If I want to have multiple references, could you please give me an example that show how my track.conf file should looks like? or should I have multiple track.conf files?


Thanks,

Mostafa




Mostafa Rahnama, PhD
Postdoctoral Scholar
Department of Plant Pathology
University of Kentucky
Lexington, KY 40546 USA
Tel:  (859) 218-0728


________________________________
From: Lbl <nat...@lb...>
Sent: Sunday, May 5, 2019 10:14:53 PM
To: Rahnama, Mostafa
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] Setting up the directory in Mac

That should work unless the server is not on.

Nathan

On May 5, 2019, at 8:13 AM, Rahnama, Mostafa <Mos...@uk...<mailto:Mos...@uk...>> wrote:


Dear Sir/Madam,


I'm trying to setup Jbrowse in my iMac (Retina 5K) and I followed all the steps as mentioned in your page. Every commands run properly but I have a problem for loading the website.

I think the problem is finding /var/www/html/ directory.

I think mac doesn't have that so I put the jbrowse in /Library/WebServer/Documents/.


Could you please let me know how I can solve this problem?


Best regards,

Mostafa



Mostafa Rahnama, PhD
Postdoctoral Scholar
Department of Plant Pathology
University of Kentucky
Lexington, KY 40546 USA
Tel:  (859) 218-0728


_______________________________________________
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Re: [Gmod-ajax] Setting up the directory in Mac

[Lbl <nat...@lb...>]

That should work unless the server is not on.

Nathan

> On May 5, 2019, at 8:13 AM, Rahnama, Mostafa <Mos...@uk...> wrote:
> 
> Dear Sir/Madam,
> 
> I'm trying to setup Jbrowse in my iMac (Retina 5K) and I followed all the steps as mentioned in your page. Every commands run properly but I have a problem for loading the website. 
> I think the problem is finding /var/www/html/
> directory. 
> I think mac doesn't have that so I put the jbrowse in /Library/WebServer/Documents/.
> 
> Could you please let me know how I can solve this problem?
> 
> Best regards,
> Mostafa
> 
> 
> Mostafa Rahnama, PhD
> Postdoctoral Scholar
> Department of Plant Pathology 
> University of Kentucky
> Lexington, KY 40546 USA
> Tel:  (859) 218-0728 
> 
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] Setting up the directory in Mac

[Rahnama, M. <Mos...@uk...>]

Dear Sir/Madam,


I'm trying to setup Jbrowse in my iMac (Retina 5K) and I followed all the steps as mentioned in your page. Every commands run properly but I have a problem for loading the website.

I think the problem is finding /var/www/html/ directory.

I think mac doesn't have that so I put the jbrowse in /Library/WebServer/Documents/.


Could you please let me know how I can solve this problem?


Best regards,

Mostafa



Mostafa Rahnama, PhD
Postdoctoral Scholar
Department of Plant Pathology
University of Kentucky
Lexington, KY 40546 USA
Tel:  (859) 218-0728

Re: [Gmod-ajax] fasta setup

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

Hello Zhihao,

There are a few things I would check:

* Did the browser reload/refresh really work? With javascript and json
files, browsers can be very conservative about caching.  There are a few
ways to get around this: open the browser's dev tools and turn off caching
explicitly, or open the URL in a incognito/private window.
* In the data/seq directory, do you see entries in the refSeqs.json file
for both chromosomes?
* Also in the data/seq directory, do you see two directories, one for each
chromosome?

Scott


On Fri, May 3, 2019 at 8:10 AM Zhihao Ding <zhi...@gm...> wrote:

> Dear Jbrowse developers,
>
> Thanks for developing Jbrowse. I've been trying to setup an instance
> following the instructions. I am able to see the browser page, but haven't
> managed to get the reference sequence right.
>
> I've downloaded a couple of fasta files just for testing from the
> following link
> ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/
>
> I then run the following two commands:
> bin/prepare-refseqs.pl --fasta
> Homo_sapiens.GRCh38.dna_rm.chromosome.1.fa.gz
> bin/prepare-refseqs.pl --fasta
> Homo_sapiens.GRCh38.dna_rm.chromosome.2.fa.gz
>
> This is  trackList.json generated:
> {
>    "formatVersion" : 1,
>    "tracks" : [
>       {
>          "category" : "Reference sequence",
>          "chunkSize" : 20000,
>          "key" : "Reference sequence",
>          "label" : "DNA",
>          "seqType" : "dna",
>          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
>          "type" : "SequenceTrack",
>          "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
>       }
>    ]
> }
>
> On the browser page, I have only contig 1 in the dropdown list.
>
> Could anyone point me to the right directions here?
>
> Thank you,
> Zhihao
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] fasta setup

[Zhihao D. <zhi...@gm...>]

Dear Jbrowse developers,

Thanks for developing Jbrowse. I've been trying to setup an instance
following the instructions. I am able to see the browser page, but haven't
managed to get the reference sequence right.

I've downloaded a couple of fasta files just for testing from the
following link
ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/

I then run the following two commands:
bin/prepare-refseqs.pl --fasta Homo_sapiens.GRCh38.dna_rm.chromosome.1.fa.gz
bin/prepare-refseqs.pl --fasta Homo_sapiens.GRCh38.dna_rm.chromosome.2.fa.gz

This is  trackList.json generated:
{
   "formatVersion" : 1,
   "tracks" : [
      {
         "category" : "Reference sequence",
         "chunkSize" : 20000,
         "key" : "Reference sequence",
         "label" : "DNA",
         "seqType" : "dna",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "type" : "SequenceTrack",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
      }
   ]
}

On the browser page, I have only contig 1 in the dropdown list.

Could anyone point me to the right directions here?

Thank you,
Zhihao

Re: [Gmod-ajax] A problem about Jbrowse configuration showing FPKM tracks

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

The phytozome team implemented this using some custom dialog box. JBrowse
has the ability to make custom dialog box content, but I wouldn't know
without looking at their code what they used in this particular instance.

If I were implementing something like this today I would probably use the
"bigBarChart" data type as a backend
https://genome.ucsc.edu/goldenPath/help/barChart.html which is just a
special type of bigBed file (which jbrowse supports natively) and then I'd
make a special dialog box for it.

-Colin

On Sun, Apr 28, 2019 at 12:29 PM 柏胜龙 <sl...@fo...> wrote:

> Dear JBrowse development team,
>
> Thank you for developing and maintaining such a great tool.
>
> When I was configuring Jbrowse, I wanted to add FPKM, like the one shown
> by phytozome Jbrowse “Gene Atlas Gene-level Expression” track，Website
> address is:
>
> https://phytozome.jgi.doe.gov/jbrowse/index.html?data=genomes%2FPpatens&loc=Chr13%3A316001..471800&tracks=Transcripts%2CAlt_Transcripts%2CGeneExpression_GeneAtlas0_1&highlight=
> <https://phytozome.jgi.doe.gov/jbrowse/index.html?data=genomes/Ppatens&loc=Chr13:316001..471800&tracks=Transcripts,Alt_Transcripts,GeneExpression_GeneAtlas0_1&highlight=>
>
> When click on the geneid in this track, the following interface will pop
> up. I think this is great, but I didn't find out how to configure it,
>
> I hope I can get your help, thank you.
>
> Best wishes,
> Shenglong
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] A problem about Jbrowse configuration showing FPKM tracks

[柏胜龙 <sl...@fo...>]

Dear JBrowse development team,

Thank you for developing and maintaining such a great tool.

When I was configuring Jbrowse, I wanted to add FPKM, like the one shown by phytozome Jbrowse “Gene Atlas Gene-level Expression” track，Website address is:
https://phytozome.jgi.doe.gov/jbrowse/index.html?data=genomes%2FPpatens&loc=Chr13%3A316001..471800&tracks=Transcripts%2CAlt_Transcripts%2CGeneExpression_GeneAtlas0_1&highlight= <https://phytozome.jgi.doe.gov/jbrowse/index.html?data=genomes/Ppatens&loc=Chr13:316001..471800&tracks=Transcripts,Alt_Transcripts,GeneExpression_GeneAtlas0_1&highlight=>

When click on the geneid in this track, the following interface will pop up. I think this is great, but I didn't find out how to configure it, 


I hope I can get your help, thank you.

Best wishes,
Shenglong

Re: [Gmod-ajax] Call for abstracts: BOSC 2019 Bioinformatics Open Source Conference

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

Reminder: the abstract deadline for BOSC is April 11!


