gmod-ajax — JBrowse list

Re: [Gmod-ajax] Question about file formats for genome alignment visualization in JBrowse

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

Hi there,
I went ahead to try to make a converter tool from XMFA to PAF. The XMFA is
sort of an awkward format for jbrowse to support directly but I hope this
converter may help. Let me know if you have any questions about using it


https://cmdcolin.github.io/xmfa2paf/

Click the "Show help" to see a series of screenshots demonstrating usage

Xref github discussion
https://github.com/GMOD/jbrowse-components/discussions/4656

-Colin


On Thu, Nov 14, 2024 at 8:44 PM Veselina Krysteva via Gmod-ajax <
gmo...@li...> wrote:

> Hello, JBrowse team,
>
> My name is Veselina!
>
> I would like to ask you a question regarding sequence alignments viewed in
> JBrowse.
> I use the downloaded app on my computer to visualize genomes and map
> reads. I also want to visualize 2 aligned genomes. I did the alignment in
> Galaxy platform using the mauveprogressive tool that generated an xmfa
> file. Can you please advice me on how I can view this alignment. I am not
> sure how to convert the xmfa file to suitable for visualization format. I
> can convert this file to GFF3 file using Galaxy as well, but I see this is
> not working in the visualization as well.
>
> Additionally, I use windows 11 system that is very limited in
> bioinformatics. I tried to install pybigwig using python but it didn't
> worked out. Also I am not an bioinformatician, so any help that is provided
> for a wet-lab person would be highly appreciated.
>
> May be I can use another aligner for my genomes (6.8 M bp large) that will
> create suitable file formats. If so, please advice.
>
> Thank you endlessly for the time!
>
> Have a good day!
>
>
> Regards,
>
> Veselina Panova
>
> Research student at GSB, Kyoto University
> [image: Emoji]  veselin <ves...@ya...>a
> <ves...@ya...>kry...@ya...
> <ves...@ya...> | pan...@st...
>
> [image: Emoji]  080-3135-8831
> [image: Emoji]  https://www.lif.kyoto-u.ac.jp/e/research/lab/137/
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] visualization of split alignments

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

Hi there,
I think this question came through our gitter chat earlier but I'll repeat
what we said there

The screenshot showing that "Link supplementary reads" functionality was an
older demo for a poster, but it was a bit hacky so it didn't end up getting
merged unfortunately!

I put in a new feature request for this though as it would be a very useful
feature https://github.com/GMOD/jbrowse-components/issues/4659

Some alternatives to get this functionality "today" using jbrowse would be
to use the "breakpoint split view"

It can draw connections between reads in the "single row" mode. The
screenshot below shows this
[image: image.png]


[image: image.png]

There are also the "read cloud" and "read arcs" modes but these are a bit
weirder for long reads. Hope that helps, I can update this thread if we add
the "Link supplementary reads" functionality

-Colin

On Fri, Nov 15, 2024 at 11:18 AM Robert Månsson Welinder <
rob...@sc...> wrote:

> Hi,
>
> Started playing around with looking at PacBio long-read data in JBrowse 2
> (2.16.1).
>
> How do I find the option that is called "link samplementary reads" in the
> JBrowse 2 demo?
> [image: Screenshot 2024-11-15 at 13.10.28.png]
>
> [Link to demo:
> https://s3.amazonaws.com/jbrowse.org/code/jb2/beta/skbr3_demo/index.html?config=test_data%2Fconfig_demo.json&session=share-4e68d7667f204ee4dfaf01279ee488275686147d4c93c86a80fb2994ad6c43c6&password=c17703b]c1fc0d1c7508bc1af8cf42892)
>
>
> Basically looking at translocations affecting the Immunoglobulin heavy
> chain locus and then one would like the VDJ recombination events to be
> linked via "lines" as shown above for "Link supplementary reads" while the
> actual translocations are shows using the "top/bottom split-view".
>
> Thanks in advance / Robert
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] visualization of split alignments

[Robert M. W. <rob...@sc...>]

Hi,

Started playing around with looking at PacBio long-read data in JBrowse 2
(2.16.1).

How do I find the option that is called "link samplementary reads" in the
JBrowse 2 demo?
[image: Screenshot 2024-11-15 at 13.10.28.png]

[Link to demo:
https://s3.amazonaws.com/jbrowse.org/code/jb2/beta/skbr3_demo/index.html?config=test_data%2Fconfig_demo.json&session=share-4e68d7667f204ee4dfaf01279ee488275686147d4c93c86a80fb2994ad6c43c6&password=c17703b]c1fc0d1c7508bc1af8cf42892)


Basically looking at translocations affecting the Immunoglobulin heavy
chain locus and then one would like the VDJ recombination events to be
linked via "lines" as shown above for "Link supplementary reads" while the
actual translocations are shows using the "top/bottom split-view".

Thanks in advance / Robert

[Gmod-ajax] Question about file formats for genome alignment visualization in JBrowse

[Veselina K. <ves...@ya...>]

Hello, JBrowse team,
My name is Veselina!
I would like to ask you a question regarding sequence alignments viewed in JBrowse.I use the downloaded app on my computer to visualize genomes and map reads. I also want to visualize 2 aligned genomes. I did the alignment in Galaxy platform using the mauveprogressive tool that generated an xmfa file. Can you please advice me on how I can view this alignment. I am not sure how to convert the xmfa file to suitable for visualization format. I can convert this file to GFF3 file using Galaxy as well, but I see this is not working in the visualization as well.
Additionally, I use windows 11 system that is very limited in bioinformatics. I tried to install pybigwig using python but it didn't worked out. Also I am not an bioinformatician, so any help that is provided for a wet-lab person would be highly appreciated.
May be I can use another aligner for my genomes (6.8 M bp large) that will create suitable file formats. If so, please advice.
Thank you endlessly for the time!
Have a good day!

Regards,


 
VeselinaPanova
Researchstudent at GSB, Kyoto University
  ves...@ya...|pan...@st...



  080-3135-8831
  https://www.lif.kyoto-u.ac.jp/e/research/lab/137/

Re: [Gmod-ajax] JBrowse not installing: perl prerequisites issue

[Vaneet L. <van...@uc...>]

I need the JBrowse perl scripts to load and index tracks so I don’t think I can go with option a) unless there’s a different script for loading gff tabix as you say?  However then how do you index the tracks without generate-names.pl?  Even so, the volvox data failed to load too, so I’m not sure I can just ignore the errors.  I was always expecting when running the setup script that nothing actually fails but not sure if all those things are even essential for JBrowse to run, it’s a good test to see though.

For that reason, I guess I’ll try approach a).  I’m not a container expert either, so option b) wouldn’t be my first choice.  This is actually on a cloud instance but it’s using the Ubuntu OS, actually a clone of one of our VMs with Ubuntu 24 so it might already have BioPerl installed, very possible.

Will let you know if it’s still failing.

Thanks,

Vaneet



From: Colin <col...@gm...>
Sent: October 22, 2024 2:55 PM
To: Vaneet Lotay <van...@uc...>; gmod-ajax <gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse not installing: perl prerequisites issue

[△EXTERNAL]

This appears to indicate the issue


! Installing the dependencies failed: Module 'Bio::FeatureIO' is not installed, Module 'Bio::SeqFeature::Annotated' is not installed
! Bailing out the installation for JBrowse-.

I don't know exactly what is happening for you but it is likely related to a change that BioPerl made in like ~2018 where they completely changed how they do everything. our setup.sh script forces the installation of a specific BioPerl version before this change, but if your machine already has some version of BioPerl on it, it might be sensitive to it. especially if you installed BioPerl systemwide in some other way.

In order to fix it for your purposes you can either

a) choose to ignore the perl issues: you can use jbrowse 1 without perl for many purposes, so unless you need flatfile-to-json.pl<http://flatfile-to-json.pl> and generate-names.pl<http://generate-names.pl>, you can load bam, bigwig, gff tabix, etc w
b) try to fix the perl issue approach 1: remove any semblance of previous bioperl libraries from your machine. for a start, you can rm -rf ~/.cpanm, rm -rf /var/www/html/jbrowse/extlib (this is a folder listed in your setup.log), and then re-run setup.sh
c) try to fix the perl issue approach 2: use something like docker like scott cain referred to, so you don't run into any sort of weird issues with your host machine and have a container. i am not personally a container expert or even a container advocate, but it is a good option in some cases
d) try to fix the perl issue approach 3: just use a fresh cloud machine to do things instead of docker, basically you get the same fresh machine experience.


-Colin

On Tue, Oct 22, 2024 at 3:05 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Sure, here’s my setup log attached.

Vaneet

From: Colin <col...@gm...<mailto:col...@gm...>>
Sent: October 22, 2024 7:00 AM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto:gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse not installing: perl prerequisites issue

[△EXTERNAL]


can you attach the setup.log file?

On Tue, Oct 22, 2024, 3:36 AM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:

Hello,



I’m installing JBrowse on a new Ubuntu VM.  I already heeded the previous advice to use Node.js v14 as later versions were in fact causing the usual ‘node-sass’ issue.  Even though I have python3 installed, I had to install python2 since the setup script was looking for it and would fail without it.  Anyways now when I run the setup script, my Perl prerequisites fail to install:



Installing Perl prerequisites ... failed.  See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.



Formatting Volvox example data ... failed.  See setup.log file for error messages.



