gmod-ajax — JBrowse list

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...>
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/)

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
>

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

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

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] JBrowse2 dynamically changing URL?

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

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

Re: [Gmod-ajax] JBrowse 2 Configuration Options

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

Random extra note:

There is a value called "bicolorPivot" which you can configure to an
absolute value. There is mention of setting bicolorPivotValue to "mean" but
this is unimplemented actually...but is a placeholder for the origin like
JBrowse 1's feature for this...



[image: image.png]


-Colin

On Mon, Mar 18, 2024 at 4:34 PM Colin <col...@gm...> wrote:

> Hi there,
> JBrowse 2 does not have the feature for displaying variance band and
> origin for bigwig tracks
>
> If you wanted to simulate it, you could create a multibigwig track with
> flat lines for the mean and variance bands
>
> I could elaborate on this if interested, but part of the reason why they
> are not implemented is that i worry about presenting potentially misleading
> mean and variance values. The values that are presented by jbrowse 1 are
> actually pretty coarse measurements that are made from summary statistics
> on the global data distribution of the bigwig
>
>
>
> -Colin
>
> On Mon, Mar 18, 2024 at 1:32 PM <aak...@sm...> wrote:
>
>>
>> Hello,
>>
>> I am Master's student from the University of Cologne, currently
>> working on a project to update a web genome browser
>> (https://amaranthgdb.org/popamaranth.html). The first version of this
>> browser uses JBrowse1, where the "origin_color" and "variance_band"
>> options are available for BigWig tracks, as listed in the respective
>> documentation. For the update, I am working with the JBrowse2 desktop
>> app and given my limited experience with JBrowse , I was unable to add
>> the origin line and the variance band to my BigWig tracks. Hence I
>> wanted to reach out and ask if there is a straightforward way of
>> adding these configuration options that I might be missing. If not, I
>> would be grateful if you could provide me with a quick guide on how I
>> can achieve this.
>>
>> Thanks in advance!
>>
>> Aslinur Akturk
>> Institute for Plant Sciences, University of Cologne
>> Biozentrum
>> Zülpicher Str. 47b
>> 50674 Cologne/Germany
>>
>>
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] JBrowse 2 Configuration Options

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

Hi there,
JBrowse 2 does not have the feature for displaying variance band and origin
for bigwig tracks

If you wanted to simulate it, you could create a multibigwig track with
flat lines for the mean and variance bands

I could elaborate on this if interested, but part of the reason why they
are not implemented is that i worry about presenting potentially misleading
mean and variance values. The values that are presented by jbrowse 1 are
actually pretty coarse measurements that are made from summary statistics
on the global data distribution of the bigwig



-Colin

On Mon, Mar 18, 2024 at 1:32 PM <aak...@sm...> wrote:

>
> Hello,
>
> I am Master's student from the University of Cologne, currently
> working on a project to update a web genome browser
> (https://amaranthgdb.org/popamaranth.html). The first version of this
> browser uses JBrowse1, where the "origin_color" and "variance_band"
> options are available for BigWig tracks, as listed in the respective
> documentation. For the update, I am working with the JBrowse2 desktop
> app and given my limited experience with JBrowse , I was unable to add
> the origin line and the variance band to my BigWig tracks. Hence I
> wanted to reach out and ask if there is a straightforward way of
> adding these configuration options that I might be missing. If not, I
> would be grateful if you could provide me with a quick guide on how I
> can achieve this.
>
> Thanks in advance!
>
> Aslinur Akturk
> Institute for Plant Sciences, University of Cologne
> Biozentrum
> Zülpicher Str. 47b
> 50674 Cologne/Germany
>
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse 2 Configuration Options

[<aak...@sm...>]

Hello,

I am Master's student from the University of Cologne, currently  
working on a project to update a web genome browser  
(https://amaranthgdb.org/popamaranth.html). The first version of this  
browser uses JBrowse1, where the "origin_color" and "variance_band"  
options are available for BigWig tracks, as listed in the respective  
documentation. For the update, I am working with the JBrowse2 desktop  
app and given my limited experience with JBrowse , I was unable to add  
the origin line and the variance band to my BigWig tracks. Hence I  
wanted to reach out and ask if there is a straightforward way of  
adding these configuration options that I might be missing. If not, I  
would be grateful if you could provide me with a quick guide on how I  
can achieve this.

Thanks in advance!

