gmod-ajax — JBrowse list

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

Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?

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

🤷 I don't know--I haven't tried, that's why I was hedging a bit with my
response. It probably will work. If it doesn't, the other option would be
to write a plugin (which is described lower down on the same page).

On Wed, Apr 10, 2024 at 12:34 PM Vaneet Lotay <van...@uc...>
wrote:

> Well by that logic I suppose you can if you can still call the contents of
> the old field you set to null.  Like for example would I able to do this in
> the formatDetails section below?
>
>
>
>   "formatDetails": {
>     "feature": "jexl:{name:undefined, Gene_symbol:feature.name}"
>   },
>
>
>
> Does the contents of that nullified field get lost if set to null?
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Wednesday, April 10, 2024 12:35 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?
>
>
>
> [△EXTERNAL]
>
>
>
> Hi Vaneet,
>
>
>
> That is documented here:
> https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/
>
> While you can't (I don't think) "rename" a field, you can remove a field
> by setting it to null, and create a new field with a new label, which is
> (again, I think) functionally the same as renaming.
>
>
>
> Scott
>
>
>
>
>
> On Wed, Apr 10, 2024 at 11:19 AM Vaneet Lotay <van...@uc...>
> wrote:
>
> Thanks Scott.  By the way I had another question, how do you change the
> names of the actual fields in the feature details pop up box?  I realize
> there’s a way to change their values, but I didn’t see how to do it for the
> field names themselves. I remember doing it in JBrowse1.  I didn’t define
> some additional fields in my bed file so they show up as field 11, field
> 12, ..etc.
>
>
>
> Vaneet
>
>
>
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Friday, March 29, 2024 10:34 AM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?
>
>
>
> [△EXTERNAL]
>
>
>
> Hi Vaneet,
>
>
>
> You can change the mouseover by providing jexl in the 'display' block (but
> not in the 'render' block), like this:
>
>
>
>  "displays": [
>     {
>       "type": "LinearBasicDisplay",
>       "displayId":
> "Macaca_mulatta_all_genes-LinearBasicDisplay-1711729713263",
>       "mouseover": "jexl:get(feature,'gene_biotype')",
>       "renderer": {
>         "type": "SvgFeatureRenderer",
>         "color1": "jexl:get(feature,'strand')<0?'teal':'darkviolet'",
>         "color3": "#30332E",
>         "maxHeight": 5000
>       }
>     }
>   ]
>
>
>
> Scott
>
>
>
>
>
>
>
>
>
> On Thu, Mar 28, 2024 at 1:35 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello,
>
>
>
> I couldn’t find anything specific in the docs about this but is there
> anyway we can configure what is shown when you hover over a feature in a
> track, like a tooltip?  JBrowse1 had the ‘onClick’ method which I used to
> configure mouse hover functionality, so I’m wondering if that can still be
> used or is there another way to configure feature tooltips?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
> _______________________________________________
> 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/)
>
>
>
> --
>
> ------------------------------------------------------------------------
> 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/)
>


-- 
------------------------------------------------------------------------
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 tooltips/mouse-hover for features?

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

Hi Vaneet,

That is documented here:
https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/

While you can't (I don't think) "rename" a field, you can remove a field by
setting it to null, and create a new field with a new label, which is
(again, I think) functionally the same as renaming.

Scott


On Wed, Apr 10, 2024 at 11:19 AM Vaneet Lotay <van...@uc...>
wrote:

> Thanks Scott.  By the way I had another question, how do you change the
> names of the actual fields in the feature details pop up box?  I realize
> there’s a way to change their values, but I didn’t see how to do it for the
> field names themselves. I remember doing it in JBrowse1.  I didn’t define
> some additional fields in my bed file so they show up as field 11, field
> 12, ..etc.
>
>
>
> Vaneet
>
>
>
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Friday, March 29, 2024 10:34 AM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?
>
>
>
> [△EXTERNAL]
>
>
>
> Hi Vaneet,
>
>
>
> You can change the mouseover by providing jexl in the 'display' block (but
> not in the 'render' block), like this:
>
>
>
>  "displays": [
>     {
>       "type": "LinearBasicDisplay",
>       "displayId":
> "Macaca_mulatta_all_genes-LinearBasicDisplay-1711729713263",
>       "mouseover": "jexl:get(feature,'gene_biotype')",
>       "renderer": {
>         "type": "SvgFeatureRenderer",
>         "color1": "jexl:get(feature,'strand')<0?'teal':'darkviolet'",
>         "color3": "#30332E",
>         "maxHeight": 5000
>       }
>     }
>   ]
>
>
>
> Scott
>
>
>
>
>
>
>
>
>
> On Thu, Mar 28, 2024 at 1:35 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello,
>
>
>
> I couldn’t find anything specific in the docs about this but is there
> anyway we can configure what is shown when you hover over a feature in a
> track, like a tooltip?  JBrowse1 had the ‘onClick’ method which I used to
> configure mouse hover functionality, so I’m wondering if that can still be
> used or is there another way to configure feature tooltips?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
> _______________________________________________
> 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/)
>


-- 
------------------------------------------------------------------------
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 tooltips/mouse-hover for features?