I did in fact install the system prerequisites using this command:



apt install build-essential zlib1g-dev



Not sure if that’s what it’s looking for but nevertheless when executing that command now it indicates I have the latest version for all these packages.  I'd be happy to attach my setup.log file too directly, I just can't post it to the mailing list as it seems too big for the limit.



Thanks for any help you can provide!



Vaneet

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Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
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Re: [Gmod-ajax] JBrowse not installing: perl prerequisites issue

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

This appears to indicate the issue


! Installing the dependencies failed: Module 'Bio::FeatureIO' is not
installed, Module 'Bio::SeqFeature::Annotated' is not installed
! Bailing out the installation for JBrowse-.

I don't know exactly what is happening for you but it is likely related to
a change that BioPerl made in like ~2018 where they completely changed how
they do everything. our setup.sh script forces the installation of a
specific BioPerl version before this change, but if your machine already
has some version of BioPerl on it, it might be sensitive to it. especially
if you installed BioPerl systemwide in some other way.

In order to fix it for your purposes you can either

a) choose to ignore the perl issues: you can use jbrowse 1 without perl for
many purposes, so unless you need flatfile-to-json.pl and generate-names.pl,
you can load bam, bigwig, gff tabix, etc w
b) try to fix the perl issue approach 1: remove any semblance of previous
bioperl libraries from your machine. for a start, you can rm -rf ~/.cpanm,
rm -rf /var/www/html/jbrowse/extlib (this is a folder listed in your
setup.log), and then re-run setup.sh
c) try to fix the perl issue approach 2: use something like docker like
scott cain referred to, so you don't run into any sort of weird issues with
your host machine and have a container. i am not personally a container
expert or even a container advocate, but it is a good option in some cases
d) try to fix the perl issue approach 3: just use a fresh cloud machine to
do things instead of docker, basically you get the same fresh machine
experience.


-Colin

On Tue, Oct 22, 2024 at 3:05 PM Vaneet Lotay <van...@uc...>
wrote:

> Sure, here’s my setup log attached.
>
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* October 22, 2024 7:00 AM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse not installing: perl prerequisites
> issue
>
>
>
> [△EXTERNAL]
>
>
>
> can you attach the setup.log file?
>
>
>
> On Tue, Oct 22, 2024, 3:36 AM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello,
>
>
>
> I’m installing JBrowse on a new Ubuntu VM.  I already heeded the previous
> advice to use Node.js v14 as later versions were in fact causing the usual
> ‘node-sass’ issue.  Even though I have python3 installed, I had to install
> python2 since the setup script was looking for it and would fail without
> it.  Anyways now when I run the setup script, my Perl prerequisites fail to
> install:
>
>
>
> *Installing Perl prerequisites ... failed.  See setup.log file for error
> messages. As a first troubleshooting step, make sure development libraries
> and header files for GD, Zlib, and libpng are installed and try again.*
>
>
>
> *Formatting Volvox example data ... failed.  See setup.log file for error
> messages.*
>
>
>
> I did in fact install the system prerequisites using this command:
>
>
>
> apt install build-essential zlib1g-dev
>
>
>
> Not sure if that’s what it’s looking for but nevertheless when executing
> that command now it indicates I have the latest version for all these
> packages.  I'd be happy to attach my setup.log file too directly, I just
> can't post it to the mailing list as it seems too big for the limit.
>
>
>
> Thanks for any help you can provide!
>
>
>
> Vaneet
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Re: [Gmod-ajax] JBrowse not installing: perl prerequisites issue

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

<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div dir="ltr"></div><div dir="ltr">Hi Vaneet,</div><div dir="ltr"><br></div><div dir="ltr">What are you planning on using the VM for? If it’s only for serving JBrowse (and not processing data files), you can do what I did in the wormbase docker file and use the “-f” option for the setup script that causes it to skip installing the Perl prereqs:</div><div dir="ltr"><br></div><div dir="ltr"><div style="display: block;" class=""><div style="-webkit-user-select: all; -webkit-user-drag: element; display: inline-block;" class="apple-rich-link" draggable="true" role="link" data-url="https://github.com/WormBase/website-genome-browsers/blob/jbrowse-279/jbrowse/Dockerfile"><a style="border-radius:10px;font-family:-apple-system, Helvetica, Arial, sans-serif;display:block;-webkit-user-select:none;width:300px;user-select:none;-webkit-user-modify:read-only;user-modify:read-only;overflow:hidden;text-decoration:none;" class="lp-rich-link" rel="nofollow" href="https://github.com/WormBase/website-genome-browsers/blob/jbrowse-279/jbrowse/Dockerfile" dir="ltr" role="button" draggable="false" width="300"><table style="table-layout:fixed;border-collapse:collapse;width:300px;background-color:#E6E6E6;font-family:-apple-system, Helvetica, Arial, sans-serif;" class="lp-rich-link-emailBaseTable" cellpadding="0" cellspacing="0" border="0" width="300"><tbody><tr><td vertical-align="center" align="center"><img style="width:300px;filter:brightness(0.97);height:150px;" width="300" height="150" draggable="false" class="lp-rich-link-mediaImage" alt="website-genome-browsers.png" src="cid:684571C5-8664-408B-87F1-4D50DA97DFAB"></td></tr><tr><td vertical-align="center"><table bgcolor="#E6E6E6" cellpadding="0" cellspacing="0" width="300" style="table-layout:fixed;font-family:-apple-system, Helvetica, Arial, sans-serif;background-color:rgba(230, 230, 230, 1);-apple-color-filter:initial;" class="lp-rich-link-captionBar"><tbody><tr><td style="padding:8px 0px 8px 0px;" class="lp-rich-link-captionBar-textStackItem"><div style="max-width:100%;margin:0px 16px 0px 16px;overflow:hidden;" class="lp-rich-link-captionBar-textStack"><div style="word-wrap:break-word;font-weight:500;font-size:12px;overflow:hidden;text-overflow:ellipsis;text-align:left;" class="lp-rich-link-captionBar-textStack-topCaption-leading"><a rel="nofollow" href="https://github.com/WormBase/website-genome-browsers/blob/jbrowse-279/jbrowse/Dockerfile" style="text-decoration: none" draggable="false"><font color="#000000" style="color: rgba(0, 0, 0, 1);">website-genome-browsers/jbrowse/Dockerfile at jbrowse-279 · WormBase/website-genome-browsers</font></a></div><div style="word-wrap:break-word;font-weight:400;font-size:11px;overflow:hidden;text-overflow:ellipsis;text-align:left;" class="lp-rich-link-captionBar-textStack-bottomCaption-leading"><a rel="nofollow" href="https://github.com/WormBase/website-genome-browsers/blob/jbrowse-279/jbrowse/Dockerfile" style="text-decoration: none" draggable="false"><font color="#A2A2A9" style="color: rgba(60, 60, 67, 0.6);">github.com</font></a></div></div></td></tr></tbody></table></td></tr></tbody></table></a></div></div><br></div><div dir="ltr">On the other hand, if you plan on using the vm for doing data processing and thus need Perl, you can look at the Dockerfile I created for doing just that at:</div><div dir="ltr"><br></div><div dir="ltr"><div style="display: block;" class=""><div style="-webkit-user-select: all; -webkit-user-drag: element; display: inline-block;" class="apple-rich-link" draggable="true" role="link" data-url="https://github.com/alliance-genome/agr_jbrowse_container/blob/master/Dockerfile.processenv"><a style="border-radius:10px;font-family:-apple-system, Helvetica, Arial, sans-serif;display:block;-webkit-user-select:none;width:300px;user-select:none;-webkit-user-modify:read-only;user-modify:read-only;overflow:hidden;text-decoration:none;" class="lp-rich-link" rel="nofollow" href="https://github.com/alliance-genome/agr_jbrowse_container/blob/master/Dockerfile.processenv" dir="ltr" role="button" draggable="false" width="300"><table style="table-layout:fixed;border-collapse:collapse;width:300px;background-color:#E6E6E6;font-family:-apple-system, Helvetica, Arial, sans-serif;" class="lp-rich-link-emailBaseTable" cellpadding="0" cellspacing="0" border="0" width="300"><tbody><tr><td vertical-align="center" align="center"><img style="width:300px;filter:brightness(0.97);height:150px;" width="300" height="150" draggable="false" class="lp-rich-link-mediaImage" alt="agr_jbrowse_container.png" src="cid:9926C247-3CEA-4B8A-BB05-F2B7F10CF0E4"></td></tr><tr><td vertical-align="center"><table bgcolor="#E6E6E6" cellpadding="0" cellspacing="0" width="300" style="table-layout:fixed;font-family:-apple-system, Helvetica, Arial, sans-serif;background-color:rgba(230, 230, 230, 1);-apple-color-filter:initial;" class="lp-rich-link-captionBar"><tbody><tr><td style="padding:8px 0px 8px 0px;" class="lp-rich-link-captionBar-textStackItem"><div style="max-width:100%;margin:0px 16px 0px 16px;overflow:hidden;" class="lp-rich-link-captionBar-textStack"><div style="word-wrap:break-word;font-weight:500;font-size:12px;overflow:hidden;text-overflow:ellipsis;text-align:left;" class="lp-rich-link-captionBar-textStack-topCaption-leading"><a rel="nofollow" href="https://github.com/alliance-genome/agr_jbrowse_container/blob/master/Dockerfile.processenv" style="text-decoration: none" draggable="false"><font color="#000000" style="color: rgba(0, 0, 0, 1);">agr_jbrowse_container/Dockerfile.processenv at master · alliance-genome/agr_jbrowse_container</font></a></div><div style="word-wrap:break-word;font-weight:400;font-size:11px;overflow:hidden;text-overflow:ellipsis;text-align:left;" class="lp-rich-link-captionBar-textStack-bottomCaption-leading"><a rel="nofollow" href="https://github.com/alliance-genome/agr_jbrowse_container/blob/master/Dockerfile.processenv" style="text-decoration: none" draggable="false"><font color="#A2A2A9" style="color: rgba(60, 60, 67, 0.6);">github.com</font></a></div></div></td></tr></tbody></table></td></tr></tbody></table></a></div></div><br></div><div dir="ltr">Which installs an old JBrowse release (because I only need the processing scripts so it didn’t matter what version I installed) but this could help with your installation woes.&nbsp;</div><div dir="ltr"><br></div><div dir="ltr">Finally, I’ll say I much prefer separating what vm processes that data versus the vm that serves the data up in JBrowse (made easier by putting the data on a third server like AWS S3) because it makes building issues like these easier to deal with.&nbsp;</div><div dir="ltr"><br></div><div dir="ltr">One more thing and I’ll stop: I don’t know if you use AWS, but another option you might consider for serving up JBrowse is to skip the VM altogether and use Amplify, which is what I currently use for WormBase and JBrowse 1:</div><div dir="ltr"><br></div><div dir="ltr"><div style="display: block;" class=""><div style="-webkit-user-select: all; -webkit-user-drag: element; display: inline-block;" class="apple-rich-link" draggable="true" role="link" data-url="https://github.com/WormBase/amplify-wb-jbrowse1"><a style="border-radius:10px;font-family:-apple-system, Helvetica, Arial, sans-serif;display:block;-webkit-user-select:none;width:300px;user-select:none;-webkit-user-modify:read-only;user-modify:read-only;overflow:hidden;text-decoration:none;" class="lp-rich-link" rel="nofollow" href="https://github.com/WormBase/amplify-wb-jbrowse1" dir="ltr" role="button" draggable="false" width="300"><table style="table-layout:fixed;border-collapse:collapse;width:300px;background-color:#DDDDDD;font-family:-apple-system, Helvetica, Arial, sans-serif;" class="lp-rich-link-emailBaseTable" cellpadding="0" cellspacing="0" border="0" width="300"><tbody><tr><td vertical-align="center"><table bgcolor="#DDDDDD" cellpadding="0" cellspacing="0" width="300" style="table-layout:fixed;font-family:-apple-system, Helvetica, Arial, sans-serif;background-color:rgba(221, 221, 221, 1);-apple-color-filter:initial;" class="lp-rich-link-captionBar"><tbody><tr><td style="padding:8px 0px 8px 0px;" class="lp-rich-link-captionBar-textStackItem"><div style="max-width:100%;margin:0px 16px 0px 16px;overflow:hidden;" class="lp-rich-link-captionBar-textStack"><div style="word-wrap:break-word;font-weight:500;font-size:12px;overflow:hidden;text-overflow:ellipsis;text-align:left;" class="lp-rich-link-captionBar-textStack-topCaption-leading"><a rel="nofollow" href="https://github.com/WormBase/amplify-wb-jbrowse1" style="text-decoration: none" draggable="false"><font color="#000000" style="color: rgba(0, 0, 0, 1);">WormBase/amplify-wb-jbrowse1: Repo to drive AWS Amplify builds for JBrowse 1</font></a></div><div style="word-wrap:break-word;font-weight:400;font-size:11px;overflow:hidden;text-overflow:ellipsis;text-align:left;" class="lp-rich-link-captionBar-textStack-bottomCaption-leading"><a rel="nofollow" href="https://github.com/WormBase/amplify-wb-jbrowse1" style="text-decoration: none" draggable="false"><font color="#A2A2A9" style="color: rgba(60, 60, 67, 0.6);">github.com</font></a></div></div></td><td style="padding:6px 12px 6px 0px;" class="lp-rich-link-captionBar-rightIconItem" width="30"><a rel="nofollow" href="https://github.com/WormBase/amplify-wb-jbrowse1" draggable="false"><img style="pointer-events:none !important;display:inline-block;width:30px;height:30px;border-radius:3px;" width="30" height="30" draggable="false" class="lp-rich-link-captionBar-rightIcon" alt="apple-touch-icon-180x180-a80b8e11abe2.png" src="cid:8FA10AE9-EDD1-4E77-80A8-273E818BDFB2"></a></td></tr></tbody></table></td></tr></tbody></table></a></div></div><br></div><div dir="ltr">This is a slightly odd example, since it’s really serving two side by side instances of JBrowse, but since the /dist directory is already built, it doesn’t need to build JBrowse at all, I just update the trackList.json files and the JBrowse instance automatically rebuilds (again, with the data being already processed somewhere else).</div><div dir="ltr"><br></div><div dir="ltr">Scott</div><div dir="ltr"><br></div><div dir="ltr"><br><blockquote type="cite">On Oct 22, 2024, at 6:00 AM, Colin &lt;col...@gm...&gt; wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><p dir="ltr">can you attach the setup.log file?</p>
<br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Oct 22, 2024, 3:36 AM Vaneet Lotay &lt;<a href="mailto:van...@uc...">van...@uc...</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">