Aslinur Akturk
Institute for Plant Sciences, University of Cologne
Biozentrum
Zülpicher Str. 47b
50674 Cologne/Germany

Re: [Gmod-ajax] Running Apollo in JBrowse

[Dorita A. <dor...@um...>]

Dear Colin,

I thank you for clearing this issue for me. I will read a bit more about
'running a web server'.
In the meantime can you please advice me on which application to use for a
small amount of manual annotation curation of a relatively small genome
(150kbp) on a Mac?

Yours truly,
Dorita Agius B.Sc. M.Phil.
Senior Lecturer II
RM D004 Junior College
University of Malta
Phone: 00356 7938 2887
dor...@um...



On Thu, 29 Feb 2024 at 23:43, Colin <col...@gm...> wrote:

> Hi Dorita
>
> Apollo is a server side app, written in java, that basically has it's own
> installation instructions here
> https://genomearchitect.readthedocs.io/en/latest/
>
> It requires running a server, so it doens't work with JBrowse desktop, you
> would need to run a web server to set it up.
>
> The current Apollo ("Apollo v2") also only works with JBrowse 1 now, but
> we are working on a new version of Apollo ("Apollo v3") that is compatible
> with JBrowse 2
>
> Hope that helps!
> -Colin
>
>
>
> On Thu, Feb 29, 2024 at 2:52 PM Dorita Agius <dor...@um...>
> wrote:
>
>> Dear Sir or Madame,
>>
>> I am trying to run Apollo within JBrowse on desktop (MacBook Pro).
>> However in both JBrowse V2.10.2 and 1.16.11 and in both cases I cannot find
>> the plugin store for installation of Apollo.
>> What am I doing wrong please?
>>
>> If this is not the right email address to use for this difficulty can you
>> guide me to the right one please?
>>
>> [image: image.png]
>>
>>
>>
>> [image: image.png]
>>
>> Thank you
>>
>> Yours truly
>>
>> Dorita Agius B.Sc. M.Phil.
>> Senior Lecturer II
>> RM D004 Junior College
>> University of Malta
>> Phone: 00356 7938 2887
>> dor...@um...
>>
>>
>> *The contents of this email are subject to these terms
>> <https://www.um.edu.mt/disclaimer/email/>.*
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

-- 
*The contents of this email are subject to *these terms 
<https://www.um.edu.mt/disclaimer/email/>.**

Re: [Gmod-ajax] Running Apollo in JBrowse

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

Hi Dorita

Apollo is a server side app, written in java, that basically has it's own
installation instructions here
https://genomearchitect.readthedocs.io/en/latest/

It requires running a server, so it doens't work with JBrowse desktop, you
would need to run a web server to set it up.

The current Apollo ("Apollo v2") also only works with JBrowse 1 now, but we
are working on a new version of Apollo ("Apollo v3") that is compatible
with JBrowse 2

Hope that helps!
-Colin



On Thu, Feb 29, 2024 at 2:52 PM Dorita Agius <dor...@um...> wrote:

> Dear Sir or Madame,
>
> I am trying to run Apollo within JBrowse on desktop (MacBook Pro). However
> in both JBrowse V2.10.2 and 1.16.11 and in both cases I cannot find the
> plugin store for installation of Apollo.
> What am I doing wrong please?
>
> If this is not the right email address to use for this difficulty can you
> guide me to the right one please?
>
> [image: image.png]
>
>
>
> [image: image.png]
>
> Thank you
>
> Yours truly
>
> Dorita Agius B.Sc. M.Phil.
> Senior Lecturer II
> RM D004 Junior College
> University of Malta
> Phone: 00356 7938 2887
> dor...@um...
>
>
> *The contents of this email are subject to these terms
> <https://www.um.edu.mt/disclaimer/email/>.*
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Running Apollo in JBrowse

[Dorita A. <dor...@um...>]

Dear Sir or Madame,

I am trying to run Apollo within JBrowse on desktop (MacBook Pro). However
in both JBrowse V2.10.2 and 1.16.11 and in both cases I cannot find the
plugin store for installation of Apollo.
What am I doing wrong please?

If this is not the right email address to use for this difficulty can you
guide me to the right one please?

[image: image.png]



[image: image.png]

Thank you

Yours truly

Dorita Agius B.Sc. M.Phil.
Senior Lecturer II
RM D004 Junior College
University of Malta
Phone: 00356 7938 2887
dor...@um...

-- 
*The contents of this email are subject to *these terms 
<https://www.um.edu.mt/disclaimer/email/>.**

Re: [Gmod-ajax] Requirements for a GFF3 to render properly?

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

Hi Scott,

Thank you! I converted the file from GTF to GFF with agat utility. Now the tracks are properly rendering.