On Thu, Mar 28, 2019 at 8:18 PM Scott Cain <sc...@sc...> wrote:

> Hi All,
>
> I meant to send this out last week--sorry for letting it slip my mind.
> Note that the abstract deadline is April 11!
>
> Scott
>
>
> ---------- Forwarded message ---------
> From: Fields, Christopher J <cjf...@il...>
> Date: Tue, Mar 19, 2019 at 2:12 PM
> Subject: Call for abstracts: BOSC 2019 Bioinformatics Open Source
> Conference
> To: Scott Cain <sc...@sc...>
>
>
> Scott, can you suggest any email lists where this could be sent?
>
> Thanks,
>
> chris
>
> On March 19, 2019 at 4:01:52 PM, cjf...@il... (
> cjf...@il...) wrote:
>
> [image: BOSC_2019_Banner]
> BOSC 2019: Bioinformatics Open Source Conference An ISMB/ECCB Community
> of Special Interest (COSI)
>
> *BOSC 2019 Dates*: July 24-25, 2019
>
> *Location*: Basel, Switzerland
>
> *Website*:  https://www.open-bio.org/wiki/BOSC_2019 (new, improved
> website coming soon!)
>
> *Email BOSC organizers*: bo...@op...
>
> *BOSC announcements mailing list*:
> http://lists.open-bio.org/mailman/listinfo/bosc-announce
>
> *Twitter*:  @OBF_BOSC <https://twitter.com/OBF_BOSC>, #BOSC2019
> <https://twitter.com/search?f=tweets&vertical=default&q=%23BOSC2019&src=typd>
> *Key Dates*:
>
> *April 11, 2019:* Deadline for submitting talk/poster abstracts
> <https://www.open-bio.org/wiki/BOSC_Abstract_Submission>
>
> *April 15:* OBF travel fellowship
> <https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md> application
> deadline
>
> *May 9:* First-round authors notified about talk/poster acceptance
>
> *May 15:* Late poster / late-breaking lightning talk abstract deadline
>
> *May 23:* Late poster / late-breaking lightning talk authors notified
>
> *July 21-25, 2019:*  ISMB/ECCB 2019 <https://www.iscb.org/ismbeccb2019>,
> Basel, Switzerland
>
> *July 24-25 (last two days of ISMB):* BOSC 2019, Basel, Switzerland
>
> *July 26-28:* CollaborationFest (CoFest) 2019
> <https://www.open-bio.org/wiki/CoFest_2019>, Basel
> About BOSC
>
> Since 2000, the yearly Bioinformatics Open Source Conference (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.
>
> In 2018, BOSC was held jointly with GCC
> <https://f1000research.com/collections/BOSC?&selectedDomain=articles> as
> a combined GCCBOSC <https://gccbosc2018.sched.com/> conference. In 2019,
> BOSC will be part of ISMB/ECCB <https://www.iscb.org/ismbeccb2019> in
> Basel. We hope to partner with GCC again in 2020 or 2021. Read more here
> about why we decided to hold BOSC with GCC in 2018 and ISMB in 2019.
> <https://news.open-bio.org/2018/08/02/taking-turns/>
>
> ISMB now consists of multiple parallel tracks called COSIs (formerly
> SIGs). The BOSC COSI will take place the last two full days of ISMB (July
> 24-25). You can register for the full ISMB/ECCB meeting (July 21-25) or for
> just two days (there is no single-day registration option).
>
> A limited number of partial travel fellowships will be granted to some
> accepted speakers who would not otherwise be able to attend BOSC--please
> see https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md for
> more information. The travel fellowship application deadline is *April
> 15.*
> Abstract submission
>
> We encourage you to submit abstracts
> <https://www.open-bio.org/wiki/BOSC_Abstract_Submission> (*due April 11*)
> on any topic relevant to open source bioinformatics or open science. After
> review, some abstracts will be selected for lightning talks, longer talks
> and/or posters. (Only first-round abstracts are eligible for longer talks.)
>
> Abstract submission instructions and a link to the EasyChair submission
> portal can be found on
> https://www.open-bio.org/wiki/BOSC_Abstract_Submission.
>
> BOSC session 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
>    - Developer Tools and Libraries
>    - Inclusion, Outreach and Training
>    - Bioinformatics Open Source Project Reports (about new or existing
>    projects)
>
> We look forward to receiving your abstract and meeting you at BOSC 2019!
>
> Sincerely,
>
> *BOSC 2019 Organizing Committee:* Nomi Harris (chair), Heather Wiencko
> (co-chair), Peter Cock, Chris Fields, Bastian Greshake Tzovaras, Michael
> Heuer, Karsten Hokamp, Monica Munoz-Torres, Bastian Rieck, Yo Yehudi.
>
> *P.S. Don't forget to submit your BOSC abstract by April 11 at*
> https://www.open-bio.org/wiki/BOSC_Abstract_Submission !
>
> Please share this announcement with your colleagues!
>
>
>
> — chris
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] Fwd: Call for abstracts: BOSC 2019 Bioinformatics Open Source Conference

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

Hi All,

I meant to send this out last week--sorry for letting it slip my mind.
Note that the abstract deadline is April 11!

Scott


---------- Forwarded message ---------
From: Fields, Christopher J <cjf...@il...>
Date: Tue, Mar 19, 2019 at 2:12 PM
Subject: Call for abstracts: BOSC 2019 Bioinformatics Open Source Conference
To: Scott Cain <sc...@sc...>


Scott, can you suggest any email lists where this could be sent?

Thanks,

chris

On March 19, 2019 at 4:01:52 PM, cjf...@il... (
cjf...@il...) wrote:

[image: BOSC_2019_Banner]
BOSC 2019: Bioinformatics Open Source Conference An ISMB/ECCB Community of
Special Interest (COSI)

*BOSC 2019 Dates*: July 24-25, 2019

*Location*: Basel, Switzerland

*Website*:  https://www.open-bio.org/wiki/BOSC_2019 (new, improved website
coming soon!)

*Email BOSC organizers*: bo...@op...

*BOSC announcements mailing list*:
http://lists.open-bio.org/mailman/listinfo/bosc-announce

*Twitter*:  @OBF_BOSC <https://twitter.com/OBF_BOSC>, #BOSC2019
<https://twitter.com/search?f=tweets&vertical=default&q=%23BOSC2019&src=typd>
*Key Dates*:

*April 11, 2019:* Deadline for submitting talk/poster abstracts
<https://www.open-bio.org/wiki/BOSC_Abstract_Submission>

*April 15:* OBF travel fellowship
<https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md> application
deadline

*May 9:* First-round authors notified about talk/poster acceptance

*May 15:* Late poster / late-breaking lightning talk abstract deadline

*May 23:* Late poster / late-breaking lightning talk authors notified

*July 21-25, 2019:*  ISMB/ECCB 2019 <https://www.iscb.org/ismbeccb2019>,
Basel, Switzerland

*July 24-25 (last two days of ISMB):* BOSC 2019, Basel, Switzerland

*July 26-28:* CollaborationFest (CoFest) 2019
<https://www.open-bio.org/wiki/CoFest_2019>, Basel
About BOSC

Since 2000, the yearly Bioinformatics Open Source Conference (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.

In 2018, BOSC was held jointly with GCC
<https://f1000research.com/collections/BOSC?&selectedDomain=articles> as a
combined GCCBOSC <https://gccbosc2018.sched.com/> conference. In 2019, BOSC
will be part of ISMB/ECCB <https://www.iscb.org/ismbeccb2019> in Basel. We
hope to partner with GCC again in 2020 or 2021. Read more here about why we
decided to hold BOSC with GCC in 2018 and ISMB in 2019.
<https://news.open-bio.org/2018/08/02/taking-turns/>

ISMB now consists of multiple parallel tracks called COSIs (formerly SIGs).
The BOSC COSI will take place the last two full days of ISMB (July 24-25).
You can register for the full ISMB/ECCB meeting (July 21-25) or for just
two days (there is no single-day registration option).

A limited number of partial travel fellowships will be granted to some
accepted speakers who would not otherwise be able to attend BOSC--please
see https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md for
more information. The travel fellowship application deadline is *April 15.*
Abstract submission

We encourage you to submit abstracts
<https://www.open-bio.org/wiki/BOSC_Abstract_Submission> (*due April 11*)
on any topic relevant to open source bioinformatics or open science. After
review, some abstracts will be selected for lightning talks, longer talks
and/or posters. (Only first-round abstracts are eligible for longer talks.)

Abstract submission instructions and a link to the EasyChair submission
portal can be found on
https://www.open-bio.org/wiki/BOSC_Abstract_Submission.

BOSC session 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
   - Developer Tools and Libraries
   - Inclusion, Outreach and Training
   - Bioinformatics Open Source Project Reports (about new or existing
   projects)

We look forward to receiving your abstract and meeting you at BOSC 2019!

Sincerely,

*BOSC 2019 Organizing Committee:* Nomi Harris (chair), Heather Wiencko
(co-chair), Peter Cock, Chris Fields, Bastian Greshake Tzovaras, Michael
Heuer, Karsten Hokamp, Monica Munoz-Torres, Bastian Rieck, Yo Yehudi.

*P.S. Don't forget to submit your BOSC abstract by April 11 at*
https://www.open-bio.org/wiki/BOSC_Abstract_Submission !

Please share this announcement with your colleagues!



— chris



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] Loading errors for Gene Locus track

[Shabari S. <sh...@ar...>]

Hi Robert,

Looks like the error is on the side of the actual data behind the viewer,
not in the exporting itself. I will see if it happens again.