<div dir="ltr">
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Hello,</span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">&nbsp;</span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">I’m installing JBrowse on a new Ubuntu VM.&nbsp; I already heeded the previous advice to use Node.js v14 as later
 versions were in fact causing the usual ‘node-sass’ issue.&nbsp; Even though I have python3 installed, I had to install python2 since the setup script was looking for it and would fail without it.&nbsp; Anyways now when I run the setup script, my Perl prerequisites
 fail to install:</span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">&nbsp;</span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><i>Installing Perl prerequisites ... failed.&nbsp; See setup.log file for error messages. As a first troubleshooting
 step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.</i></span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><i>&nbsp;</i></span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><i>Formatting Volvox example data ... failed.&nbsp; See setup.log file for error messages.</i></span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">&nbsp;</span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">I did in fact install the system prerequisites using this command:</span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">&nbsp;</span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">apt install build-essential zlib1g-dev</span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">&nbsp;</span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Not sure if that’s what it’s looking for but nevertheless when executing that command
 now it indicates I have the latest version for all these packages.&nbsp; I'd be happy to attach my setup.log file too directly, I just can't post it to the mailing list as it seems too big for the limit.</span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">&nbsp;</span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Thanks for any help you can provide!</span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">&nbsp;</span></p>
<p><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Vaneet</span></p>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
</div>

_______________________________________________<br>
Gmod-ajax mailing list<br>
<a href="mailto:Gmo...@li..." target="_blank" rel="noreferrer">Gmo...@li...</a><br>
<a href="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" rel="noreferrer noreferrer" target="_blank">https://lists.sourceforge.net/lists/listinfo/gmod-ajax</a><br>
</blockquote></div>
<span>_______________________________________________</span><br><span>Gmod-ajax mailing list</span><br><span>Gmo...@li...</span><br><span>https://lists.sourceforge.net/lists/listinfo/gmod-ajax</span><br></div></blockquote></body></html>

Re: [Gmod-ajax] JBrowse not installing: perl prerequisites issue

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

can you attach the setup.log file?

On Tue, Oct 22, 2024, 3:36 AM Vaneet Lotay <van...@uc...> wrote:

> Hello,
>
>
>
> I’m installing JBrowse on a new Ubuntu VM.  I already heeded the previous
> advice to use Node.js v14 as later versions were in fact causing the usual
> ‘node-sass’ issue.  Even though I have python3 installed, I had to install
> python2 since the setup script was looking for it and would fail without
> it.  Anyways now when I run the setup script, my Perl prerequisites fail to
> install:
>
>
>
> *Installing Perl prerequisites ... failed.  See setup.log file for error
> messages. As a first troubleshooting step, make sure development libraries
> and header files for GD, Zlib, and libpng are installed and try again.*
>
>
>
> *Formatting Volvox example data ... failed.  See setup.log file for error
> messages.*
>
>
>
> I did in fact install the system prerequisites using this command:
>
>
>
> apt install build-essential zlib1g-dev
>
>
>
> Not sure if that’s what it’s looking for but nevertheless when executing
> that command now it indicates I have the latest version for all these
> packages.  I'd be happy to attach my setup.log file too directly, I just
> can't post it to the mailing list as it seems too big for the limit.
>
>
>
> Thanks for any help you can provide!
>
>
>
> Vaneet
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse not installing: perl prerequisites issue

[Vaneet L. <van...@uc...>]

Hello,



I’m installing JBrowse on a new Ubuntu VM.  I already heeded the previous advice to use Node.js v14 as later versions were in fact causing the usual ‘node-sass’ issue.  Even though I have python3 installed, I had to install python2 since the setup script was looking for it and would fail without it.  Anyways now when I run the setup script, my Perl prerequisites fail to install:



Installing Perl prerequisites ... failed.  See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.



Formatting Volvox example data ... failed.  See setup.log file for error messages.



I did in fact install the system prerequisites using this command:



apt install build-essential zlib1g-dev



Not sure if that’s what it’s looking for but nevertheless when executing that command now it indicates I have the latest version for all these packages.  I'd be happy to attach my setup.log file too directly, I just can't post it to the mailing list as it seems too big for the limit.



Thanks for any help you can provide!