Betss,
-Hans
________________________________
From: Scott Cain <sc...@sc...>
Sent: Thursday, January 11, 2024 3:01 PM
To: Hans Vasquez-Gross <hva...@un...>
Cc: gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] Requirements for a GFF3 to render properly?


[EXTERNAL EMAIL]

Another thing I should have mentioned when I said this looked like GTF: GTF is frequently called GFF2.5. What you posted would also pass as GFF 2.

On Thu, Jan 11, 2024 at 2:45 PM Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Hans,

I'd say the problem is primarily that the snippet you've shown isn't GFF3; it looks much more like GTF (GFF3 would have "tag=value;tag2=value2" in the ninth column, as opposed to 'tag "value"; tag2 "value2"' in the ninth column). While JBrowse 2 does support GTF, it has some drawbacks, the biggest of which is there isn't an indexed form of it, so the tracks will load very slowly since JBrowse has to load the entire file and parse it in order to draw any portion of it. If you had GFF3, each of the exon features would have a "Parent" tag that pointed to the ID of the parent transcript.

The other thing that jumps out at me for the data snippet you provided is that all of the transcripts appear to share the same start and end coordinates of the child exons, so they would only show up as individual exons anyway. I would guess that elsewhere in your GTF file you have more complicated examples with transcripts that have multiple exon children.

So, it's hard to say what I would expect to see without a better example of your GTF, but you probably want to look at generated GFF3 anyway, so that you can take advantage of tabix indexing of the GFF3 files.

Of course, feel free to follow up with more questions or example data and we can figure out where to go from there.

Scott


On Thu, Jan 11, 2024 at 2:29 PM Hans Vasquez-Gross <hva...@un...<mailto:hva...@un...>> wrote:
Hello All,

I have the output from isoseq collapse then pigeon index to create a sorted .gff3 file for a new assembly. Currently, this gff3 file has transcript and exon definitions.  However, when I load this track data on JBrowse2, it shows the transcripts as one large unit and the exons as a separate unit. It doesn't seem to correct render the intron/exon boundaries. The annotation track is on top in yellow and the isoseq_reads bam file is below.

Example data:
##pacbio-collapse-version 1.0
##date Thu Jan 11 00:10:30 2024 UTC
ctg_p_c_003493_0_75000_89999  PacBio      transcript  11587 12122 .     -     .     gene_id "PB.32086"; transcript_id "PB.32086.1";
ctg_p_c_003493_0_75000_89999  PacBio      exon  11587 12122 .     -     .     gene_id "PB.32086"; transcript_id "PB.32086.1";
ctg_p_c_033075_0  PacBio      transcript  20564 22031 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.1";
ctg_p_c_033075_0  PacBio      exon  20564 22031 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.1";
ctg_p_c_033075_0  PacBio      transcript  20564 21887 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.2";
ctg_p_c_033075_0  PacBio      exon  20564 21887 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.2";
ctg_p_c_033075_0  PacBio      transcript  20564 21758 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.3";
ctg_p_c_033075_0  PacBio      exon  20564 21758 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.3";


Any suggestions?

Thank you,
-Hans


--



[signature_998258195]

Hans Vasquez-Gross, Ph.D

Bioinformatics Scientist,
Nevada Bioinformatics Center

https://www.unr.edu/bioinformatics

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

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


--
------------------------------------------------------------------------
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/)

This email originated outside of the University of Nevada, Reno. Do not click on links or attachments unless you recognize the sender and know the content is safe. Report suspicious emails to the Office of Information Technology (OIT) at ab...@un....

Re: [Gmod-ajax] Requirements for a GFF3 to render properly?

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

Hi Hans,

I'd say the problem is primarily that the snippet you've shown isn't GFF3;
it looks much more like GTF (GFF3 would have "tag=value;tag2=value2" in the
ninth column, as opposed to 'tag "value"; tag2 "value2"' in the ninth
column). While JBrowse 2 does support GTF, it has some drawbacks, the
biggest of which is there isn't an indexed form of it, so the tracks will
load very slowly since JBrowse has to load the entire file and parse it in
order to draw any portion of it. If you had GFF3, each of the exon features
would have a "Parent" tag that pointed to the ID of the parent transcript.

The other thing that jumps out at me for the data snippet you provided is
that all of the transcripts appear to share the same start and end
coordinates of the child exons, so they would only show up as individual
exons anyway. I would guess that elsewhere in your GTF file you have more
complicated examples with transcripts that have multiple exon children.