Best
-shabari

On Tue, Mar 26, 2019 at 7:01 PM Robert Buels <rb...@gm...> wrote:

> I couldn't quite follow what we found out here. Is there a problem with
> the JBrowse 1 GFF3 exporting?
>
> On Tue, Mar 26, 2019 at 4:36 PM Shabari Subramaniam <
> sh...@ar...> wrote:
>
>> That did the trick. Thanks for the help.
>>
>> On Tue, Mar 26, 2019 at 3:31 PM Shabari Subramaniam <
>> sh...@ar...> wrote:
>>
>>> Hi Colin,
>>>
>>> Thank you so much for the suggestion. I will remove the NaN lines
>>> reload.
>>>
>>> Best
>>> -shabari
>>>
>>> On Tue, Mar 26, 2019 at 3:15 PM Colin <col...@gm...> wrote:
>>>
>>>> I'd assert that the track on araport is somehow corrupted. You can see
>>>> if you click "View details" on any given feature that it has weird
>>>> subfeatures with NaN values.
>>>>
>>>> In this sense, jbrowse is doing it's best here :)
>>>>
>>>> I would just "grep -v" all the lines with NaN before trying to load
>>>> your track with flatfile-to-json.
>>>>
>>>> You might also want to perform "delete Array.prototype.values" in the
>>>> your javascript console before doing Save track data if you want to fix the
>>>> issue of "function() { [values] }" in the exported GFF. Newer jbrowse
>>>> versions contain a bugfix for this but older JBrowse versions do not (the
>>>> bug was introduced only recently by browsers due to changes in how the
>>>> javascript language has evolved over the years...)
>>>>
>>>> -Colin
>>>>
>>>> On Tue, Mar 26, 2019 at 6:05 PM Shabari Subramaniam <
>>>> sh...@ar...> wrote:
>>>>
>>>>> Thanks Scott. Here is the link.
>>>>>
>>>>>
>>>>> https://apps.araport.org/jbrowse/?data=arabidopsis&loc=Chr1%3A24330927..24332945&tracks=Araport11_Loci&highlight=
>>>>>
>>>>> Click on the dropdown on the track label 'Araport11 Gene Locus' and
>>>>> select 'Save Track Data'. Then you select 'Whole reference sequence' and
>>>>> 'GFF3' as the format option. (Screenshot attached).
>>>>>
>>>>> Thanks for your help.
>>>>>
>>>>> Best
>>>>> -shabari
>>>>>
>>>>> On Tue, Mar 26, 2019 at 12:51 PM Scott Cain <sc...@sc...>
>>>>> wrote:
>>>>>
>>>>>> Hi Shabari,
>>>>>>
>>>>>> I'm sending this to the JBrowse mailing list too, so others can chime
>>>>>> in with suggestions.  The problem is almost certainly with the GFF: it is
>>>>>> really screwed up (periods in the type column for all of the child
>>>>>> features, NAN for the start coordinates and periods for the end
>>>>>> coordinates).  I'd say addressing that will go a long way to fixing any
>>>>>> problems. You said you dumped this GFF out of a JBrowse instance.  Can you
>>>>>> provide the URL for that instance? Maybe there is something wrong with it.
>>>>>>
>>>>>> Thanks,
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> On Tue, Mar 26, 2019 at 11:53 AM Shabari Subramaniam <
>>>>>> sh...@ar...> wrote:
>>>>>>
>>>>>>> Hi Scott,
>>>>>>> I am getting errors when i try to upload the data from the
>>>>>>> 'Araport11 Gene Locus' track. I downloaded the data from the Jbrowse track
>>>>>>> on Araport11's Jbrowse viewer in gff format. I removed the 'Chr' from the
>>>>>>> gff file. The gff file is attached.
>>>>>>>
>>>>>>> The problem may be the -type is not the right one. The file only has
>>>>>>> 'gene' as type so i tried '--type gene' (below) and no type defined. I am
>>>>>>> getting the same error (attached). What am i doing wrong? Let me know if
>>>>>>> you need access to the machine to check this out.
>>>>>>>
>>>>>>> [ec2-user@ip-172-31-31-73 JBrowse-1.16.2]$ bin/flatfile-to-json.pl
>>>>>>> --gff ./arabidopsis/raw/Araport11\ -\ Gene\ Locus-Chr1-1..30427671.gff3
>>>>>>> --tracklabel 'Araport11 Gene Locus' --metadata '{"Source": "Araport11
>>>>>>> Release (Jun 2016)", "Description": "Araport11 Protein-coding,
>>>>>>> Transposable-element, and Non-coding gene loci", "category": "Araport Data
>>>>>>> / Araport11 / Annotation (Jun 2016)"}' --type gene
>>>>>>>
>>>>>>>
>>>>>>> I am not getting this error when i load the 'Araport11 Protein
>>>>>>> Coding Genes' track data with --type as exon.
>>>>>>>
>>>>>>>
>>>>>>> Thanks for your help.
>>>>>>>
>>>>>>> -shabari
>>>>>>>
>>>>>>> --
>>>>>>> ---------------------------------------------------
>>>>>>> Sabarinath Subramaniam, Ph.D.
>>>>>>> Director of Business Development
>>>>>>> Phoenix Bioinformatics
>>>>>>> 39221 Paseo Padre Parkway, Ste. J
>>>>>>> Fremont, CA 94583, USA
>>>>>>> Email: sh...@ar...
>>>>>>> SkypeID:  shabarinath
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>>
>>>>>> ------------------------------------------------------------------------
>>>>>> Scott Cain, Ph. D.                                   scott at
>>>>>> scottcain dot net
>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>> Ontario Institute for Cancer Research
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ---------------------------------------------------
>>>>> Sabarinath Subramaniam, Ph.D.
>>>>> Director of Business Development
>>>>> Phoenix Bioinformatics
>>>>> 39221 Paseo Padre Parkway, Ste. J
>>>>> Fremont, CA 94583, USA
>>>>> Email: sh...@ar...
>>>>> SkypeID:  shabarinath
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>
>>>>
>>>
>>> --
>>> ---------------------------------------------------
>>> Sabarinath Subramaniam, Ph.D.
>>> Director of Business Development
>>> Phoenix Bioinformatics
>>> 39221 Paseo Padre Parkway, Ste. J
>>> Fremont, CA 94583, USA
>>> Email: sh...@ar...
>>> SkypeID:  shabarinath
>>>
>>
>>
>> --
>> ---------------------------------------------------
>> Sabarinath Subramaniam, Ph.D.
>> Director of Business Development
>> Phoenix Bioinformatics
>> 39221 Paseo Padre Parkway, Ste. J
>> Fremont, CA 94583, USA
>> Email: sh...@ar...
>> SkypeID:  shabarinath
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

-- 
---------------------------------------------------
Sabarinath Subramaniam, Ph.D.
Director of Business Development
Phoenix Bioinformatics
39221 Paseo Padre Parkway, Ste. J
Fremont, CA 94583, USA
Email: sh...@ar...
SkypeID:  shabarinath

Re: [Gmod-ajax] Loading errors for Gene Locus track

[Robert B. <rb...@gm...>]

I couldn't quite follow what we found out here. Is there a problem with the
JBrowse 1 GFF3 exporting?

On Tue, Mar 26, 2019 at 4:36 PM Shabari Subramaniam <sh...@ar...>
wrote:

> That did the trick. Thanks for the help.
>
> On Tue, Mar 26, 2019 at 3:31 PM Shabari Subramaniam <
> sh...@ar...> wrote:
>
>> Hi Colin,
>>
>> Thank you so much for the suggestion. I will remove the NaN lines reload.
>>
>> Best
>> -shabari
>>
>> On Tue, Mar 26, 2019 at 3:15 PM Colin <col...@gm...> wrote:
>>
>>> I'd assert that the track on araport is somehow corrupted. You can see
>>> if you click "View details" on any given feature that it has weird
>>> subfeatures with NaN values.
>>>
>>> In this sense, jbrowse is doing it's best here :)
>>>
>>> I would just "grep -v" all the lines with NaN before trying to load your
>>> track with flatfile-to-json.
>>>
>>> You might also want to perform "delete Array.prototype.values" in the
>>> your javascript console before doing Save track data if you want to fix the
>>> issue of "function() { [values] }" in the exported GFF. Newer jbrowse
>>> versions contain a bugfix for this but older JBrowse versions do not (the
>>> bug was introduced only recently by browsers due to changes in how the
>>> javascript language has evolved over the years...)
>>>
>>> -Colin
>>>
>>> On Tue, Mar 26, 2019 at 6:05 PM Shabari Subramaniam <
>>> sh...@ar...> wrote:
>>>
>>>> Thanks Scott. Here is the link.
>>>>
>>>>
>>>> https://apps.araport.org/jbrowse/?data=arabidopsis&loc=Chr1%3A24330927..24332945&tracks=Araport11_Loci&highlight=
>>>>
>>>> Click on the dropdown on the track label 'Araport11 Gene Locus' and
>>>> select 'Save Track Data'. Then you select 'Whole reference sequence' and
>>>> 'GFF3' as the format option. (Screenshot attached).
>>>>
>>>> Thanks for your help.
>>>>
>>>> Best
>>>> -shabari
>>>>
>>>> On Tue, Mar 26, 2019 at 12:51 PM Scott Cain <sc...@sc...>
>>>> wrote:
>>>>
>>>>> Hi Shabari,
>>>>>
>>>>> I'm sending this to the JBrowse mailing list too, so others can chime
>>>>> in with suggestions.  The problem is almost certainly with the GFF: it is
>>>>> really screwed up (periods in the type column for all of the child
>>>>> features, NAN for the start coordinates and periods for the end
>>>>> coordinates).  I'd say addressing that will go a long way to fixing any
>>>>> problems. You said you dumped this GFF out of a JBrowse instance.  Can you
>>>>> provide the URL for that instance? Maybe there is something wrong with it.
>>>>>
>>>>> Thanks,
>>>>> Scott
>>>>>
>>>>>
>>>>> On Tue, Mar 26, 2019 at 11:53 AM Shabari Subramaniam <
>>>>> sh...@ar...> wrote:
>>>>>
>>>>>> Hi Scott,
>>>>>> I am getting errors when i try to upload the data from the 'Araport11
>>>>>> Gene Locus' track. I downloaded the data from the Jbrowse track on
>>>>>> Araport11's Jbrowse viewer in gff format. I removed the 'Chr' from the gff
>>>>>> file. The gff file is attached.
>>>>>>
>>>>>> The problem may be the -type is not the right one. The file only has
>>>>>> 'gene' as type so i tried '--type gene' (below) and no type defined. I am
>>>>>> getting the same error (attached). What am i doing wrong? Let me know if
>>>>>> you need access to the machine to check this out.
>>>>>>
>>>>>> [ec2-user@ip-172-31-31-73 JBrowse-1.16.2]$ bin/flatfile-to-json.pl
>>>>>> --gff ./arabidopsis/raw/Araport11\ -\ Gene\ Locus-Chr1-1..30427671.gff3
>>>>>> --tracklabel 'Araport11 Gene Locus' --metadata '{"Source": "Araport11
>>>>>> Release (Jun 2016)", "Description": "Araport11 Protein-coding,
>>>>>> Transposable-element, and Non-coding gene loci", "category": "Araport Data
>>>>>> / Araport11 / Annotation (Jun 2016)"}' --type gene
>>>>>>
>>>>>>
>>>>>> I am not getting this error when i load the 'Araport11 Protein Coding
>>>>>> Genes' track data with --type as exon.
>>>>>>
>>>>>>
>>>>>> Thanks for your help.
>>>>>>
>>>>>> -shabari
>>>>>>
>>>>>> --
>>>>>> ---------------------------------------------------
>>>>>> Sabarinath Subramaniam, Ph.D.
>>>>>> Director of Business Development
>>>>>> Phoenix Bioinformatics
>>>>>> 39221 Paseo Padre Parkway, Ste. J
>>>>>> Fremont, CA 94583, USA
>>>>>> Email: sh...@ar...
>>>>>> SkypeID:  shabarinath
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at
>>>>> scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>>>
>>>>
>>>>
>>>> --
>>>> ---------------------------------------------------
>>>> Sabarinath Subramaniam, Ph.D.
>>>> Director of Business Development
>>>> Phoenix Bioinformatics
>>>> 39221 Paseo Padre Parkway, Ste. J
>>>> Fremont, CA 94583, USA
>>>> Email: sh...@ar...
>>>> SkypeID:  shabarinath
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>
>>
>> --
>> ---------------------------------------------------
>> Sabarinath Subramaniam, Ph.D.
>> Director of Business Development
>> Phoenix Bioinformatics
>> 39221 Paseo Padre Parkway, Ste. J
>> Fremont, CA 94583, USA
>> Email: sh...@ar...
>> SkypeID:  shabarinath
>>
>
>
> --
> ---------------------------------------------------
> Sabarinath Subramaniam, Ph.D.
> Director of Business Development
> Phoenix Bioinformatics
> 39221 Paseo Padre Parkway, Ste. J
> Fremont, CA 94583, USA
> Email: sh...@ar...
> SkypeID:  shabarinath
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Loading errors for Gene Locus track

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

But that will mean any subfeatures are lost. Is it possible to get the original gff?

> On Mar 26, 2019, at 3:31 PM, Shabari Subramaniam <sh...@ar...> wrote:
> 
> Hi Colin,
> 
> Thank you so much for the suggestion. I will remove the NaN lines reload. 
> 
> Best
> -shabari
> 
>> On Tue, Mar 26, 2019 at 3:15 PM Colin <col...@gm...> wrote:
>> I'd assert that the track on araport is somehow corrupted. You can see if you click "View details" on any given feature that it has weird subfeatures with NaN values.
>> 
>> In this sense, jbrowse is doing it's best here :)
>> 
>> I would just "grep -v" all the lines with NaN before trying to load your track with flatfile-to-json.
>> 
>> You might also want to perform "delete Array.prototype.values" in the your javascript console before doing Save track data if you want to fix the issue of "function() { [values] }" in the exported GFF. Newer jbrowse versions contain a bugfix for this but older JBrowse versions do not (the bug was introduced only recently by browsers due to changes in how the javascript language has evolved over the years...)
>> 
>> -Colin
>> 
>>> On Tue, Mar 26, 2019 at 6:05 PM Shabari Subramaniam <sh...@ar...> wrote:
>>> Thanks Scott. Here is the link. 
>>> 
>>> https://apps.araport.org/jbrowse/?data=arabidopsis&loc=Chr1%3A24330927..24332945&tracks=Araport11_Loci&highlight=
>>> 
>>> Click on the dropdown on the track label 'Araport11 Gene Locus' and select 'Save Track Data'. Then you select 'Whole reference sequence' and  'GFF3' as the format option. (Screenshot attached).
>>> 
>>> Thanks for your help.
>>> 
>>> Best
>>> -shabari
>>> 
>>>> On Tue, Mar 26, 2019 at 12:51 PM Scott Cain <sc...@sc...> wrote:
>>>> Hi Shabari,
>>>> 
>>>> I'm sending this to the JBrowse mailing list too, so others can chime in with suggestions.  The problem is almost certainly with the GFF: it is really screwed up (periods in the type column for all of the child features, NAN for the start coordinates and periods for the end coordinates).  I'd say addressing that will go a long way to fixing any problems. You said you dumped this GFF out of a JBrowse instance.  Can you provide the URL for that instance? Maybe there is something wrong with it.
>>>> 
>>>> Thanks,
>>>> Scott
>>>> 
>>>> 
>>>>> On Tue, Mar 26, 2019 at 11:53 AM Shabari Subramaniam <sh...@ar...> wrote:
>>>>> Hi Scott,
>>>>> I am getting errors when i try to upload the data from the 'Araport11 Gene Locus' track. I downloaded the data from the Jbrowse track on Araport11's Jbrowse viewer in gff format. I removed the 'Chr' from the gff file. The gff file is attached. 
>>>>> 
>>>>> The problem may be the -type is not the right one. The file only has 'gene' as type so i tried '--type gene' (below) and no type defined. I am getting the same error (attached). What am i doing wrong? Let me know if you need access to the machine to check this out. 
>>>>> 
>>>>> [ec2-user@ip-172-31-31-73 JBrowse-1.16.2]$ bin/flatfile-to-json.pl --gff ./arabidopsis/raw/Araport11\ -\ Gene\ Locus-Chr1-1..30427671.gff3 --tracklabel 'Araport11 Gene Locus' --metadata '{"Source": "Araport11 Release (Jun 2016)", "Description": "Araport11 Protein-coding, Transposable-element, and Non-coding gene loci", "category": "Araport Data / Araport11 / Annotation (Jun 2016)"}' --type gene
>>>>> 
>>>>> I am not getting this error when i load the 'Araport11 Protein Coding Genes' track data with --type as exon. 
>>>>> 
>>>>> Thanks for your help.
>>>>> 
>>>>> -shabari
>>>>> 
>>>>> -- 
>>>>> ---------------------------------------------------
>>>>> Sabarinath Subramaniam, Ph.D.
>>>>> Director of Business Development
>>>>> Phoenix Bioinformatics
>>>>> 39221 Paseo Padre Parkway, Ste. J
>>>>> Fremont, CA 94583, USA
>>>>> Email: sh...@ar...
>>>>> SkypeID:  shabarinath
>>>> 
>>>> 
>>>> -- 
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>> 
>>> 
>>> -- 
>>> ---------------------------------------------------
>>> Sabarinath Subramaniam, Ph.D.
>>> Director of Business Development
>>> Phoenix Bioinformatics
>>> 39221 Paseo Padre Parkway, Ste. J
>>> Fremont, CA 94583, USA
>>> Email: sh...@ar...
>>> SkypeID:  shabarinath
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> 
> 
> -- 
> ---------------------------------------------------
> Sabarinath Subramaniam, Ph.D.
> Director of Business Development
> Phoenix Bioinformatics
> 39221 Paseo Padre Parkway, Ste. J
> Fremont, CA 94583, USA
> Email: sh...@ar...
> SkypeID:  shabarinath

Re: [Gmod-ajax] Loading errors for Gene Locus track

[Shabari S. <sh...@ar...>]

That did the trick. Thanks for the help.