Vaneet

Re: [Gmod-ajax] [Gmod-gbrowse] Server change for gmod.org and an announcement

[Fields, C. J <cjf...@il...>]

Hi Scott, I just wanted to say a tremendous ‘thank you’ for essentially leading GMOD efforts over the last 20+ years.  Wow, has it been that long!?! (I’m getting old).  You should be incredibly proud of the work you and all GMOD projects and developers have accomplished; it’s a tremendous accomplishment.

Hope to see you still out there somewhere in the open-bio world, and best of luck on your next steps in your career!

Best,

Chris


From: Scott Cain <sc...@sc...>
Date: Tuesday, July 23, 2024 at 1:19 PM
To: gmod-announce <gmo...@li...>, gmod-devel <gmo...@li...>, gmod-ajax <gmo...@li...>, GMOD Tripal <gmo...@li...>, Gbrowse (E-mail) <gmo...@li...>, GMOD Schema/Chado List <gmo...@li...>
Subject: [Gmod-gbrowse] Server change for gmod.org and an announcement
Hello all,

For several years, I've wanted to port the gmod.org<https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> MediaWiki instance to something else but was daunted by the task. Events have finally conspired to force me to do it, so I've spent the last month porting the content at gmod.org<https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> to a github.io<https://urldefense.com/v3/__http:/github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtQUw79P0$> hosted page. It was a real slog, but thank goodness for recursive wget, Pandoc and command line Perl to allow me to change thousands of markdown files at a time.

Since gmod.org<https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> is now hosted at github.io<https://urldefense.com/v3/__http:/github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtQUw79P0$>, changes to this page can now be made with commits to the https://github.com/GMOD/gmod.github.io<https://urldefense.com/v3/__https:/github.com/GMOD/gmod.github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtU5TvTYs$> repo. That means that fixes and additions can be made by creating and editing markdown files in the gmod.github.io<https://urldefense.com/v3/__http:/gmod.github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtViLqSVk$> repo and merging the changes into the main branch.

AND NOW THE ANNOUNCEMENT

At the end of July, I will be stepping away from my role as GMOD project coordinator, which on one hand, makes me very sad, but on the other, fills me with immense pride in what we as the GMOD community have achieved over the last 22 years. We have truly democratized organism genomics, allowing a small lab to distribute data on whatever organisms are of interest to them with (relatively) little effort. We can compare that to the MODs that existed in the early aughts, that had staffs of many software developers to make the same thing happen. We all did that, and I think the world is a better place for it.

I can't say yet where I'm going, as I have a few opportunities on the table that haven't been finalized, but I hope to be fulfilling a similar role in another community.  If you're really interested, you can follow me on Mastodon at @sco...@ge...cial.

Thank you to all of you--I have really enjoyed working with and growing this community,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott at scottcain dot net
GMOD Project Manager (http://gmod.org/<https://urldefense.com/v3/__http:/gmod.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLt_a75Ac4$>)                            216-392-3087
WormBase Developer (http://wormbase.org/<https://urldefense.com/v3/__http:/wormbase.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtqyOTGjk$>)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/<https://urldefense.com/v3/__http:/alliancegenome.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtfgzLlII$>)
VirusSeq Project Manager (https://virusseq-dataportal.ca/<https://urldefense.com/v3/__https:/virusseq-dataportal.ca/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLt7Qo4Y2Y$>)
Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/<https://urldefense.com/v3/__https:/hcmi-searchable-catalog.nci.nih.gov/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtmGSQ6iE$>)

[Gmod-ajax] Server change for gmod.org and an announcement

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

Hello all,

For several years, I've wanted to port the gmod.org MediaWiki instance to
something else but was daunted by the task. Events have finally conspired
to force me to do it, so I've spent the last month porting the content at
gmod.org to a github.io hosted page. It was a real slog, but thank goodness
for recursive wget, Pandoc and command line Perl to allow me to change
thousands of markdown files at a time.

Since gmod.org is now hosted at github.io, changes to this page can now be
made with commits to the https://github.com/GMOD/gmod.github.io repo. That
means that fixes and additions can be made by creating and editing markdown
files in the gmod.github.io repo and merging the changes into the main
branch.

AND NOW THE ANNOUNCEMENT

At the end of July, I will be stepping away from my role as GMOD project
coordinator, which on one hand, makes me very sad, but on the other, fills
me with immense pride in what we as the GMOD community have achieved over
the last 22 years. We have truly democratized organism genomics, allowing a
small lab to distribute data on whatever organisms are of interest to them
with (relatively) little effort. We can compare that to the MODs that
existed in the early aughts, that had staffs of many software developers to
make the same thing happen. We all did that, and I think the world is a
better place for it.

I can't say yet where I'm going, as I have a few opportunities on the table
that haven't been finalized, but I hope to be fulfilling a similar role in
another community.  If you're really interested, you can follow me on
Mastodon at @sco...@ge...cial.

Thank you to all of you--I have really enjoyed working with and growing
this community,
Scott


-- 
------------------------------------------------------------------------
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] JBrowse2 about this track box

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

Hi Vaneet

The "About track" dialog in JBrowse 2 will display HTML in any of the track
config using a "sanitization" (which didn't exist in JBrowse 1) so HTML
should allow it by default without any special flags.
Here is an example I made which loads tracks from UCSC which have a bunch
of HTML in the track "metadata"

https://jbrowse.org/code/jb2/main/?config=%2Fdemos%2Fucsc%2Fconfig.json&session=share-sIwvn8cwM4&password=GTdhe

That track config looks like this

{
      "type": "FeatureTrack",
      "trackId": "augustusGene_hg19",
      "name": "AUGUSTUS ab initio gene predictions v3.1",
      "assemblyNames": ["hg19"],
      "adapter": {
        "type": "BedTabixAdapter",
        "bedGzLocation": {
          "uri": "hg19/augustusGene.bed.gz"
        },
        "index": {
          "location": {
            "uri": "hg19/augustusGene.bed.gz.tbi"
          }
        }
      },
      "metadata": {
        "tableName": "augustusGene",
        "shortLabel": "AUGUSTUS",
        "type": "genePred",
        "visibility": "3",
        "priority": "100",
        "colorR": "12",
        "colorG": "105",
        "colorB": "0",
        "altColorR": "133",
        "altColorG": "180",
        "altColorB": "127",
        "useScore": "0",
        "private": "0",
        "restrictCount": "0",
        "restrictList": "",
        "url": "",
        "canPack": "1",
        "html": "<h2>Description</h2>\n\n<p>\n  This track shows <i>ab
initio</i> predictions from the program\n  <a href=\"
http://bioinf.uni-greifswald.de/augustus/\" target=\"_blank\">AUGUSTUS</a>
(version 3.1).\n  The predictions are based on the genome sequence
alone.\n</p>\n\n<p>\nFor more information on the different gene tracks, see
our <a target=_blank \nhref=\"/FAQ/FAQgenes.html\">Genes
FAQ</a>.</p>\n\n<h2>Methods</h2>\n\n<p>\nStatistical signal models were
built for splice sites, branch-point\npatterns, translation start sites,
and the poly-A signal.\nFurthermore, models were built for the sequence
content of\nprotein-coding and non-coding regions as well as for the length
distributions\nof different exon and intron types. Detailed descriptions of
most of these different models\ncan be found in Mario Stanke's\n<a href=\"
https://ediss.uni-goettingen.de/handle/11858/00-1735-0000-0006-B3F8-4\"
target=\"_blank\">dissertation</a>.\nThis track shows the most likely gene
structure according to a\nSemi-Markov Conditional Random Field
model.\nAlternative splicing transcripts were obtained with\na sampling
algorithm (<tt>--alternatives-from-sampling=true --sample=100
--minexonintronprob=0.2\n--minmeanexonintronprob=0.5 --maxtracks=3
--temperature=2</tt>).\n</p>\n\n<p>\nThe different models used by Augustus
were trained on a number of different species-specific\ngene sets, which
included 1000-2000 training gene structures. The <tt>--species</tt> option
allows\none to choose the species used for training the models. Different
training species were used\nfor the <tt>--species</tt> option when
generating these predictions for different groups of\nassemblies.\n<table
class=\"stdTbl\">\n <tr>\n  <td align=center><b>Assembly Group</b></td>\n
 <td align=center><b>Training Species</b></td>\n </tr>\n <tr>\n  <td
align=center>Fish</td>\n  <td align=center><tt>zebrafish</tt>\n </tr>\n
<tr>\n  <td align=center>Birds</td>\n  <td align=center><tt>chicken</tt>\n
</tr>\n <tr>\n  <td align=center>Human and all other vertebrates</td>\n
 <td align=center><tt>human</tt>\n </tr>\n <tr>\n  <td
align=center>Nematodes</td>\n  <td
align=center><tt>caenorhabditis</tt></td>\n </tr>\n <tr>\n  <td
align=center>Drosophila</td>\n  <td align=center><tt>fly</tt></td>\n
</tr>\n <tr>\n  <td align=center><em>A. mellifera</em></td>\n  <td
align=center><tt>honeybee1</tt></td>\n </tr>\n <tr>\n  <td
align=center><em>A. gambiae</em></td>\n  <td
align=center><tt>culex</tt></td>\n </tr>\n <tr>\n  <td align=center><em>S.
cerevisiae</em></td>\n  <td align=center><tt>saccharomyces</tt></td>\n
</tr>\n</table>\n<p>\nThis table describes which training species was used
for a particular group of assemblies.\nWhen available, the closest related
training species was used.\n</p>\n\n<h2>Credits</h2>\n\nThanks to the\n<a
href=\"
https://math-inf.uni-greifswald.de/en/department/about-us/employees/prof-dr-mario-stanke-english/\"\ntarget=\"_blank\">Stanke
lab</a>\nfor providing the AUGUSTUS program.  The training for the
<tt>chicken</tt> version was\ndone by Stefanie K&ouml;nig and the training
for the\n<tt>human</tt> and <tt>zebrafish</tt> versions was done by Mario
Stanke.\n\n<h2>References</h2>\n\n<p>\nStanke M, Diekhans M, Baertsch R,
Haussler D.\n<a href=\"
https://academic.oup.com/bioinformatics/article/24/5/637/202844/Using-native-and-syntenically-mapped-cDNA\"\ntarget=\"_blank\">\nUsing
native and syntenically mapped cDNA alignments to improve de novo gene
finding</a>.\n<em>Bioinformatics</em>. 2008 Mar 1;24(5):637-44.\nPMID: <a
href=\"https://www.ncbi.nlm.nih.gov/pubmed/18218656\"
target=\"_blank\">18218656</a>\n</p>\n\n<p>\nStanke M, Waack S.\n<a href=\"
https://academic.oup.com/bioinformatics/article/19/suppl_2/ii215/180603/Gene-prediction-with-a-hidden-Markov-model-and-a\"\ntarget=\"_blank\">\nGene
prediction with a hidden Markov model and a new intron
submodel</a>.\n<em>Bioinformatics</em>. 2003 Oct;19 Suppl
2:ii215-25.\nPMID: <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/14534192\"
target=\"_blank\">14534192</a>\n</p>\n"
      },
      "category": ["genes"]
    },