So, it's hard to say what I would expect to see without a better example of
your GTF, but you probably want to look at generated GFF3 anyway, so that
you can take advantage of tabix indexing of the GFF3 files.

Of course, feel free to follow up with more questions or example data and
we can figure out where to go from there.

Scott


On Thu, Jan 11, 2024 at 2:29 PM Hans Vasquez-Gross <hva...@un...>
wrote:

> Hello All,
>
> I have the output from isoseq collapse then pigeon index to create a
> sorted .gff3 file for a new assembly. Currently, this gff3 file has
> transcript and exon definitions.  However, when I load this track data on
> JBrowse2, it shows the transcripts as one large unit and the exons as a
> separate unit. It doesn't seem to correct render the intron/exon
> boundaries. The annotation track is on top in yellow and the isoseq_reads
> bam file is below.
>
> Example data:
> ##pacbio-collapse-version 1.0
> ##date Thu Jan 11 00:10:30 2024 UTC
> ctg_p_c_003493_0_75000_89999 PacBio transcript 11587 12122 . - . gene_id
> "PB.32086"; transcript_id "PB.32086.1";
> ctg_p_c_003493_0_75000_89999 PacBio exon 11587 12122 . - . gene_id
> "PB.32086"; transcript_id "PB.32086.1";
> ctg_p_c_033075_0 PacBio transcript 20564 22031 . + . gene_id "PB.31043";
> transcript_id "PB.31043.1";
> ctg_p_c_033075_0 PacBio exon 20564 22031 . + . gene_id "PB.31043";
> transcript_id "PB.31043.1";
> ctg_p_c_033075_0 PacBio transcript 20564 21887 . + . gene_id "PB.31043";
> transcript_id "PB.31043.2";
> ctg_p_c_033075_0 PacBio exon 20564 21887 . + . gene_id "PB.31043";
> transcript_id "PB.31043.2";
> ctg_p_c_033075_0 PacBio transcript 20564 21758 . + . gene_id "PB.31043";
> transcript_id "PB.31043.3";
> ctg_p_c_033075_0 PacBio exon 20564 21758 . + . gene_id "PB.31043";
> transcript_id "PB.31043.3";
>
>
> Any suggestions?
>
> Thank you,
> -Hans
>
> --
>
>
>
> [image: signature_998258195]
>
> *Hans Vasquez-Gross, Ph.D*
>
> Bioinformatics Scientist,
> Nevada Bioinformatics Center
>
> https://www.unr.edu/bioinformatics
>
> hva...@un...
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
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] Requirements for a GFF3 to render properly?

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

Another thing I should have mentioned when I said this looked like GTF: GTF
is frequently called GFF2.5. What you posted would also pass as GFF 2.

On Thu, Jan 11, 2024 at 2:45 PM Scott Cain <sc...@sc...> wrote:

> Hi Hans,
>
> I'd say the problem is primarily that the snippet you've shown isn't GFF3;
> it looks much more like GTF (GFF3 would have "tag=value;tag2=value2" in the
> ninth column, as opposed to 'tag "value"; tag2 "value2"' in the ninth
> column). While JBrowse 2 does support GTF, it has some drawbacks, the
> biggest of which is there isn't an indexed form of it, so the tracks will
> load very slowly since JBrowse has to load the entire file and parse it in
> order to draw any portion of it. If you had GFF3, each of the exon features
> would have a "Parent" tag that pointed to the ID of the parent transcript.
>
> The other thing that jumps out at me for the data snippet you provided is
> that all of the transcripts appear to share the same start and end
> coordinates of the child exons, so they would only show up as individual
> exons anyway. I would guess that elsewhere in your GTF file you have more
> complicated examples with transcripts that have multiple exon children.
>
> So, it's hard to say what I would expect to see without a better example
> of your GTF, but you probably want to look at generated GFF3 anyway, so
> that you can take advantage of tabix indexing of the GFF3 files.
>
> Of course, feel free to follow up with more questions or example data and
> we can figure out where to go from there.
>
> Scott
>
>
> On Thu, Jan 11, 2024 at 2:29 PM Hans Vasquez-Gross <hva...@un...>
> wrote:
>
>> Hello All,
>>
>> I have the output from isoseq collapse then pigeon index to create a
>> sorted .gff3 file for a new assembly. Currently, this gff3 file has
>> transcript and exon definitions.  However, when I load this track data on
>> JBrowse2, it shows the transcripts as one large unit and the exons as a
>> separate unit. It doesn't seem to correct render the intron/exon
>> boundaries. The annotation track is on top in yellow and the isoseq_reads
>> bam file is below.
>>
>> Example data:
>> ##pacbio-collapse-version 1.0
>> ##date Thu Jan 11 00:10:30 2024 UTC
>> ctg_p_c_003493_0_75000_89999 PacBio transcript 11587 12122 . - . gene_id
>> "PB.32086"; transcript_id "PB.32086.1";
>> ctg_p_c_003493_0_75000_89999 PacBio exon 11587 12122 . - . gene_id
>> "PB.32086"; transcript_id "PB.32086.1";
>> ctg_p_c_033075_0 PacBio transcript 20564 22031 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.1";
>> ctg_p_c_033075_0 PacBio exon 20564 22031 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.1";
>> ctg_p_c_033075_0 PacBio transcript 20564 21887 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.2";
>> ctg_p_c_033075_0 PacBio exon 20564 21887 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.2";
>> ctg_p_c_033075_0 PacBio transcript 20564 21758 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.3";
>> ctg_p_c_033075_0 PacBio exon 20564 21758 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.3";
>>
>>
>> Any suggestions?
>>
>> Thank you,
>> -Hans
>>
>> --
>>
>>
>>
>> [image: signature_998258195]
>>
>> *Hans Vasquez-Gross, Ph.D*
>>
>> Bioinformatics Scientist,
>> Nevada Bioinformatics Center
>>
>> https://www.unr.edu/bioinformatics
>>
>> hva...@un...
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> --
> ------------------------------------------------------------------------
> 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/)