On Tue, Mar 26, 2019 at 3:31 PM Shabari Subramaniam <sh...@ar...>
wrote:

> Hi Colin,
>
> Thank you so much for the suggestion. I will remove the NaN lines reload.
>
> Best
> -shabari
>
> On Tue, Mar 26, 2019 at 3:15 PM Colin <col...@gm...> wrote:
>
>> I'd assert that the track on araport is somehow corrupted. You can see if
>> you click "View details" on any given feature that it has weird subfeatures
>> with NaN values.
>>
>> In this sense, jbrowse is doing it's best here :)
>>
>> I would just "grep -v" all the lines with NaN before trying to load your
>> track with flatfile-to-json.
>>
>> You might also want to perform "delete Array.prototype.values" in the
>> your javascript console before doing Save track data if you want to fix the
>> issue of "function() { [values] }" in the exported GFF. Newer jbrowse
>> versions contain a bugfix for this but older JBrowse versions do not (the
>> bug was introduced only recently by browsers due to changes in how the
>> javascript language has evolved over the years...)
>>
>> -Colin
>>
>> On Tue, Mar 26, 2019 at 6:05 PM Shabari Subramaniam <
>> sh...@ar...> wrote:
>>
>>> Thanks Scott. Here is the link.
>>>
>>>
>>> https://apps.araport.org/jbrowse/?data=arabidopsis&loc=Chr1%3A24330927..24332945&tracks=Araport11_Loci&highlight=
>>>
>>> Click on the dropdown on the track label 'Araport11 Gene Locus' and
>>> select 'Save Track Data'. Then you select 'Whole reference sequence' and
>>> 'GFF3' as the format option. (Screenshot attached).
>>>
>>> Thanks for your help.
>>>
>>> Best
>>> -shabari
>>>
>>> On Tue, Mar 26, 2019 at 12:51 PM Scott Cain <sc...@sc...> wrote:
>>>
>>>> Hi Shabari,
>>>>
>>>> I'm sending this to the JBrowse mailing list too, so others can chime
>>>> in with suggestions.  The problem is almost certainly with the GFF: it is
>>>> really screwed up (periods in the type column for all of the child
>>>> features, NAN for the start coordinates and periods for the end
>>>> coordinates).  I'd say addressing that will go a long way to fixing any
>>>> problems. You said you dumped this GFF out of a JBrowse instance.  Can you
>>>> provide the URL for that instance? Maybe there is something wrong with it.
>>>>
>>>> Thanks,
>>>> Scott
>>>>
>>>>
>>>> On Tue, Mar 26, 2019 at 11:53 AM Shabari Subramaniam <
>>>> sh...@ar...> wrote:
>>>>
>>>>> Hi Scott,
>>>>> I am getting errors when i try to upload the data from the 'Araport11
>>>>> Gene Locus' track. I downloaded the data from the Jbrowse track on
>>>>> Araport11's Jbrowse viewer in gff format. I removed the 'Chr' from the gff
>>>>> file. The gff file is attached.
>>>>>
>>>>> The problem may be the -type is not the right one. The file only has
>>>>> 'gene' as type so i tried '--type gene' (below) and no type defined. I am
>>>>> getting the same error (attached). What am i doing wrong? Let me know if
>>>>> you need access to the machine to check this out.
>>>>>
>>>>> [ec2-user@ip-172-31-31-73 JBrowse-1.16.2]$ bin/flatfile-to-json.pl
>>>>> --gff ./arabidopsis/raw/Araport11\ -\ Gene\ Locus-Chr1-1..30427671.gff3
>>>>> --tracklabel 'Araport11 Gene Locus' --metadata '{"Source": "Araport11
>>>>> Release (Jun 2016)", "Description": "Araport11 Protein-coding,
>>>>> Transposable-element, and Non-coding gene loci", "category": "Araport Data
>>>>> / Araport11 / Annotation (Jun 2016)"}' --type gene
>>>>>
>>>>>
>>>>> I am not getting this error when i load the 'Araport11 Protein Coding
>>>>> Genes' track data with --type as exon.
>>>>>
>>>>>
>>>>> Thanks for your help.
>>>>>
>>>>> -shabari
>>>>>
>>>>> --
>>>>> ---------------------------------------------------
>>>>> Sabarinath Subramaniam, Ph.D.
>>>>> Director of Business Development
>>>>> Phoenix Bioinformatics
>>>>> 39221 Paseo Padre Parkway, Ste. J
>>>>> Fremont, CA 94583, USA
>>>>> Email: sh...@ar...
>>>>> SkypeID:  shabarinath
>>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>> dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>>
>>>
>>>
>>> --
>>> ---------------------------------------------------
>>> Sabarinath Subramaniam, Ph.D.
>>> Director of Business Development
>>> Phoenix Bioinformatics
>>> 39221 Paseo Padre Parkway, Ste. J
>>> Fremont, CA 94583, USA
>>> Email: sh...@ar...
>>> SkypeID:  shabarinath
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>
> --
> ---------------------------------------------------
> Sabarinath Subramaniam, Ph.D.
> Director of Business Development
> Phoenix Bioinformatics
> 39221 Paseo Padre Parkway, Ste. J
> Fremont, CA 94583, USA
> Email: sh...@ar...
> SkypeID:  shabarinath
>


-- 
---------------------------------------------------
Sabarinath Subramaniam, Ph.D.
Director of Business Development
Phoenix Bioinformatics
39221 Paseo Padre Parkway, Ste. J
Fremont, CA 94583, USA
Email: sh...@ar...
SkypeID:  shabarinath

Re: [Gmod-ajax] Loading errors for Gene Locus track

[Shabari S. <sh...@ar...>]

Hi Colin,

Thank you so much for the suggestion. I will remove the NaN lines reload.

Best
-shabari

On Tue, Mar 26, 2019 at 3:15 PM Colin <col...@gm...> wrote:

> I'd assert that the track on araport is somehow corrupted. You can see if
> you click "View details" on any given feature that it has weird subfeatures
> with NaN values.
>
> In this sense, jbrowse is doing it's best here :)
>
> I would just "grep -v" all the lines with NaN before trying to load your
> track with flatfile-to-json.
>
> You might also want to perform "delete Array.prototype.values" in the your
> javascript console before doing Save track data if you want to fix the
> issue of "function() { [values] }" in the exported GFF. Newer jbrowse
> versions contain a bugfix for this but older JBrowse versions do not (the
> bug was introduced only recently by browsers due to changes in how the
> javascript language has evolved over the years...)
>
> -Colin
>
> On Tue, Mar 26, 2019 at 6:05 PM Shabari Subramaniam <
> sh...@ar...> wrote:
>
>> Thanks Scott. Here is the link.
>>
>>
>> https://apps.araport.org/jbrowse/?data=arabidopsis&loc=Chr1%3A24330927..24332945&tracks=Araport11_Loci&highlight=
>>
>> Click on the dropdown on the track label 'Araport11 Gene Locus' and
>> select 'Save Track Data'. Then you select 'Whole reference sequence' and
>> 'GFF3' as the format option. (Screenshot attached).
>>
>> Thanks for your help.
>>
>> Best
>> -shabari
>>
>> On Tue, Mar 26, 2019 at 12:51 PM Scott Cain <sc...@sc...> wrote:
>>
>>> Hi Shabari,
>>>
>>> I'm sending this to the JBrowse mailing list too, so others can chime in
>>> with suggestions.  The problem is almost certainly with the GFF: it is
>>> really screwed up (periods in the type column for all of the child
>>> features, NAN for the start coordinates and periods for the end
>>> coordinates).  I'd say addressing that will go a long way to fixing any
>>> problems. You said you dumped this GFF out of a JBrowse instance.  Can you
>>> provide the URL for that instance? Maybe there is something wrong with it.
>>>
>>> Thanks,
>>> Scott
>>>
>>>
>>> On Tue, Mar 26, 2019 at 11:53 AM Shabari Subramaniam <
>>> sh...@ar...> wrote:
>>>
>>>> Hi Scott,
>>>> I am getting errors when i try to upload the data from the 'Araport11
>>>> Gene Locus' track. I downloaded the data from the Jbrowse track on
>>>> Araport11's Jbrowse viewer in gff format. I removed the 'Chr' from the gff
>>>> file. The gff file is attached.
>>>>
>>>> The problem may be the -type is not the right one. The file only has
>>>> 'gene' as type so i tried '--type gene' (below) and no type defined. I am
>>>> getting the same error (attached). What am i doing wrong? Let me know if
>>>> you need access to the machine to check this out.
>>>>
>>>> [ec2-user@ip-172-31-31-73 JBrowse-1.16.2]$ bin/flatfile-to-json.pl
>>>> --gff ./arabidopsis/raw/Araport11\ -\ Gene\ Locus-Chr1-1..30427671.gff3
>>>> --tracklabel 'Araport11 Gene Locus' --metadata '{"Source": "Araport11
>>>> Release (Jun 2016)", "Description": "Araport11 Protein-coding,
>>>> Transposable-element, and Non-coding gene loci", "category": "Araport Data
>>>> / Araport11 / Annotation (Jun 2016)"}' --type gene
>>>>
>>>>
>>>> I am not getting this error when i load the 'Araport11 Protein Coding
>>>> Genes' track data with --type as exon.
>>>>
>>>>
>>>> Thanks for your help.
>>>>
>>>> -shabari
>>>>
>>>> --
>>>> ---------------------------------------------------
>>>> Sabarinath Subramaniam, Ph.D.
>>>> Director of Business Development
>>>> Phoenix Bioinformatics
>>>> 39221 Paseo Padre Parkway, Ste. J
>>>> Fremont, CA 94583, USA
>>>> Email: sh...@ar...
>>>> SkypeID:  shabarinath
>>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>
>>
>> --
>> ---------------------------------------------------
>> Sabarinath Subramaniam, Ph.D.
>> Director of Business Development
>> Phoenix Bioinformatics
>> 39221 Paseo Padre Parkway, Ste. J
>> Fremont, CA 94583, USA
>> Email: sh...@ar...
>> SkypeID:  shabarinath
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

-- 
---------------------------------------------------
Sabarinath Subramaniam, Ph.D.
Director of Business Development
Phoenix Bioinformatics
39221 Paseo Padre Parkway, Ste. J
Fremont, CA 94583, USA
Email: sh...@ar...
SkypeID:  shabarinath

Re: [Gmod-ajax] Loading errors for Gene Locus track

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

I'd assert that the track on araport is somehow corrupted. You can see if
you click "View details" on any given feature that it has weird subfeatures
with NaN values.