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

Well by that logic I suppose you can if you can still call the contents of the old field you set to null.  Like for example would I able to do this in the formatDetails section below?

  "formatDetails": {
    "feature": "jexl:{name:undefined, Gene_symbol:feature.name}"
  },

Does the contents of that nullified field get lost if set to null?

Thanks,

Vaneet

From: Scott Cain <sc...@sc...>
Sent: Wednesday, April 10, 2024 12:35 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?

[△EXTERNAL]

Hi Vaneet,

That is documented here: https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/
While you can't (I don't think) "rename" a field, you can remove a field by setting it to null, and create a new field with a new label, which is (again, I think) functionally the same as renaming.

Scott


On Wed, Apr 10, 2024 at 11:19 AM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Thanks Scott.  By the way I had another question, how do you change the names of the actual fields in the feature details pop up box?  I realize there’s a way to change their values, but I didn’t see how to do it for the field names themselves. I remember doing it in JBrowse1.  I didn’t define some additional fields in my bed file so they show up as field 11, field 12, ..etc.

Vaneet

From: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Sent: Friday, March 29, 2024 10:34 AM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto:gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?

[△EXTERNAL]

Hi Vaneet,

You can change the mouseover by providing jexl in the 'display' block (but not in the 'render' block), like this:

 "displays": [
    {
      "type": "LinearBasicDisplay",
      "displayId": "Macaca_mulatta_all_genes-LinearBasicDisplay-1711729713263",
      "mouseover": "jexl:get(feature,'gene_biotype')",
      "renderer": {
        "type": "SvgFeatureRenderer",
        "color1": "jexl:get(feature,'strand')<0?'teal':'darkviolet'",
        "color3": "#30332E",
        "maxHeight": 5000
      }
    }
  ]

Scott




On Thu, Mar 28, 2024 at 1:35 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I couldn’t find anything specific in the docs about this but is there anyway we can configure what is shown when you hover over a feature in a track, like a tooltip?  JBrowse1 had the ‘onClick’ method which I used to configure mouse hover functionality, so I’m wondering if that can still be used or is there another way to configure feature tooltips?

Thanks,

Vaneet
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto: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/)


--
------------------------------------------------------------------------
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 tooltips/mouse-hover for features?

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

Thanks Scott.  By the way I had another question, how do you change the names of the actual fields in the feature details pop up box?  I realize there’s a way to change their values, but I didn’t see how to do it for the field names themselves. I remember doing it in JBrowse1.  I didn’t define some additional fields in my bed file so they show up as field 11, field 12, ..etc.

Vaneet

From: Scott Cain <sc...@sc...>
Sent: Friday, March 29, 2024 10:34 AM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?

[△EXTERNAL]

Hi Vaneet,

You can change the mouseover by providing jexl in the 'display' block (but not in the 'render' block), like this:

 "displays": [
    {
      "type": "LinearBasicDisplay",
      "displayId": "Macaca_mulatta_all_genes-LinearBasicDisplay-1711729713263",
      "mouseover": "jexl:get(feature,'gene_biotype')",
      "renderer": {
        "type": "SvgFeatureRenderer",
        "color1": "jexl:get(feature,'strand')<0?'teal':'darkviolet'",
        "color3": "#30332E",
        "maxHeight": 5000
      }
    }
  ]

Scott




On Thu, Mar 28, 2024 at 1:35 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I couldn’t find anything specific in the docs about this but is there anyway we can configure what is shown when you hover over a feature in a track, like a tooltip?  JBrowse1 had the ‘onClick’ method which I used to configure mouse hover functionality, so I’m wondering if that can still be used or is there another way to configure feature tooltips?

Thanks,

Vaneet
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
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--
------------------------------------------------------------------------
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 tooltips/mouse-hover for features?