[Gmod-ajax] Requirements for a GFF3 to render properly?

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

Hello All,

I have the output from isoseq collapse then pigeon index to create a sorted .gff3 file for a new assembly. Currently, this gff3 file has transcript and exon definitions.  However, when I load this track data on JBrowse2, it shows the transcripts as one large unit and the exons as a separate unit. It doesn't seem to correct render the intron/exon boundaries. The annotation track is on top in yellow and the isoseq_reads bam file is below.

Example data:
##pacbio-collapse-version 1.0
##date Thu Jan 11 00:10:30 2024 UTC
ctg_p_c_003493_0_75000_89999  PacBio      transcript  11587 12122 .     -     .     gene_id "PB.32086"; transcript_id "PB.32086.1";
ctg_p_c_003493_0_75000_89999  PacBio      exon  11587 12122 .     -     .     gene_id "PB.32086"; transcript_id "PB.32086.1";
ctg_p_c_033075_0  PacBio      transcript  20564 22031 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.1";
ctg_p_c_033075_0  PacBio      exon  20564 22031 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.1";
ctg_p_c_033075_0  PacBio      transcript  20564 21887 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.2";
ctg_p_c_033075_0  PacBio      exon  20564 21887 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.2";
ctg_p_c_033075_0  PacBio      transcript  20564 21758 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.3";
ctg_p_c_033075_0  PacBio      exon  20564 21758 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.3";


Any suggestions?

Thank you,
-Hans


--



[signature_998258195]

Hans Vasquez-Gross, Ph.D

Bioinformatics Scientist,
Nevada Bioinformatics Center

https://www.unr.edu/bioinformatics

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

Re: [Gmod-ajax] text-index problem

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

Hi,

After upgrading Node.js to 20, the index function is fully restored (tested
with various options).

Thanks for the help from the developers!

Ke

On Wed, Dec 6, 2023 at 10:14 PM Ke Jiang <bio...@gm...> wrote:

> Thanks, Colin! I’ll give upgrading node.js a try and report back how it
> works.
>
> On Wed, Dec 6, 2023 at 6:12 PM Colin <col...@gm...> wrote:
>
>> Sorry there was a typo in the last email, I meant to say node 14 and 16
>> are end of life, 18 is not, so upgrading to 18 or 20 is safe (those are the
>> current "LTS" versions)
>>
>> -Colin
>>
>> On Wed, Dec 6, 2023 at 7:11 PM Colin <col...@gm...> wrote:
>>
>>> Hi there,
>>> It looks like replaceAll was added in nodejs 15. If you run node
>>> --version you can check which version you have. I would imagine that
>>> upgrading could help if e.g. you are node 14 (both node 16 and node 18 are
>>> now officially "end of life" so it is good to stay updated if possible)
>>>
>>> We can probably do a better job in our CLI trying to report errors with
>>> this. We can maybe also even consider trying to support older node or at
>>> least not using bleeding edge features all the time, as I know it is kind
>>> of tricky to stay updated
>>>
>>> -Colin
>>>
>>> On Wed, Dec 6, 2023 at 3:52 PM Ke Jiang <bio...@gm...> wrote:
>>>
>>>> Hi,
>>>>
>>>> I tried to rebuild some indice with new tracks added, but experienced
>>>> the following error message:
>>>>
>>>> UnhandledPromiseRejectionWarning: TypeError:
>>>> JSON.stringify(...).replaceAll is not a function
>>>>
>>>> Even after cleaning up the old indice JSON chunk, I keep having this
>>>> error with "text-index" with all new tracks. Based on some searches, it
>>>> looks like this is caused by an older version of node.js. Does anyone have
>>>> similar problems? If so, does upgrading the node.js solve it? I'm on
>>>> JBrowse2 2.8.0.
>>>>
>>>> Thanks!
>>>>
>>>> Ke
>>>>
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>