In this sense, jbrowse is doing it's best here :)

I would just "grep -v" all the lines with NaN before trying to load your
track with flatfile-to-json.

You might also want to perform "delete Array.prototype.values" in the your
javascript console before doing Save track data if you want to fix the
issue of "function() { [values] }" in the exported GFF. Newer jbrowse
versions contain a bugfix for this but older JBrowse versions do not (the
bug was introduced only recently by browsers due to changes in how the
javascript language has evolved over the years...)

-Colin

On Tue, Mar 26, 2019 at 6:05 PM Shabari Subramaniam <sh...@ar...>
wrote:

> Thanks Scott. Here is the link.
>
>
> https://apps.araport.org/jbrowse/?data=arabidopsis&loc=Chr1%3A24330927..24332945&tracks=Araport11_Loci&highlight=
>
> Click on the dropdown on the track label 'Araport11 Gene Locus' and select
> 'Save Track Data'. Then you select 'Whole reference sequence' and  'GFF3'
> as the format option. (Screenshot attached).
>
> Thanks for your help.
>
> Best
> -shabari
>
> On Tue, Mar 26, 2019 at 12:51 PM Scott Cain <sc...@sc...> wrote:
>
>> Hi Shabari,
>>
>> I'm sending this to the JBrowse mailing list too, so others can chime in
>> with suggestions.  The problem is almost certainly with the GFF: it is
>> really screwed up (periods in the type column for all of the child
>> features, NAN for the start coordinates and periods for the end
>> coordinates).  I'd say addressing that will go a long way to fixing any
>> problems. You said you dumped this GFF out of a JBrowse instance.  Can you
>> provide the URL for that instance? Maybe there is something wrong with it.
>>
>> Thanks,
>> Scott
>>
>>
>> On Tue, Mar 26, 2019 at 11:53 AM Shabari Subramaniam <
>> sh...@ar...> wrote:
>>
>>> Hi Scott,
>>> I am getting errors when i try to upload the data from the 'Araport11
>>> Gene Locus' track. I downloaded the data from the Jbrowse track on
>>> Araport11's Jbrowse viewer in gff format. I removed the 'Chr' from the gff
>>> file. The gff file is attached.
>>>
>>> The problem may be the -type is not the right one. The file only has
>>> 'gene' as type so i tried '--type gene' (below) and no type defined. I am
>>> getting the same error (attached). What am i doing wrong? Let me know if
>>> you need access to the machine to check this out.
>>>
>>> [ec2-user@ip-172-31-31-73 JBrowse-1.16.2]$ bin/flatfile-to-json.pl
>>> --gff ./arabidopsis/raw/Araport11\ -\ Gene\ Locus-Chr1-1..30427671.gff3
>>> --tracklabel 'Araport11 Gene Locus' --metadata '{"Source": "Araport11
>>> Release (Jun 2016)", "Description": "Araport11 Protein-coding,
>>> Transposable-element, and Non-coding gene loci", "category": "Araport Data
>>> / Araport11 / Annotation (Jun 2016)"}' --type gene
>>>
>>>
>>> I am not getting this error when i load the 'Araport11 Protein Coding
>>> Genes' track data with --type as exon.
>>>
>>>
>>> Thanks for your help.
>>>
>>> -shabari
>>>
>>> --
>>> ---------------------------------------------------
>>> Sabarinath Subramaniam, Ph.D.
>>> Director of Business Development
>>> Phoenix Bioinformatics
>>> 39221 Paseo Padre Parkway, Ste. J
>>> Fremont, CA 94583, USA
>>> Email: sh...@ar...
>>> SkypeID:  shabarinath
>>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>
>
> --
> ---------------------------------------------------
> Sabarinath Subramaniam, Ph.D.
> Director of Business Development
> Phoenix Bioinformatics
> 39221 Paseo Padre Parkway, Ste. J
> Fremont, CA 94583, USA
> Email: sh...@ar...
> SkypeID:  shabarinath
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Loading errors for Gene Locus track

[Shabari S. <sh...@ar...>]

Thanks Scott. Here is the link.

https://apps.araport.org/jbrowse/?data=arabidopsis&loc=Chr1%3A24330927..24332945&tracks=Araport11_Loci&highlight=

Click on the dropdown on the track label 'Araport11 Gene Locus' and select
'Save Track Data'. Then you select 'Whole reference sequence' and  'GFF3'
as the format option. (Screenshot attached).

Thanks for your help.

Best
-shabari

On Tue, Mar 26, 2019 at 12:51 PM Scott Cain <sc...@sc...> wrote:

> Hi Shabari,
>
> I'm sending this to the JBrowse mailing list too, so others can chime in
> with suggestions.  The problem is almost certainly with the GFF: it is
> really screwed up (periods in the type column for all of the child
> features, NAN for the start coordinates and periods for the end
> coordinates).  I'd say addressing that will go a long way to fixing any
> problems. You said you dumped this GFF out of a JBrowse instance.  Can you
> provide the URL for that instance? Maybe there is something wrong with it.
>
> Thanks,
> Scott
>
>
> On Tue, Mar 26, 2019 at 11:53 AM Shabari Subramaniam <
> sh...@ar...> wrote:
>
>> Hi Scott,
>> I am getting errors when i try to upload the data from the 'Araport11
>> Gene Locus' track. I downloaded the data from the Jbrowse track on
>> Araport11's Jbrowse viewer in gff format. I removed the 'Chr' from the gff
>> file. The gff file is attached.
>>
>> The problem may be the -type is not the right one. The file only has
>> 'gene' as type so i tried '--type gene' (below) and no type defined. I am
>> getting the same error (attached). What am i doing wrong? Let me know if
>> you need access to the machine to check this out.
>>
>> [ec2-user@ip-172-31-31-73 JBrowse-1.16.2]$ bin/flatfile-to-json.pl --gff
>> ./arabidopsis/raw/Araport11\ -\ Gene\ Locus-Chr1-1..30427671.gff3
>> --tracklabel 'Araport11 Gene Locus' --metadata '{"Source": "Araport11
>> Release (Jun 2016)", "Description": "Araport11 Protein-coding,
>> Transposable-element, and Non-coding gene loci", "category": "Araport Data
>> / Araport11 / Annotation (Jun 2016)"}' --type gene
>>
>>
>> I am not getting this error when i load the 'Araport11 Protein Coding
>> Genes' track data with --type as exon.
>>
>>
>> Thanks for your help.
>>
>> -shabari
>>
>> --
>> ---------------------------------------------------
>> Sabarinath Subramaniam, Ph.D.
>> Director of Business Development
>> Phoenix Bioinformatics
>> 39221 Paseo Padre Parkway, Ste. J
>> Fremont, CA 94583, USA
>> Email: sh...@ar...
>> SkypeID:  shabarinath
>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>


-- 
---------------------------------------------------
Sabarinath Subramaniam, Ph.D.
Director of Business Development
Phoenix Bioinformatics
39221 Paseo Padre Parkway, Ste. J
Fremont, CA 94583, USA
Email: sh...@ar...
SkypeID:  shabarinath

Re: [Gmod-ajax] Loading errors for Gene Locus track

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

Hi Shabari,

I'm sending this to the JBrowse mailing list too, so others can chime in
with suggestions.  The problem is almost certainly with the GFF: it is
really screwed up (periods in the type column for all of the child
features, NAN for the start coordinates and periods for the end
coordinates).  I'd say addressing that will go a long way to fixing any
problems. You said you dumped this GFF out of a JBrowse instance.  Can you
provide the URL for that instance? Maybe there is something wrong with it.

Thanks,
Scott


On Tue, Mar 26, 2019 at 11:53 AM Shabari Subramaniam <
sh...@ar...> wrote:

> Hi Scott,
> I am getting errors when i try to upload the data from the 'Araport11 Gene
> Locus' track. I downloaded the data from the Jbrowse track on Araport11's
> Jbrowse viewer in gff format. I removed the 'Chr' from the gff file. The
> gff file is attached.
>
> The problem may be the -type is not the right one. The file only has
> 'gene' as type so i tried '--type gene' (below) and no type defined. I am
> getting the same error (attached). What am i doing wrong? Let me know if
> you need access to the machine to check this out.
>
> [ec2-user@ip-172-31-31-73 JBrowse-1.16.2]$ bin/flatfile-to-json.pl --gff
> ./arabidopsis/raw/Araport11\ -\ Gene\ Locus-Chr1-1..30427671.gff3
> --tracklabel 'Araport11 Gene Locus' --metadata '{"Source": "Araport11
> Release (Jun 2016)", "Description": "Araport11 Protein-coding,
> Transposable-element, and Non-coding gene loci", "category": "Araport Data
> / Araport11 / Annotation (Jun 2016)"}' --type gene
>
>
> I am not getting this error when i load the 'Araport11 Protein Coding
> Genes' track data with --type as exon.
>
>
> Thanks for your help.
>
> -shabari
>
> --
> ---------------------------------------------------
> Sabarinath Subramaniam, Ph.D.
> Director of Business Development
> Phoenix Bioinformatics
> 39221 Paseo Padre Parkway, Ste. J
> Fremont, CA 94583, USA
> Email: sh...@ar...
> SkypeID:  shabarinath
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] variable speed of generate-names on similar GFF3Tabix files

[Jorge D. <to...@gm...>]

 - JBrowse version 1.16.0

i am runing generate-names on similar genomes with similar GFF3Tabix files
and one is runing reasonnably slowly, but the other one is tremendously
slow (see details bellow).

the stats printed for the reasonnably slow one:
Sampled input stats:
                   avg record text bytes 16.2100898570142
                      name input records 43291
        operation stream estimated count 981961604
           record stream estimated count 75535508
                     total namerec bytes 701751
                       total input bytes 1224437376
                         operations made 50005
                       namerecs buffered 43291
        namerecs converted to operations 3827

the stats printed for the very slow one:
Sampled input stats:
                   avg record text bytes 0.53713464302827
                      name input records 2092
        operation stream estimated count 24720969515
           record stream estimated count 2247360865
                     total namerec bytes 2242
                       total input bytes 1207135376
                         operations made 50009
                       namerecs buffered 4174
        namerecs converted to operations 4174


How come there are so big differences between the two runs ?