Here is another example from our volvox test data
https://jbrowse.org/code/jb2/v2.12.3/?config=test_data%2Fvolvox%2Fconfig.json&session=share-vckBej0yhi&password=DsB1j
This track has HTML in the track name, and metadata added by a plugin, and
also has a special panel in the about track dialog named "More info" that
is added via a plugin. That extra panel allows arbitrary React to be
rendered as a custom about track panel.
This could be useful if you need to make a very advanced custom panel like
one that fetches data or something like this
https://github.com/GMOD/jbrowse-components/blob/7815547783b473b72fff92988c8bc4da4d580c65/test_data/volvox/umd_plugin.js#L44-L52

Hope that helps
-Colin

On Fri, Jul 19, 2024 at 3:19 PM Vaneet Lotay <van...@uc...>
wrote:

> Hello all,
>
>
>
> How do I add new fields to the ‘About this track’ window that can be
> selected from the track label.  I wanted to add source information or how
> the track was created.  Also, if there’s a way to add it, how do we ensure
> that the text shows web links or other HTML characters like ‘<br>’.  In
> JBrowse this was achieved by setting a config parameter to true ->
> ‘unsafePopup: true’.
>
>
>
> Thanks,
>
>
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse2 about this track box

[Vaneet L. <van...@uc...>]

Hello all,

How do I add new fields to the 'About this track' window that can be selected from the track label.  I wanted to add source information or how the track was created.  Also, if there's a way to add it, how do we ensure that the text shows web links or other HTML characters like '<br>'.  In JBrowse this was achieved by setting a config parameter to true -> 'unsafePopup: true'.

Thanks,

Vaneet

Re: [Gmod-ajax] Use JBrowse browser on the Galaxy Kirin operating system

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

Hello,

I think Kirin is based on FreeBSD, so I imagine it would work just fine.
The server side is fairly straightforward with few dependencies, so
installing it shouldn't be a problem. Please let us know if there are any
issues you run into.

Thanks,
Scott


On Mon, Jun 24, 2024 at 12:37 PM 李静 <my2...@16...> wrote:

> Dear，
>       Hello！I am a JBrowse browser user and currently we would like to use
> it on the Galaxy Kirin operating system. Do we support deployment in the
> Galaxy Kirin environment?
>       Thank you.
> _______________________________________________
> 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] Use JBrowse browser on the Galaxy Kirin operating system

[李静 <my2...@16...>]

Dear，

      Hello！I am a JBrowse browser user and currently we would like to use it on the Galaxy Kirin operating system. Do we support deployment in the Galaxy Kirin environment?
      Thank you.

Re: [Gmod-ajax] JBrowse fmtDetailValue error

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

Glad it works now. :) these are the 'considerations' for the functions in
the .conf format
https://jbrowse.org/docs/configuration_file_formats.html#callback-function-specific-considerations-for-the-text-based-conf-format-


I also found that jbrowse can be made to create source maps for production
builds using this change to webpack.config.js

diff --git a/webpack.config.js b/webpack.config.js
index 6d1bfa685..0dd90ce97 100644
--- a/webpack.config.js
+++ b/webpack.config.js
@@ -19,6 +19,7 @@ var webpackConf = {
         main: "src/JBrowse/main",
         browser: "src/JBrowse/standalone"
     },
+    devtool:'source-map',
     plugins: [
         new CleanWebpackPlugin(['dist']),

This will generate new ".map" files in the "dist" directory when you run
setup.sh or the build, and these will improve the error messages in e.g.
chrome devtools or the javascript console

-Colin

On Mon, May 6, 2024 at 3:31 PM Vaneet Lotay <van...@uc...>
wrote:

> For some reason it works now.  Maybe it was a hidden character that went
> away once I recopied from another source.
>
>
>
> I’m pretty sure I do have a dev-build of jbrowse since I’ve added plugins
> and done some minor modifications to the source js files.  How do I make
> sure I get more informative error messages?  That would be great.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Friday, May 3, 2024 8:08 AM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse fmtDetailValue error
>
>
>
> [△EXTERNAL]
>
>
>
> You'll likely get this error if there is a problem such as a syntax error
> with your function in functions.conf
>
>
>
> You didn't attach your functions.conf so hard to know but this is the
> likely case
>
>
>
> Also note that you can get better error messages if you use a "dev" build
> of jbrowse, this will have regular function names and actual line numbers
> instead of mangled names and minified single line compressed bundles
>
>
>
>
>
> -Colin
>
>
>
> On Fri, May 3, 2024 at 3:47 AM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello,
>
>
>
> I’m getting a strange error when trying to reference a callback function
> to replace my dbxref field, something I’ve done many times for every other
> genome using the same code and syntax without fail using this line:
>
>
>
> "fmtDetailValue_Dbxref" : "{dbxLinks}",
>
>
>
> I also have the include statement referencing which file contains my
> functions added into this genome’s trackList.json file:
>
>
>
>    "include" : "functions.conf",
>
>
>
> Here’s the error I get when trying to click on a gene model to view its
> details:
>
>
>
> Uncaught TypeError: u is not a function
>
>     at Object.renderDetailValue (1.bundle.js:1:555217)
>
>     at Object.renderDetailField (1.bundle.js:1:554833)
>
>     at 1.bundle.js:1:388369
>
>     at Array.forEach (<anonymous>)
>
>     at Object._renderAdditionalTagsDetail (1.bundle.js:1:388346)
>
>     at Object.defaultFeatureDetail (1.bundle.js:1:386667)
>
>     at Object.<anonymous> (0.bundle.js:1:20292)
>
>     at Object._evalConf (1.bundle.js:1:285747)
>
>     at Object._openDialog (1.bundle.js:1:286530)
>
>     at Object.n (1.bundle.js:1:283338)
>
>
>
> I’m not sure which ‘u’ it’s referring to, I’m just hoping one of you has
> seen this error before.  The strange part is if I remove the ‘include’
> statement, the error remains.  If I change the ‘dbxLinks’ to anything else
> or any random set of letters, it still fails with the same error.  If I set
> it to an empty string between the double quotes it at least allows me to
> open the gene model details but obviously doesn’t change the dbxref field.
> If I manually write a function in there instead of referencing a function
> in an external file, it seems to work.  I don’t understand why this time it
> has a problem with me referencing a callback function when I’ve used the
> same function and code so many times with no issue.
>
>
>
> Thanks
>
>
>
> Vaneet
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Re: [Gmod-ajax] JBrowse fmtDetailValue error

[Vaneet L. <van...@uc...>]

For some reason it works now.  Maybe it was a hidden character that went away once I recopied from another source.

I’m pretty sure I do have a dev-build of jbrowse since I’ve added plugins and done some minor modifications to the source js files.  How do I make sure I get more informative error messages?  That would be great.

Thanks,

Vaneet

From: Colin <col...@gm...>
Sent: Friday, May 3, 2024 8:08 AM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse fmtDetailValue error

[△EXTERNAL]

You'll likely get this error if there is a problem such as a syntax error with your function in functions.conf

You didn't attach your functions.conf so hard to know but this is the likely case

Also note that you can get better error messages if you use a "dev" build of jbrowse, this will have regular function names and actual line numbers instead of mangled names and minified single line compressed bundles


-Colin

On Fri, May 3, 2024 at 3:47 AM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I’m getting a strange error when trying to reference a callback function to replace my dbxref field, something I’ve done many times for every other genome using the same code and syntax without fail using this line:

"fmtDetailValue_Dbxref" : "{dbxLinks}",

I also have the include statement referencing which file contains my functions added into this genome’s trackList.json file:

   "include" : "functions.conf",

Here’s the error I get when trying to click on a gene model to view its details:

Uncaught TypeError: u is not a function
    at Object.renderDetailValue (1.bundle.js:1:555217)
    at Object.renderDetailField (1.bundle.js:1:554833)
    at 1.bundle.js:1:388369
    at Array.forEach (<anonymous>)
    at Object._renderAdditionalTagsDetail (1.bundle.js:1:388346)
    at Object.defaultFeatureDetail (1.bundle.js:1:386667)
    at Object.<anonymous> (0.bundle.js:1:20292)
    at Object._evalConf (1.bundle.js:1:285747)
    at Object._openDialog (1.bundle.js:1:286530)
    at Object.n (1.bundle.js:1:283338)

I’m not sure which ‘u’ it’s referring to, I’m just hoping one of you has seen this error before.  The strange part is if I remove the ‘include’ statement, the error remains.  If I change the ‘dbxLinks’ to anything else or any random set of letters, it still fails with the same error.  If I set it to an empty string between the double quotes it at least allows me to open the gene model details but obviously doesn’t change the dbxref field.  If I manually write a function in there instead of referencing a function in an external file, it seems to work.  I don’t understand why this time it has a problem with me referencing a callback function when I’ve used the same function and code so many times with no issue.