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

Hi Vaneet,

You can change the mouseover by providing jexl in the 'display' block (but
not in the 'render' block), like this:

 "displays": [
    {
      "type": "LinearBasicDisplay",
      "displayId":
"Macaca_mulatta_all_genes-LinearBasicDisplay-1711729713263",
      "mouseover": "jexl:get(feature,'gene_biotype')",
      "renderer": {
        "type": "SvgFeatureRenderer",
        "color1": "jexl:get(feature,'strand')<0?'teal':'darkviolet'",
        "color3": "#30332E",
        "maxHeight": 5000
      }
    }
  ]

Scott




On Thu, Mar 28, 2024 at 1:35 PM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
>
>
> I couldn’t find anything specific in the docs about this but is there
> anyway we can configure what is shown when you hover over a feature in a
> track, like a tooltip?  JBrowse1 had the ‘onClick’ method which I used to
> configure mouse hover functionality, so I’m wondering if that can still be
> used or is there another way to configure feature tooltips?
>
>
>
> Thanks,
>
>
>
> Vaneet
> _______________________________________________
> 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] JBrowse2 tooltips/mouse-hover for features?

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

Hello,

I couldn't find anything specific in the docs about this but is there anyway we can configure what is shown when you hover over a feature in a track, like a tooltip?  JBrowse1 had the 'onClick' method which I used to configure mouse hover functionality, so I'm wondering if that can still be used or is there another way to configure feature tooltips?

Thanks,

Vaneet

Re: [Gmod-ajax] JBrowse2 dynamically changing URL?

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

During normal operation, the session is local to your browser, specifically
using browser localStorage.

 When you use the share button, your session is encrypted, copied to our
server, and then a short url is generated referring to that copy that is
online. We do not not plan to delete sessions and session sgare urls should
be alive as long as we stay online :)

Short faq entry
https://jbrowse.org/jb2/docs/faq/#how-does-the-session-sharing-work-with-shortened-urls-work-in-jbrowse-web


-Colin

On Wed, Mar 27, 2024, 12:37 PM Vaneet Lotay <van...@uc...>
wrote:

> Thanks guys for the detailed explanation.  So for sessions....isn't that
> saved local to my browser or is it possible to share it with another user?
> If so how long can the session be shared for before it's removed from the
> server?  Do you have to create a session JSON file to properly store it in
> the server to make sure it doesn't get deleted before sharing it with
> someone?
>
> Vaneet
> ------------------------------
> *From:* Colin <col...@gm...>
> *Sent:* March 27, 2024 9:10 AM
> *To:* Scott Cain <sc...@sc...>
> *Cc:* Vaneet Lotay <van...@uc...>;
> gmo...@li... <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] JBrowse2 dynamically changing URL?
>
> [△EXTERNAL]
>
> Basically what Scott says, but just to add a little more perspective
>
> As a  comparison, JBrowse 1 did have the auto-updating url, and it was a
> relatively simple system that just stored the current "&loc=chr:1-100" type
> location that you are viewing in the url. That was pretty much all that was
> stored...that and tracks and data directory...
>
> With JBrowse 2, we have the ability to have multiple views, and all sorts
> of  2 just became a kind of complex app with multiple views, and each view
> can have subviews (think synteny view) and so it became hard to port over
> the notion of having a simple URL.
>
> I know this is a little unfortunate that the URL bar is not copyable at
> any time, but as Scott said, we do have the "Share" button that lets you
> get shareable URL.
>
> If the Share button was undesirable, and someone really wanted live
> updating URLs they could conceivably....
>
> a) make a plugin that keeps a minimal set of url params in the url, so it
> can always be copied
> b) use the @jbrowse/react-app package, which does not assume anything
> about the URL, and custom code that feature
>
> -Colin
>
> On Tue, Mar 26, 2024 at 10:07 PM Scott Cain <sc...@sc...> wrote:
>
> Hi Vaneet,
>
> A JBrowse 2 url puts everything in the session into it, so it is *very*
> long. You can get that url from hitting the share link at the top of the
> page and selecting the “long url” option (the short option makes use of a
> url shortener at jbrowse.org) but generally speaking, that long url isn’t
> too useful.
>
> It’s possible to write urls that go into JBrowse 2 that tell it what
> tracks to open and what assembly to use but that gets immediately converted
> to a session.
>
> I hope that helps,
> Scott
>
>
> On Mar 26, 2024, at 2:36 PM, Vaneet Lotay <van...@uc...>
> wrote:
>
> 
>
> Hello all,
>
>
>
> I was just wondering in JBrowse2, is it possible for the URL in my browser
> to dynamically change when I’m selecting different tracks, changing
> location, or even entering different views like the linear synteny view?
> So far it just stays the same once I start from my default session.  It
> would be nice if there’s at least a button that can reveal the true long
> form URL at any point but not sure if that’s possible.  JBrowse 1 had the
> changing URL so that’s why I’m wondering if it’s still accessible somehow.
> This would be a nice feature as it to have as it will make easier to share
> URLs for specific track arrangements with other users.
>
>
>
> Thanks,
>
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Re: [Gmod-ajax] JBrowse2 dynamically changing URL?