Thanks for the help in understanding what's going on and how to speed up
the second run.

[Gmod-ajax] variable speed of generate-names on similar GFF3Tabix files

[Jorge D. <to...@gm...>]

- JBrowse version 1.16.0

i am runing generate-names on similar genomes with similar GFF3Tabix files
and one is runing reasonnably slowly, but the other one is tremendously
slow (see details bellow).

the stats printed for the reasonnably slow one:
Sampled input stats:
                   avg record text bytes 16.2100898570142
                      name input records 43291
        operation stream estimated count 981961604
           record stream estimated count 75535508
                     total namerec bytes 701751
                       total input bytes 1224437376
                         operations made 50005
                       namerecs buffered 43291
        namerecs converted to operations 3827

the stats printed for the very slow one:
Sampled input stats:
                   avg record text bytes 0.53713464302827
                      name input records 2092
        operation stream estimated count 24720969515
           record stream estimated count 2247360865
                     total namerec bytes 2242
                       total input bytes 1207135376
                         operations made 50009
                       namerecs buffered 4174
        namerecs converted to operations 4174


How come there are so big differences between the two runs ?

Thanks for the help in understanding what's going on and how to speed up
the second run.

Jorge

Re: [Gmod-ajax] Jbrowse 1.16.4 Setup issue

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

I believe this issue is cross-posted here and solved
https://github.com/GMOD/jbrowse/issues/1325 (the email here was probably
just suspended in email filters)


-Colin

On Tue, Mar 5, 2019 at 12:03 PM Nalabolu, Harika Srividya <
hsn...@mc...> wrote:

> Hi Team,
>
>
>
> I have issues with installing the Jbrowse 1.16.4.
>
> Steps followed:
>
>    1. Got the Jbrowse zip file from
>    https://github.com/GMOD/jbrowse/archive/1.16.3-release.zip
>    2. Unzipped the file
>    3. Removed comments for sample_data tracks on jbrowse.conf
>    4. Ran setup.sh script. It ran successfully without any issues.
>
>
>
> When I open the Jbrowse for the sample_data tracks on the server, it gave
> me the below error. Could you please let me know whats wrong with the set
> up.
>
>
>
>
>
> [image: error]
>
>
>
>
>
> Thanks,
>
> Harika
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Jbrowse 1.16.4 Setup issue

[Nalabolu, H. S. <hsn...@mc...>]

Hi Team,

I have issues with installing the Jbrowse 1.16.4.
Steps followed:

  1.  Got the Jbrowse zip file from https://github.com/GMOD/jbrowse/archive/1.16.3-release.zip
  2.  Unzipped the file
  3.  Removed comments for sample_data tracks on jbrowse.conf
  4.  Ran setup.sh script. It ran successfully without any issues.

When I open the Jbrowse for the sample_data tracks on the server, it gave me the below error. Could you please let me know whats wrong with the set up.


[error]


Thanks,
Harika

Re: [Gmod-ajax] jbrowse1.16.3 plugin not found

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

No worries

One other note, I think Hans had mentioned there might be some
compatibility issue between this plugin and the latest version of JBrowse
due to some upgrades that were made to the VCF parser. If you find this can
you document it?

Thanks

-Colin

On Thu, Feb 28, 2019 at 3:20 PM thomas <
tsi...@re...> wrote:

> Damn! That's what it was. It works now. Thanks very much for your help and
> sorry to have bothered you with such a rookie mistake.
>
> Best,
>
> Thomas
> On 2019-02-28 12:02 p.m., Colin wrote:
>
> Have you tried clearing browser cache and refreshing by chance?
>
>
>
> -Colin
>
> On Thu, Feb 28, 2019 at 2:36 PM thomas <
> tsi...@re...> wrote:
>
>> Hi Colin,
>>
>>
>> Thanks for your prompt answer and your help.
>>
>> I effectively use the JBrowse-1.16.3-dev.zip
>> <https://github.com/GMOD/jbrowse/archive/1.16.3-release.zip>
>> (jbrowse-1.16.3-release once unzipped, sorry for the confusion). I also
>> tried to build from source (git clone https://github.com/GMOD/jbrowse)
>> but although the setup runs fine, the plugin still fails to load (the
>> browser works fine without any plugin listed in jbrowse.conf).
>>
>> The plugins seems to be taken into account during setup during as shown
>> log file (line ~50):
>>
>>
>> $ webpack
>> clean-webpack-plugin: /var/www/jbrowse/dist has been removed.
>> jbrowse-glob-loader: building 205 JBrowse modules
>> jbrowse-glob-loader: adding plugin module
>> VariantEffectPlugin/View/Track/CanvasEffectVariants
>> jbrowse-glob-loader: adding plugin module
>> VariantEffectPlugin/View/Track/_VariantDetailMixin
>> jbrowse-glob-loader: adding plugin module VariantEffectPlugin/main
>> jbrowse-glob-loader: adding plugin module
>> RegexSequenceSearch/View/SearchSeqDialog
>> jbrowse-glob-loader: adding plugin module
>> RegexSequenceSearch/Store/SeqFeature/RegexSearch
>> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
>> jbrowse-glob-loader: adding plugin module
>> NeatHTMLFeatures/View/Track/NeatFeatures
>> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
>> jbrowse-glob-loader: adding plugin module
>> NeatCanvasFeatures/View/Track/NeatFeatures
>> jbrowse-glob-loader: adding plugin module
>> NeatCanvasFeatures/View/FeatureGlyph/UnprocessedTranscript
>> jbrowse-glob-loader: adding plugin module
>> NeatCanvasFeatures/View/FeatureGlyph/Segments
>> jbrowse-glob-loader: adding plugin module
>> NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
>> jbrowse-glob-loader: adding plugin module
>> NeatCanvasFeatures/View/FeatureGlyph/Gene
>> jbrowse-glob-loader: adding plugin module
>> NeatCanvasFeatures/View/FeatureGlyph/Box
>> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
>> jbrowse-glob-loader: adding plugin module HideTrackLabels/main
>> jbrowse-glob-loader: adding plugin module DebugEvents/main
>> jbrowse-glob-loader: adding plugin module CategoryUrl/main
>> jbrowse-glob-loader: discovered a total of 223 modules
>> jbrowse-glob-loader: skipping entry point module JBrowse/standalone
>> jbrowse-glob-loader: skipping entry point module JBrowse/main
>> jbrowse-glob-loader: skipping entry point module JBrowse/standalone
>> jbrowse-glob-loader: skipping entry point module JBrowse/main
>> Hash: 4c7633339ca7b9824f57
>> Version: webpack 4.26.1
>> Time: 41529ms
>> Built at: 02/28/2019 6:52:02 PM
>>
>>
>> the log file is attached to this message as well as a screen shot of my
>> browser (with the error message).
>>
>> Thanks again for your help.
>>
>>
>> Best,
>>
>>
>> Thomas
>>
>>
>>
>>
>> On 2019-02-28 10:33 a.m., Colin wrote:
>>
>> That looks about right, wondering are you using the "-dev" version of the
>> code?
>>
>> The release pages here say something to the effect of
>>
>> "JBrowse-1.16.3-dev.zip - use this if you modify jbrowse source code or
>> use plugins"
>>
>> Only the -dev version or a github clone of the jbrowse repo will perform
>> the rebuild with the plugins properly
>>
>> Hope that helps.. the whole reason for this is the webpack modernization
>> of our code that got us to where we don't dynamically load plugins but
>> instead bundle them at build time.
>>
>>
>> -Colin
>>
>> On Thu, Feb 28, 2019 at 1:14 PM thomas <
>> tsi...@re...> wrote:
>>
>>> Hello all,
>>>
>>> I am fairly new to Jbrowse. I have installed the latest version
>>> (jbrowse-1.16.3-release) in a docker container (ubuntu xenial) and it
>>> works fine.
>>>
>>> Problems arise when I try to install a plugin. I am trying to install
>>> and use VariantEffectPlugin
>>> (https://github.com/hans-vg/jbplugin-varianteffect).
>>>
>>> I copied the plugin folder into the jbrowse/plugins directory, added the
>>> plugin to jbrowse.conf and ran ./setup.sh again - and get an error
>>> "plugin VariantEffectPlugin not found, please ensure the plugin was
>>> included in this jbrowse unit".
>>>
>>> I tried to add the plugin using many syntaxes in jbrowse.conf:
>>>
>>> in [GENERAL]
>>>
>>> plugins += VariantEffectPlugin
>>>
>>> or
>>>
>>> [plugins.VariantEffectPlugin]
>>> location = plugins/VariantEffectPlugin
>>>
>>> or
>>>
>>> [plugins.VariantEffectPlugin]
>>> location = /var/www/jbrowse/plugins/VariantEffectPlugin
>>>
>>>
>>> The files exists and the plugin folder is open in reading.
>>>
>>>
>>> I cannot seem to figure out what am I doing wrong.
>>>
>>> is jbrowse-1.16.3-release the right version to use with plugins?
>>>
>>> is there something that I'm missing to load the plugins properly?
>>>
>>>
>>> Best regards,
>>>
>>>
>>> Thomas
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>

Re: [Gmod-ajax] jbrowse1.16.3 plugin not found

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

Have you tried clearing browser cache and refreshing by chance?