Thanks

Vaneet
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] JBrowse fmtDetailValue error

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

You'll likely get this error if there is a problem such as a syntax error
with your function in functions.conf

You didn't attach your functions.conf so hard to know but this is the
likely case

Also note that you can get better error messages if you use a "dev" build
of jbrowse, this will have regular function names and actual line numbers
instead of mangled names and minified single line compressed bundles


-Colin

On Fri, May 3, 2024 at 3:47 AM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
>
>
> I’m getting a strange error when trying to reference a callback function
> to replace my dbxref field, something I’ve done many times for every other
> genome using the same code and syntax without fail using this line:
>
>
>
> "fmtDetailValue_Dbxref" : "{dbxLinks}",
>
>
>
> I also have the include statement referencing which file contains my
> functions added into this genome’s trackList.json file:
>
>
>
>    "include" : "functions.conf",
>
>
>
> Here’s the error I get when trying to click on a gene model to view its
> details:
>
>
>
> Uncaught TypeError: u is not a function
>
>     at Object.renderDetailValue (1.bundle.js:1:555217)
>
>     at Object.renderDetailField (1.bundle.js:1:554833)
>
>     at 1.bundle.js:1:388369
>
>     at Array.forEach (<anonymous>)
>
>     at Object._renderAdditionalTagsDetail (1.bundle.js:1:388346)
>
>     at Object.defaultFeatureDetail (1.bundle.js:1:386667)
>
>     at Object.<anonymous> (0.bundle.js:1:20292)
>
>     at Object._evalConf (1.bundle.js:1:285747)
>
>     at Object._openDialog (1.bundle.js:1:286530)
>
>     at Object.n (1.bundle.js:1:283338)
>
>
>
> I’m not sure which ‘u’ it’s referring to, I’m just hoping one of you has
> seen this error before.  The strange part is if I remove the ‘include’
> statement, the error remains.  If I change the ‘dbxLinks’ to anything else
> or any random set of letters, it still fails with the same error.  If I set
> it to an empty string between the double quotes it at least allows me to
> open the gene model details but obviously doesn’t change the dbxref field.
> If I manually write a function in there instead of referencing a function
> in an external file, it seems to work.  I don’t understand why this time it
> has a problem with me referencing a callback function when I’ve used the
> same function and code so many times with no issue.
>
>
>
> Thanks
>
>
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse fmtDetailValue error

[Vaneet L. <van...@uc...>]

Hello,

I'm getting a strange error when trying to reference a callback function to replace my dbxref field, something I've done many times for every other genome using the same code and syntax without fail using this line:

"fmtDetailValue_Dbxref" : "{dbxLinks}",

I also have the include statement referencing which file contains my functions added into this genome's trackList.json file:

   "include" : "functions.conf",

Here's the error I get when trying to click on a gene model to view its details:

Uncaught TypeError: u is not a function
    at Object.renderDetailValue (1.bundle.js:1:555217)
    at Object.renderDetailField (1.bundle.js:1:554833)
    at 1.bundle.js:1:388369
    at Array.forEach (<anonymous>)
    at Object._renderAdditionalTagsDetail (1.bundle.js:1:388346)
    at Object.defaultFeatureDetail (1.bundle.js:1:386667)
    at Object.<anonymous> (0.bundle.js:1:20292)
    at Object._evalConf (1.bundle.js:1:285747)
    at Object._openDialog (1.bundle.js:1:286530)
    at Object.n (1.bundle.js:1:283338)

I'm not sure which 'u' it's referring to, I'm just hoping one of you has seen this error before.  The strange part is if I remove the 'include' statement, the error remains.  If I change the 'dbxLinks' to anything else or any random set of letters, it still fails with the same error.  If I set it to an empty string between the double quotes it at least allows me to open the gene model details but obviously doesn't change the dbxref field.  If I manually write a function in there instead of referencing a function in an external file, it seems to work.  I don't understand why this time it has a problem with me referencing a callback function when I've used the same function and code so many times with no issue.

Thanks

Vaneet

Re: [Gmod-ajax] JBrowse2 loading human hg38

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

It looks like your gff3 lines referring to parent  features that basically
don't exist (or in some cases, exist on entirely other chromosomes which is
not sensible to jbrowse at least)

Example DPPA2P2 exists on chr1_KN196473v1_fix but it is "referred to" on
chr1

chr1    ncbiRefSeq.2022-10-28   transcript      26519117        26520264
     .       -       .       ID=DPPA2P2_2;Parent=DPPA2P2;

Likely, this transcript should not even have a parent tag as your gff3 file
does not have "gene" level features

I would suggest using gffread to convert gtf to gff3, example here from
jbrowse 1 docs
https://jbrowse.org/docs/faq_data_loading.html#how-do-i-convert-gtf-to-gff

The gffread method does not make "gene level" features either. I don't know
any gtf to gff that do this anyways though

-Colin

On Wed, Apr 17, 2024 at 5:25 PM Vaneet Lotay <van...@uc...>
wrote:

> I loaded the track with GFF3Tabix.  This gff3 attachment is bgzipped and
> 20MB so I’m not sure if it will go through to you.
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Wednesday, April 17, 2024 1:46 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse2 loading human hg38
>
>
>
> [△EXTERNAL]
>
>
>
> Additionally if you can describe how you loaded the track (e.g. as
> plaintext GFF3 or as GFF3Tabix) it might help also
>
>
>
> -Colin
>
>
>
> On Wed, Apr 17, 2024 at 3:44 PM Colin <col...@gm...> wrote:
>
> I would prefer to avoid speaking in generalities about the error message
> if there is a particular thing :)
>
>
>
> How did you do the gtf to gff3 conversion? Then I can just try it , or if
> you want to upload the GFF3 then I can inspect it.
>
>
>
> -Colin
>
>
>
> On Wed, Apr 17, 2024 at 2:30 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> The fasta and a gtf file was sourced from here:
>
>
>
> https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/
>
>
>
> I just learned my colleague had to convert the gtf to gff3 format, maybe
> there’s something that went wrong during the conversion?
>
>
>
> What does that error usually indicate though?  I assumed it was gene
> models that referenced a parent ID that doesn’t exist in the file anywhere,
> but I couldn’t find any examples of that.
>
>
>
> Thanks,
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Wednesday, April 17, 2024 10:43 AM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse2 loading human hg38
>
>
>
> [△EXTERNAL]
>
>
>
> what is the source of "hg38.ncbiRefSeq.gff3.gz"?
>
>
>
> -Colin
>
>
>
> On Wed, Apr 17, 2024 at 12:36 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello,
>
>
>
> Not sure if this is a JBrowse issue or one with the human genome or gene
> models, but this being human, it’s a fairly common genome so I though I’d
> ask the community in case they have ran into any issues when loading hg38
> and its gene models.
>
>
>
> So, I loaded the human hg38 version genome assembly (hg38.masked.fa.gz)
> and that worked fine.  I loaded the NCBI RefSeq gene models track (hg38.ncbiRefSeq.gff3.gz)
> for hg38 next and that seemed to load fine.  However, when I go to any of
> the standard chromosomes which have a short sequence ID (chr1, chr2,
> ..etc.) as opposed to the appended longer sequence IDs
> (chr8_KI270815v1_alt, chr9_GL383540v1_alt) I get this error (stack trace):
>
>
>
>
>
> *Error: some features reference other features that do not exist in the
> file (or in the same '###' scope).
> PRAMEF30P,RNU6-1072P,PRAMEF29P,PRAMEF28P,PRAMEF35P,PRAMEF31P,PRAMEF32P,RNU6-771P,MT1XP1,RPL22P3,RNU1-6P,TRV-CAC11-1,PDE4DIPP8,LOC101056699,EIF1AXP1,TRV-CAC13-1,CROCCP4,PDE4DIPP9,TRV-CAC11-2,LOC124903860,RNU1-5P,LOC107985101,RPL29P6,DPPA2P2,RN7SL679P,RPL36AP9,RPL31P12,LOC100131348,SLC25A24P1,NBPF5P,SLC25A24P2,ST13P21,LOC100420170,LOC124904641,LOC107985110,GEMIN2P1,RN7SL372P,LOC645965,MTX1P1,MPTX1,OR10J2P,OR10J7P,OR10J8P,OR10J9P,LOC100996886,PEBP1P3,ST13P19,RNASEH1P3,RNU5A-8P,BPNT2P1,RPL23AP15,H2BU2P,RNA5SP19,RNA5SP18,LOC124900442,FTH1P2,LOC100418822,RPS21P1,MTCYBP14,MTND6P14,MTND5P19,MTND4P10,MTND4LP21,MTND3P8,MTCO3P46,SEPTIN14P21,CICP21,RNU6-747P,FCF1P7,FABP7P1,VN1R17P,OR2AS2P,OR2AS1P*
>
> *_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867
> <_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867>*
>
> *finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856
> <finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856>*
>
> *parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409
> <parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409>*
>
> *getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706
> <getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706>*
>
>
>
> *JBrowse 2.10.3*
>
>
>
> This error was on chr1 but as I said it happens for pretty much any
> standard chromosome I go to.  When I go to the ‘alt’ or ‘random’ sequences
> with the longer sequence names, they seem to load gene models fine.  When I
> check those mentioned gene models in the error, I can’t seem to find
> anything wrong with its references.
>
>
>
> Just wanted to check in case someone has ran into the same error and how
> it was resolved.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Re: [Gmod-ajax] JBrowse2 loading human hg38