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

Thanks guys for the detailed explanation.  So for sessions....isn't that saved local to my browser or is it possible to share it with another user?  If so how long can the session be shared for before it's removed from the server?  Do you have to create a session JSON file to properly store it in the server to make sure it doesn't get deleted before sharing it with someone?

Vaneet
________________________________
From: Colin <col...@gm...>
Sent: March 27, 2024 9:10 AM
To: Scott Cain <sc...@sc...>
Cc: Vaneet Lotay <van...@uc...>; gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse2 dynamically changing URL?

[△EXTERNAL]


Basically what Scott says, but just to add a little more perspective

As a  comparison, JBrowse 1 did have the auto-updating url, and it was a relatively simple system that just stored the current "&loc=chr:1-100" type location that you are viewing in the url. That was pretty much all that was stored...that and tracks and data directory...

With JBrowse 2, we have the ability to have multiple views, and all sorts of  2 just became a kind of complex app with multiple views, and each view can have subviews (think synteny view) and so it became hard to port over the notion of having a simple URL.

I know this is a little unfortunate that the URL bar is not copyable at any time, but as Scott said, we do have the "Share" button that lets you get shareable URL.

If the Share button was undesirable, and someone really wanted live updating URLs they could conceivably....

a) make a plugin that keeps a minimal set of url params in the url, so it can always be copied
b) use the @jbrowse/react-app package, which does not assume anything about the URL, and custom code that feature

-Colin

On Tue, Mar 26, 2024 at 10:07 PM Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Vaneet,

A JBrowse 2 url puts everything in the session into it, so it is *very* long. You can get that url from hitting the share link at the top of the page and selecting the “long url” option (the short option makes use of a url shortener at jbrowse.org<http://jbrowse.org>) but generally speaking, that long url isn’t too useful.

It’s possible to write urls that go into JBrowse 2 that tell it what tracks to open and what assembly to use but that gets immediately converted to a session.

I hope that helps,
Scott


On Mar 26, 2024, at 2:36 PM, Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:



Hello all,



I was just wondering in JBrowse2, is it possible for the URL in my browser to dynamically change when I’m selecting different tracks, changing location, or even entering different views like the linear synteny view?  So far it just stays the same once I start from my default session.  It would be nice if there’s at least a button that can reveal the true long form URL at any point but not sure if that’s possible.  JBrowse 1 had the changing URL so that’s why I’m wondering if it’s still accessible somehow.  This would be a nice feature as it to have as it will make easier to share URLs for specific track arrangements with other users.



Thanks,

Vaneet

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

Re: [Gmod-ajax] JBrowse2 dynamically changing URL?

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

Basically what Scott says, but just to add a little more perspective

As a  comparison, JBrowse 1 did have the auto-updating url, and it was a
relatively simple system that just stored the current "&loc=chr:1-100" type
location that you are viewing in the url. That was pretty much all that was
stored...that and tracks and data directory...

With JBrowse 2, we have the ability to have multiple views, and all sorts
of  2 just became a kind of complex app with multiple views, and each view
can have subviews (think synteny view) and so it became hard to port over
the notion of having a simple URL.

I know this is a little unfortunate that the URL bar is not copyable at any
time, but as Scott said, we do have the "Share" button that lets you get
shareable URL.

If the Share button was undesirable, and someone really wanted live
updating URLs they could conceivably....

a) make a plugin that keeps a minimal set of url params in the url, so it
can always be copied
b) use the @jbrowse/react-app package, which does not assume anything about
the URL, and custom code that feature

-Colin

On Tue, Mar 26, 2024 at 10:07 PM Scott Cain <sc...@sc...> wrote:

> Hi Vaneet,
>
> A JBrowse 2 url puts everything in the session into it, so it is *very*
> long. You can get that url from hitting the share link at the top of the
> page and selecting the “long url” option (the short option makes use of a
> url shortener at jbrowse.org) but generally speaking, that long url isn’t
> too useful.
>
> It’s possible to write urls that go into JBrowse 2 that tell it what
> tracks to open and what assembly to use but that gets immediately converted
> to a session.
>
> I hope that helps,
> Scott
>
>
> On Mar 26, 2024, at 2:36 PM, Vaneet Lotay <van...@uc...>
> wrote:
>
> 
>
> Hello all,
>
>
>
> I was just wondering in JBrowse2, is it possible for the URL in my browser
> to dynamically change when I’m selecting different tracks, changing
> location, or even entering different views like the linear synteny view?
> So far it just stays the same once I start from my default session.  It
> would be nice if there’s at least a button that can reveal the true long
> form URL at any point but not sure if that’s possible.  JBrowse 1 had the
> changing URL so that’s why I’m wondering if it’s still accessible somehow.
> This would be a nice feature as it to have as it will make easier to share
> URLs for specific track arrangements with other users.
>
>
>
> Thanks,
>
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>