Re: [Gmod-ajax] JBrowse URL params: specify height

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

Currently, the url params don't allow specifying height, but that is a good
idea, to provide various parameters. However you can pre-configure the
height of the track in the config.json as an alternative

Example of pre-configuring height on a track with height on the display

  {
      "type": "FeatureTrack",
      "trackId": "mygenes",
      "assemblyNames": ["hg19"],
      "name": "genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": { "uri": "volvox.sort.gff3.gz" },
        "index": { "location": {"uri": "volvox.sort.gff3.gz.tbi" } }
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "height": 600,
          "displayId": "mygenes_LinearBasicDisplay"
        }
      ]
    }



Also, we may look into auto-adjusting the track height to the contents of
the track or something of that sort
https://github.com/GMOD/jbrowse-components/issues/534


-Colin

On Wed, Dec 20, 2023 at 4:58 PM Vaneet Lotay <van...@uc...>
wrote:

> Hi all,
>
>
>
> I was looking at this doc page for JBrowse2:
>
>
>
> https://jbrowse.org/jb2/docs/urlparams/
>
>
>
> I was just wondering is there a way to specify additional parameters via
> URL besides the 5 that were mentioned?  Specifically, I’m thinking of track
> height, since when I tried using some specific parameters in the URL to go
> to the position of a gene model, the track height wasn’t long enough to
> cover all the transcripts in the gene model, it was cut off.
>
>
>
> Thanks,
>
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse URL params: specify height

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

Hi all,

I was looking at this doc page for JBrowse2:

https://jbrowse.org/jb2/docs/urlparams/

I was just wondering is there a way to specify additional parameters via URL besides the 5 that were mentioned?  Specifically, I'm thinking of track height, since when I tried using some specific parameters in the URL to go to the position of a gene model, the track height wasn't long enough to cover all the transcripts in the gene model, it was cut off.

Thanks,

Vaneet

Re: [Gmod-ajax] Callback function error with dbxrefs

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

 No worries, I'm glad you found this workaround.

it is actually really good to hear about any issues people might have with
CLI so we can potentially find ways to fix.

I know nodejs isn't very common in bioinformatics so for some people
installing jbrowse CLI is people's first experience with nodejs, so we want
to make sure it's easy. I considered possibly making a single file binary
version of jbrowse CLI for example

-Colin

On Tue, Dec 12, 2023 at 2:37 PM Vaneet Lotay <van...@uc...>
wrote:

> Sorry this dragged on so long Colin.  So I find out that when using ‘npm
> install -g’ it installs the @jbrowse/cli tool in 3 different places when
> I’m using sudo or root user.  One of the places “/usr/local/bin/jbrowse”
> was the old v2.6.3 while the other two were the latest v2.9.  So I removed
> the symlink that was in /usr/local/bin, which actually points to a
> directory under /usr/local/lib.  Afterwards when trying to run the jbrowse
> command it unfortunately only looks in the /usr/local/bin/ directory again,
> even though the other two locations where the v2.9.0 was installed are
> clearly in my PATH.  Anyways I simply recreated that symlink under
> /usr/local/bin for JBrowse but pointed it to one of the v2.9.0 executables
> in the other location.  Now when checking the version I get the right
> release #:
>
>
>
> jbrowse --version
>
> @jbrowse/cli/2.9.0 linux-x64 node-v20.10.0
>
>
>
> Hopefully, this workaround functions ok when I upgrade the client tool in
> the future, I’ll have to see.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Monday, December 11, 2023 5:29 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Callback function error with dbxrefs
>
>
>
> [△EXTERNAL]
>
>
>
> I was mostly referring to how you installed the @jbrowse/cli tool
>
>
>
> I think because you have a version of @jbrowse/cli in "/usr/lib/" because
> that is listed by npm list -g in your previous post, which suggests to me
> that you have used "sudo npm install -g @jbrowse/cli" or run "npm install
> -g @jbrowse/cli" under a root or privileged account. This is ok. And, that
> one looks like the latest correct version. But, you might also have another
> version installed somewhere else too, and that is the v2.6.3 version. Try
> identifying where that v2.6.3 version is installed perhaps, with commands
> like "which jbrowse" or npm list -g like mentioned previously. And then you
> can try uninstalling that version (npm uninstall -g @jbrowse/cli is a valid
> command)
>
>
>
> Hope that helps :)
>
>
>
> -Colin
>
>
>
> On Mon, Dec 11, 2023 at 7:12 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey Colin,
>
>
>
> Are you referring to how I installed npm or Node.js? Or how I
> installed/unpacked JBrowse2? I believe JBrowse2 was done under my user but
> perhaps npm was installed using root. I'll have to double check but I
> suppose that can cause some discrepancies.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> Get Outlook for Android <https://aka.ms/AAb9ysg>
> ------------------------------
>
> *From:* Colin <col...@gm...>
> *Sent:* Monday, December 11, 2023 4:40:06 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] Callback function error with dbxrefs
>
>
>
> [△EXTERNAL]
>
>
>
> The note that you made about running as root may be a clue. You might have
> somehow installed it twice, once as a root user, and once as a non-root
> user. I would just try to be consistent, e.g. always use the root account
> (or equivalently basically, always use "sudo jbrowse ...") or always
> unpriviledged. There may be some way to "only install as a root, and then
> run the rest of the time as a non-root user" but I can't necessarily advise
> on all the cases on how this may affect. You might have installed a version
> as a non-root user, for example, my email above actually is an example of
> that, my library is in
>
> /home/cdiesh/.fnm/node-versions/v20.10.0/installation/lib because I use
> "fnm" for managing multiple node versions and so that could be where your
> v2.6.3 is coming from, and that shadows the system version of v2.9.0
>
>
>
>
>
>
>
>
>
> On Mon, Dec 11, 2023 at 4:47 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey Colin,
>
>
>
> I get the same output from the ‘npm install’ command as you except that
> it’s “changed 297 packages” instead of added so I assume it’s working but
> the version check doesn’t show the new version number.  Perhaps this might
> give more of a clue to what’s going on, when I run the ‘npm list’ command I
> get this:
>
>
>
> XenJBrowse2# npm list -g
>
> /usr/lib
>
> ├── @jbrowse/cli@2.9.0
>
> ├── corepack@0.22.0
>
> └── npm@10.2.3
>
>
>
> Interesting that here it lists the latest JBrowse release #, but I’m not
> seeing that change in my main JBrowse 2 folder.  Does this give any other
> clue to what might be going on?  I need to switch to root when running the
> npm install command to have access to the full suite of npm commands, but
> not sure if that conflicts with anything here.
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Friday, December 8, 2023 3:29 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Callback function error with dbxrefs
>
>
>
> [△EXTERNAL]
>
>
>
> Hi there,
>
> Running the "npm install -g @jbrowse/cli" should get the latest version,
> so then, running "jbrowse --version" should report the latest version
> (currently, 2.9.0)
>
>
>
> So for me
>
>
>
> % npm install -g @jbrowse/cli
>
> added 297 packages in 12s
>
> 45 packages are looking for funding
>   run `npm fund` for details
>
> ~ took 12s
> % jbrowse --version
> @jbrowse/cli/2.9.0 linux-x64 node-v20.10.0
>
>
>
> I am not sure why this is not happening in your case. You can try running
>
>
>
> "npm list -g"
>
>
>
> This will list globally installed npm packages and their locations. So for
> me, it outputs a folder named
>
>
>
> /home/cdiesh/.fnm/node-versions/v20.10.0/installation/lib
>
>
>