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

Additionally if you can describe how you loaded the track (e.g. as
plaintext GFF3 or as GFF3Tabix) it might help also

-Colin

On Wed, Apr 17, 2024 at 3:44 PM Colin <col...@gm...> wrote:

> I would prefer to avoid speaking in generalities about the error message
> if there is a particular thing :)
>
> How did you do the gtf to gff3 conversion? Then I can just try it , or if
> you want to upload the GFF3 then I can inspect it.
>
> -Colin
>
> On Wed, Apr 17, 2024 at 2:30 PM Vaneet Lotay <van...@uc...>
> wrote:
>
>> The fasta and a gtf file was sourced from here:
>>
>>
>>
>> https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/
>>
>>
>>
>> I just learned my colleague had to convert the gtf to gff3 format, maybe
>> there’s something that went wrong during the conversion?
>>
>>
>>
>> What does that error usually indicate though?  I assumed it was gene
>> models that referenced a parent ID that doesn’t exist in the file anywhere,
>> but I couldn’t find any examples of that.
>>
>>
>>
>> Thanks,
>>
>> Vaneet
>>
>>
>>
>> *From:* Colin <col...@gm...>
>> *Sent:* Wednesday, April 17, 2024 10:43 AM
>> *To:* Vaneet Lotay <van...@uc...>
>> *Cc:* gmo...@li...
>> *Subject:* Re: [Gmod-ajax] JBrowse2 loading human hg38
>>
>>
>>
>> [△EXTERNAL]
>>
>>
>>
>> what is the source of "hg38.ncbiRefSeq.gff3.gz"?
>>
>>
>>
>> -Colin
>>
>>
>>
>> On Wed, Apr 17, 2024 at 12:36 PM Vaneet Lotay <van...@uc...>
>> wrote:
>>
>> Hello,
>>
>>
>>
>> Not sure if this is a JBrowse issue or one with the human genome or gene
>> models, but this being human, it’s a fairly common genome so I though I’d
>> ask the community in case they have ran into any issues when loading hg38
>> and its gene models.
>>
>>
>>
>> So, I loaded the human hg38 version genome assembly (hg38.masked.fa.gz)
>> and that worked fine.  I loaded the NCBI RefSeq gene models track (hg38.ncbiRefSeq.gff3.gz)
>> for hg38 next and that seemed to load fine.  However, when I go to any of
>> the standard chromosomes which have a short sequence ID (chr1, chr2,
>> ..etc.) as opposed to the appended longer sequence IDs
>> (chr8_KI270815v1_alt, chr9_GL383540v1_alt) I get this error (stack trace):
>>
>>
>>
>>
>>
>> *Error: some features reference other features that do not exist in the
>> file (or in the same '###' scope).
>> PRAMEF30P,RNU6-1072P,PRAMEF29P,PRAMEF28P,PRAMEF35P,PRAMEF31P,PRAMEF32P,RNU6-771P,MT1XP1,RPL22P3,RNU1-6P,TRV-CAC11-1,PDE4DIPP8,LOC101056699,EIF1AXP1,TRV-CAC13-1,CROCCP4,PDE4DIPP9,TRV-CAC11-2,LOC124903860,RNU1-5P,LOC107985101,RPL29P6,DPPA2P2,RN7SL679P,RPL36AP9,RPL31P12,LOC100131348,SLC25A24P1,NBPF5P,SLC25A24P2,ST13P21,LOC100420170,LOC124904641,LOC107985110,GEMIN2P1,RN7SL372P,LOC645965,MTX1P1,MPTX1,OR10J2P,OR10J7P,OR10J8P,OR10J9P,LOC100996886,PEBP1P3,ST13P19,RNASEH1P3,RNU5A-8P,BPNT2P1,RPL23AP15,H2BU2P,RNA5SP19,RNA5SP18,LOC124900442,FTH1P2,LOC100418822,RPS21P1,MTCYBP14,MTND6P14,MTND5P19,MTND4P10,MTND4LP21,MTND3P8,MTCO3P46,SEPTIN14P21,CICP21,RNU6-747P,FCF1P7,FABP7P1,VN1R17P,OR2AS2P,OR2AS1P*
>>
>> *_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867
>> <_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867>*
>>
>> *finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856
>> <finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856>*
>>
>> *parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409
>> <parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409>*
>>
>> *getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706
>> <getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706>*
>>
>>
>>
>> *JBrowse 2.10.3*
>>
>>
>>
>> This error was on chr1 but as I said it happens for pretty much any
>> standard chromosome I go to.  When I go to the ‘alt’ or ‘random’ sequences
>> with the longer sequence names, they seem to load gene models fine.  When I
>> check those mentioned gene models in the error, I can’t seem to find
>> anything wrong with its references.
>>
>>
>>
>> Just wanted to check in case someone has ran into the same error and how
>> it was resolved.
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Vaneet
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>

Re: [Gmod-ajax] JBrowse2 loading human hg38

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

I would prefer to avoid speaking in generalities about the error message if
there is a particular thing :)

How did you do the gtf to gff3 conversion? Then I can just try it , or if
you want to upload the GFF3 then I can inspect it.

-Colin

On Wed, Apr 17, 2024 at 2:30 PM Vaneet Lotay <van...@uc...>
wrote:

> The fasta and a gtf file was sourced from here:
>
>
>
> https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/
>
>
>
> I just learned my colleague had to convert the gtf to gff3 format, maybe
> there’s something that went wrong during the conversion?
>
>
>
> What does that error usually indicate though?  I assumed it was gene
> models that referenced a parent ID that doesn’t exist in the file anywhere,
> but I couldn’t find any examples of that.
>
>
>
> Thanks,
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Wednesday, April 17, 2024 10:43 AM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse2 loading human hg38
>
>
>
> [△EXTERNAL]
>
>
>
> what is the source of "hg38.ncbiRefSeq.gff3.gz"?
>
>
>
> -Colin
>
>
>
> On Wed, Apr 17, 2024 at 12:36 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello,
>
>
>
> Not sure if this is a JBrowse issue or one with the human genome or gene
> models, but this being human, it’s a fairly common genome so I though I’d
> ask the community in case they have ran into any issues when loading hg38
> and its gene models.
>
>
>
> So, I loaded the human hg38 version genome assembly (hg38.masked.fa.gz)
> and that worked fine.  I loaded the NCBI RefSeq gene models track (hg38.ncbiRefSeq.gff3.gz)
> for hg38 next and that seemed to load fine.  However, when I go to any of
> the standard chromosomes which have a short sequence ID (chr1, chr2,
> ..etc.) as opposed to the appended longer sequence IDs
> (chr8_KI270815v1_alt, chr9_GL383540v1_alt) I get this error (stack trace):
>
>
>
>
>
> *Error: some features reference other features that do not exist in the
> file (or in the same '###' scope).
> PRAMEF30P,RNU6-1072P,PRAMEF29P,PRAMEF28P,PRAMEF35P,PRAMEF31P,PRAMEF32P,RNU6-771P,MT1XP1,RPL22P3,RNU1-6P,TRV-CAC11-1,PDE4DIPP8,LOC101056699,EIF1AXP1,TRV-CAC13-1,CROCCP4,PDE4DIPP9,TRV-CAC11-2,LOC124903860,RNU1-5P,LOC107985101,RPL29P6,DPPA2P2,RN7SL679P,RPL36AP9,RPL31P12,LOC100131348,SLC25A24P1,NBPF5P,SLC25A24P2,ST13P21,LOC100420170,LOC124904641,LOC107985110,GEMIN2P1,RN7SL372P,LOC645965,MTX1P1,MPTX1,OR10J2P,OR10J7P,OR10J8P,OR10J9P,LOC100996886,PEBP1P3,ST13P19,RNASEH1P3,RNU5A-8P,BPNT2P1,RPL23AP15,H2BU2P,RNA5SP19,RNA5SP18,LOC124900442,FTH1P2,LOC100418822,RPS21P1,MTCYBP14,MTND6P14,MTND5P19,MTND4P10,MTND4LP21,MTND3P8,MTCO3P46,SEPTIN14P21,CICP21,RNU6-747P,FCF1P7,FABP7P1,VN1R17P,OR2AS2P,OR2AS1P*
>
> *_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867
> <_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867>*
>
> *finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856
> <finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856>*
>
> *parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409
> <parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409>*
>
> *getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706
> <getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706>*
>
>
>
> *JBrowse 2.10.3*
>
>
>
> This error was on chr1 but as I said it happens for pretty much any
> standard chromosome I go to.  When I go to the ‘alt’ or ‘random’ sequences
> with the longer sequence names, they seem to load gene models fine.  When I
> check those mentioned gene models in the error, I can’t seem to find
> anything wrong with its references.
>
>
>
> Just wanted to check in case someone has ran into the same error and how
> it was resolved.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Re: [Gmod-ajax] JBrowse2 loading human hg38

[Vaneet L. <van...@uc...>]

The fasta and a gtf file was sourced from here:

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/

I just learned my colleague had to convert the gtf to gff3 format, maybe there’s something that went wrong during the conversion?