-Colin

On Thu, Feb 28, 2019 at 2:36 PM thomas <
tsi...@re...> wrote:

> Hi Colin,
>
>
> Thanks for your prompt answer and your help.
>
> I effectively use the JBrowse-1.16.3-dev.zip
> <https://github.com/GMOD/jbrowse/archive/1.16.3-release.zip>
> (jbrowse-1.16.3-release once unzipped, sorry for the confusion). I also
> tried to build from source (git clone https://github.com/GMOD/jbrowse)
> but although the setup runs fine, the plugin still fails to load (the
> browser works fine without any plugin listed in jbrowse.conf).
>
> The plugins seems to be taken into account during setup during as shown
> log file (line ~50):
>
>
> $ webpack
> clean-webpack-plugin: /var/www/jbrowse/dist has been removed.
> jbrowse-glob-loader: building 205 JBrowse modules
> jbrowse-glob-loader: adding plugin module
> VariantEffectPlugin/View/Track/CanvasEffectVariants
> jbrowse-glob-loader: adding plugin module
> VariantEffectPlugin/View/Track/_VariantDetailMixin
> jbrowse-glob-loader: adding plugin module VariantEffectPlugin/main
> jbrowse-glob-loader: adding plugin module
> RegexSequenceSearch/View/SearchSeqDialog
> jbrowse-glob-loader: adding plugin module
> RegexSequenceSearch/Store/SeqFeature/RegexSearch
> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
> jbrowse-glob-loader: adding plugin module
> NeatHTMLFeatures/View/Track/NeatFeatures
> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
> jbrowse-glob-loader: adding plugin module
> NeatCanvasFeatures/View/Track/NeatFeatures
> jbrowse-glob-loader: adding plugin module
> NeatCanvasFeatures/View/FeatureGlyph/UnprocessedTranscript
> jbrowse-glob-loader: adding plugin module
> NeatCanvasFeatures/View/FeatureGlyph/Segments
> jbrowse-glob-loader: adding plugin module
> NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
> jbrowse-glob-loader: adding plugin module
> NeatCanvasFeatures/View/FeatureGlyph/Gene
> jbrowse-glob-loader: adding plugin module
> NeatCanvasFeatures/View/FeatureGlyph/Box
> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
> jbrowse-glob-loader: adding plugin module HideTrackLabels/main
> jbrowse-glob-loader: adding plugin module DebugEvents/main
> jbrowse-glob-loader: adding plugin module CategoryUrl/main
> jbrowse-glob-loader: discovered a total of 223 modules
> jbrowse-glob-loader: skipping entry point module JBrowse/standalone
> jbrowse-glob-loader: skipping entry point module JBrowse/main
> jbrowse-glob-loader: skipping entry point module JBrowse/standalone
> jbrowse-glob-loader: skipping entry point module JBrowse/main
> Hash: 4c7633339ca7b9824f57
> Version: webpack 4.26.1
> Time: 41529ms
> Built at: 02/28/2019 6:52:02 PM
>
>
> the log file is attached to this message as well as a screen shot of my
> browser (with the error message).
>
> Thanks again for your help.
>
>
> Best,
>
>
> Thomas
>
>
>
>
> On 2019-02-28 10:33 a.m., Colin wrote:
>
> That looks about right, wondering are you using the "-dev" version of the
> code?
>
> The release pages here say something to the effect of
>
> "JBrowse-1.16.3-dev.zip - use this if you modify jbrowse source code or
> use plugins"
>
> Only the -dev version or a github clone of the jbrowse repo will perform
> the rebuild with the plugins properly
>
> Hope that helps.. the whole reason for this is the webpack modernization
> of our code that got us to where we don't dynamically load plugins but
> instead bundle them at build time.
>
>
> -Colin
>
> On Thu, Feb 28, 2019 at 1:14 PM thomas <
> tsi...@re...> wrote:
>
>> Hello all,
>>
>> I am fairly new to Jbrowse. I have installed the latest version
>> (jbrowse-1.16.3-release) in a docker container (ubuntu xenial) and it
>> works fine.
>>
>> Problems arise when I try to install a plugin. I am trying to install
>> and use VariantEffectPlugin
>> (https://github.com/hans-vg/jbplugin-varianteffect).
>>
>> I copied the plugin folder into the jbrowse/plugins directory, added the
>> plugin to jbrowse.conf and ran ./setup.sh again - and get an error
>> "plugin VariantEffectPlugin not found, please ensure the plugin was
>> included in this jbrowse unit".
>>
>> I tried to add the plugin using many syntaxes in jbrowse.conf:
>>
>> in [GENERAL]
>>
>> plugins += VariantEffectPlugin
>>
>> or
>>
>> [plugins.VariantEffectPlugin]
>> location = plugins/VariantEffectPlugin
>>
>> or
>>
>> [plugins.VariantEffectPlugin]
>> location = /var/www/jbrowse/plugins/VariantEffectPlugin
>>
>>
>> The files exists and the plugin folder is open in reading.
>>
>>
>> I cannot seem to figure out what am I doing wrong.
>>
>> is jbrowse-1.16.3-release the right version to use with plugins?
>>
>> is there something that I'm missing to load the plugins properly?
>>
>>
>> Best regards,
>>
>>
>> Thomas
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] jbrowse1.16.3 plugin not found

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

That looks about right, wondering are you using the "-dev" version of the
code?

The release pages here say something to the effect of

"JBrowse-1.16.3-dev.zip - use this if you modify jbrowse source code or use
plugins"

Only the -dev version or a github clone of the jbrowse repo will perform
the rebuild with the plugins properly

Hope that helps.. the whole reason for this is the webpack modernization of
our code that got us to where we don't dynamically load plugins but instead
bundle them at build time.


-Colin

On Thu, Feb 28, 2019 at 1:14 PM thomas <
tsi...@re...> wrote:

> Hello all,
>
> I am fairly new to Jbrowse. I have installed the latest version
> (jbrowse-1.16.3-release) in a docker container (ubuntu xenial) and it
> works fine.
>
> Problems arise when I try to install a plugin. I am trying to install
> and use VariantEffectPlugin
> (https://github.com/hans-vg/jbplugin-varianteffect).
>
> I copied the plugin folder into the jbrowse/plugins directory, added the
> plugin to jbrowse.conf and ran ./setup.sh again - and get an error
> "plugin VariantEffectPlugin not found, please ensure the plugin was
> included in this jbrowse unit".
>
> I tried to add the plugin using many syntaxes in jbrowse.conf:
>
> in [GENERAL]
>
> plugins += VariantEffectPlugin
>
> or
>
> [plugins.VariantEffectPlugin]
> location = plugins/VariantEffectPlugin
>
> or
>
> [plugins.VariantEffectPlugin]
> location = /var/www/jbrowse/plugins/VariantEffectPlugin
>
>
> The files exists and the plugin folder is open in reading.
>
>
> I cannot seem to figure out what am I doing wrong.
>
> is jbrowse-1.16.3-release the right version to use with plugins?
>
> is there something that I'm missing to load the plugins properly?
>
>
> Best regards,
>
>
> Thomas
>
>
>
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] jbrowse1.16.3 plugin not found

[thomas <tsi...@re...>]

Hello all,

I am fairly new to Jbrowse. I have installed the latest version 
(jbrowse-1.16.3-release) in a docker container (ubuntu xenial) and it 
works fine.

Problems arise when I try to install a plugin. I am trying to install 
and use VariantEffectPlugin 
(https://github.com/hans-vg/jbplugin-varianteffect).

I copied the plugin folder into the jbrowse/plugins directory, added the 
plugin to jbrowse.conf and ran ./setup.sh again - and get an error 
"plugin VariantEffectPlugin not found, please ensure the plugin was 
included in this jbrowse unit".

I tried to add the plugin using many syntaxes in jbrowse.conf:

in [GENERAL]

plugins += VariantEffectPlugin

or

[plugins.VariantEffectPlugin]
location = plugins/VariantEffectPlugin

or

[plugins.VariantEffectPlugin]
location = /var/www/jbrowse/plugins/VariantEffectPlugin


The files exists and the plugin folder is open in reading.


I cannot seem to figure out what am I doing wrong.

is jbrowse-1.16.3-release the right version to use with plugins?

is there something that I'm missing to load the plugins properly?


Best regards,


Thomas