> And then a folder in that same directory is where all the binaries that
> are in your path should be
>
>
>
> /home/cdiesh/.fnm/node-versions/v20.10.0/installation/bin
>
>
>
> If you have manually manipulated your PATH variable to try to add npm
> binaries to your PATH, you might consider adjusting that or removing the
> custom PATH for npm entirely (it should be automatic under most
> installations)
>
>
>
> Note: we removed the gt gff3 -sortlines because it outputted inaccurate
> sorting that would be rejected by tabix under certain circumstances. There
> was also an awk command and this also was bugged. We replaced it with a new
> built-in jbrowse CLI command, the sort-gff
>
>  to try to avoid the external dependency and make it easier to run
> (hopefully!)
>
>
>
> Let me know if that helps
>
> -Colin
>
>
>
> On Fri, Dec 8, 2023 at 2:53 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey Colin,
>
>
>
> Speaking of changes to the doc pages, I noticed someone might have changed
> the tutorial page for adding JBrowse tracks? This page:
>
>
>
>
> https://jbrowse.org/jb2/docs/quickstart_web/#adding-a-gff3-file-with-gff3tabix
>
>
>
> I believe it used to say ‘gt gff3 …..’ for the command to initially sort
> the gff3.  Now it uses the ‘jbrowse sort-gff’ command which I don’t seem to
> have in my release of JBrowse tools.  This relates to my issue.  I
> attempted to upgrade JBrowse to the latest release, also it because has
> some addons/fixes I’m interested in, but it didn’t seem to work.  I used
> these commands from the tutorial page:
>
>
>
> jbrowse upgrade
>
> npm install -g @jbrowse/cli
>
>
>
> I didn’t receive any errors.  However when I try the new jbrowse sort-gff
> command it’s not found.  My version is still listed as such:
>
>
>
> jbrowse --version
>
> @jbrowse/cli/2.6.3 linux-x64 node-v20.9.0
>
>
>
> Do you know if I’m missing something needed to upgrade to the latest
> release?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *From:* Vaneet Lotay <van...@uc...>
> *Sent:* Monday, November 27, 2023 4:41 PM
> *To:* Colin <col...@gm...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Callback function error with dbxrefs
>
>
>
> [△EXTERNAL]
>
>
>
> That was the issue for me, thank you for fixing this! My dbxref links work
> fine now.
>
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Monday, November 27, 2023 3:43 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Callback function error with dbxrefs
>
>
>
> [△EXTERNAL]
>
>
>
> I made a code fix to this link
> https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/#example-a-generalized-solution-to-dbxrefs
> just yesterday after I saw this thread, the diff was
>
>
>
>
>
> old
>
>   ;(typeof self !== 'undefined' ? self : window).JBrowsePluginMyPlugin = {
>     default: Plugin, // this variable "Plugin" wasn't defined
>   }
>
>
>
> new
>
>
>
>
>   ;(typeof self !== 'undefined' ? self : window).JBrowsePluginMyPlugin = {
>     default: MyPlugin, // fixed! this refers to class MyPlugin. change to
> DbxrefPlugin or whatever the name of your class is
>   }
>
>
>
> On Mon, Nov 27, 2023 at 4:59 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey Colin,
>
>
>
> Thanks I did catch that mistake for the plugin name, which I forgot to
> change in one place.  Now I’ve got this error in the browser:
>
>
>
> TypeError: Illegal constructor.
>
>
>
> I tried to see what could be causing this but haven’t located it yet. Any
> ideas?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Sunday, November 26, 2023 8:03 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Callback function error with dbxrefs
>
>
>
> [△EXTERNAL]
>
>
>
> Hi there
>
> I think if you copied from here
> https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/#example-a-generalized-solution-to-dbxrefs
> then also have to rename JBrowsePluginMyPlugin ->
> JBrowsePluginDbxrefPlugin. You can see that the error message is looking
> for that variable name because that is what you named it in your
> config.json (it looks for the name JBrowsePlugin+name from the
> config.json), so I think that should help
>
>
>
> -Colin
>
>
>
>
>
> Footnote: it is definitely a little tricky that you have to meticulously
> have the right name for the plugin in so many places. Hopefully in the
> future it might not require this if we switch to so called "esm plugins".
> ESM plugins are already supported by jbrowse 2 but some browsers don't have
> great support for them yet, so they aren't our default example in the
> documentation, but we may update our examples to them in the future
>
>
>
> On Thu, Nov 23, 2023 at 3:15 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hi all,
>
>
>
> I followed the same structure that was outlined in the docs section at
> jbrowse.org (‘generalized solution to dbxrefs’) with different content
> obviously.  I created a dbxrefPlugin.js file with a ‘linkout’ function
> under a plugin named DbxrefPlugin.  When trying to load the genome for
> which I’m attempting to use the callback function I see this error:
>
>
>
> *Failed to load UMD bundle for DbxrefPlugin, JBrowsePluginDbxrefPlugin is
> undefined*
>
>
>
> Any idea where I’m going wrong?  I can attach some code if it’s not
> something simple or obvious I’m missing here.
>
>
>
> Just at the preliminary stages of trying to understand how JBrowse2
> functions behind the scenes, so I may have other moments like this in the
> future 😊
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>