What does that error usually indicate though?  I assumed it was gene models that referenced a parent ID that doesn’t exist in the file anywhere, but I couldn’t find any examples of that.

Thanks,

Vaneet

From: Colin <col...@gm...>
Sent: Wednesday, April 17, 2024 10:43 AM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse2 loading human hg38

[△EXTERNAL]

what is the source of "hg38.ncbiRefSeq.gff3.gz"?

-Colin

On Wed, Apr 17, 2024 at 12:36 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

Not sure if this is a JBrowse issue or one with the human genome or gene models, but this being human, it’s a fairly common genome so I though I’d ask the community in case they have ran into any issues when loading hg38 and its gene models.

So, I loaded the human hg38 version genome assembly (hg38.masked.fa.gz) and that worked fine.  I loaded the NCBI RefSeq gene models track (hg38.ncbiRefSeq.gff3.gz) for hg38 next and that seemed to load fine.  However, when I go to any of the standard chromosomes which have a short sequence ID (chr1, chr2, ..etc.) as opposed to the appended longer sequence IDs (chr8_KI270815v1_alt, chr9_GL383540v1_alt) I get this error (stack trace):


Error: some features reference other features that do not exist in the file (or in the same '###' scope). PRAMEF30P,RNU6-1072P,PRAMEF29P,PRAMEF28P,PRAMEF35P,PRAMEF31P,PRAMEF32P,RNU6-771P,MT1XP1,RPL22P3,RNU1-6P,TRV-CAC11-1,PDE4DIPP8,LOC101056699,EIF1AXP1,TRV-CAC13-1,CROCCP4,PDE4DIPP9,TRV-CAC11-2,LOC124903860,RNU1-5P,LOC107985101,RPL29P6,DPPA2P2,RN7SL679P,RPL36AP9,RPL31P12,LOC100131348,SLC25A24P1,NBPF5P,SLC25A24P2,ST13P21,LOC100420170,LOC124904641,LOC107985110,GEMIN2P1,RN7SL372P,LOC645965,MTX1P1,MPTX1,OR10J2P,OR10J7P,OR10J8P,OR10J9P,LOC100996886,PEBP1P3,ST13P19,RNASEH1P3,RNU5A-8P,BPNT2P1,RPL23AP15,H2BU2P,RNA5SP19,RNA5SP18,LOC124900442,FTH1P2,LOC100418822,RPS21P1,MTCYBP14,MTND6P14,MTND5P19,MTND4P10,MTND4LP21,MTND3P8,MTCO3P46,SEPTIN14P21,CICP21,RNU6-747P,FCF1P7,FABP7P1,VN1R17P,OR2AS2P,OR2AS1P
_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867<mailto:_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867>
finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856<mailto:finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856>
parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409<mailto:parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409>
getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706<mailto:getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706>

JBrowse 2.10.3

This error was on chr1 but as I said it happens for pretty much any standard chromosome I go to.  When I go to the ‘alt’ or ‘random’ sequences with the longer sequence names, they seem to load gene models fine.  When I check those mentioned gene models in the error, I can’t seem to find anything wrong with its references.

Just wanted to check in case someone has ran into the same error and how it was resolved.

Thanks,

Vaneet
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] JBrowse2 loading human hg38

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

what is the source of "hg38.ncbiRefSeq.gff3.gz"?

-Colin

On Wed, Apr 17, 2024 at 12:36 PM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
>
>
> Not sure if this is a JBrowse issue or one with the human genome or gene
> models, but this being human, it’s a fairly common genome so I though I’d
> ask the community in case they have ran into any issues when loading hg38
> and its gene models.
>
>
>
> So, I loaded the human hg38 version genome assembly (hg38.masked.fa.gz)
> and that worked fine.  I loaded the NCBI RefSeq gene models track (hg38.ncbiRefSeq.gff3.gz)
> for hg38 next and that seemed to load fine.  However, when I go to any of
> the standard chromosomes which have a short sequence ID (chr1, chr2,
> ..etc.) as opposed to the appended longer sequence IDs
> (chr8_KI270815v1_alt, chr9_GL383540v1_alt) I get this error (stack trace):
>
>
>
>
>
> *Error: some features reference other features that do not exist in the
> file (or in the same '###' scope).
> PRAMEF30P,RNU6-1072P,PRAMEF29P,PRAMEF28P,PRAMEF35P,PRAMEF31P,PRAMEF32P,RNU6-771P,MT1XP1,RPL22P3,RNU1-6P,TRV-CAC11-1,PDE4DIPP8,LOC101056699,EIF1AXP1,TRV-CAC13-1,CROCCP4,PDE4DIPP9,TRV-CAC11-2,LOC124903860,RNU1-5P,LOC107985101,RPL29P6,DPPA2P2,RN7SL679P,RPL36AP9,RPL31P12,LOC100131348,SLC25A24P1,NBPF5P,SLC25A24P2,ST13P21,LOC100420170,LOC124904641,LOC107985110,GEMIN2P1,RN7SL372P,LOC645965,MTX1P1,MPTX1,OR10J2P,OR10J7P,OR10J8P,OR10J9P,LOC100996886,PEBP1P3,ST13P19,RNASEH1P3,RNU5A-8P,BPNT2P1,RPL23AP15,H2BU2P,RNA5SP19,RNA5SP18,LOC124900442,FTH1P2,LOC100418822,RPS21P1,MTCYBP14,MTND6P14,MTND5P19,MTND4P10,MTND4LP21,MTND3P8,MTCO3P46,SEPTIN14P21,CICP21,RNU6-747P,FCF1P7,FABP7P1,VN1R17P,OR2AS2P,OR2AS1P*
>
> *_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867
> <_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867>*
>
> *finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856
> <finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856>*
>
> *parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409
> <parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409>*
>
> *getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706
> <getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706>*
>
>
>
> *JBrowse 2.10.3*
>
>
>
> This error was on chr1 but as I said it happens for pretty much any
> standard chromosome I go to.  When I go to the ‘alt’ or ‘random’ sequences
> with the longer sequence names, they seem to load gene models fine.  When I
> check those mentioned gene models in the error, I can’t seem to find
> anything wrong with its references.
>
>
>
> Just wanted to check in case someone has ran into the same error and how
> it was resolved.
>
>
>
> Thanks,
>
>
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse2 loading human hg38

[Vaneet L. <van...@uc...>]

Hello,

Not sure if this is a JBrowse issue or one with the human genome or gene models, but this being human, it's a fairly common genome so I though I'd ask the community in case they have ran into any issues when loading hg38 and its gene models.

So, I loaded the human hg38 version genome assembly (hg38.masked.fa.gz) and that worked fine.  I loaded the NCBI RefSeq gene models track (hg38.ncbiRefSeq.gff3.gz) for hg38 next and that seemed to load fine.  However, when I go to any of the standard chromosomes which have a short sequence ID (chr1, chr2, ..etc.) as opposed to the appended longer sequence IDs (chr8_KI270815v1_alt, chr9_GL383540v1_alt) I get this error (stack trace):


Error: some features reference other features that do not exist in the file (or in the same '###' scope). PRAMEF30P,RNU6-1072P,PRAMEF29P,PRAMEF28P,PRAMEF35P,PRAMEF31P,PRAMEF32P,RNU6-771P,MT1XP1,RPL22P3,RNU1-6P,TRV-CAC11-1,PDE4DIPP8,LOC101056699,EIF1AXP1,TRV-CAC13-1,CROCCP4,PDE4DIPP9,TRV-CAC11-2,LOC124903860,RNU1-5P,LOC107985101,RPL29P6,DPPA2P2,RN7SL679P,RPL36AP9,RPL31P12,LOC100131348,SLC25A24P1,NBPF5P,SLC25A24P2,ST13P21,LOC100420170,LOC124904641,LOC107985110,GEMIN2P1,RN7SL372P,LOC645965,MTX1P1,MPTX1,OR10J2P,OR10J7P,OR10J8P,OR10J9P,LOC100996886,PEBP1P3,ST13P19,RNASEH1P3,RNU5A-8P,BPNT2P1,RPL23AP15,H2BU2P,RNA5SP19,RNA5SP18,LOC124900442,FTH1P2,LOC100418822,RPS21P1,MTCYBP14,MTND6P14,MTND5P19,MTND4P10,MTND4LP21,MTND3P8,MTCO3P46,SEPTIN14P21,CICP21,RNU6-747P,FCF1P7,FABP7P1,VN1R17P,OR2AS2P,OR2AS1P
_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867<mailto:_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867>
finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856<mailto:finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856>
parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409<mailto:parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409>
getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706<mailto:getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706>

JBrowse 2.10.3

This error was on chr1 but as I said it happens for pretty much any standard chromosome I go to.  When I go to the 'alt' or 'random' sequences with the longer sequence names, they seem to load gene models fine.  When I check those mentioned gene models in the error, I can't seem to find anything wrong with its references.

Just wanted to check in case someone has ran into the same error and how it was resolved.

Thanks,

Vaneet