gmod-ajax — JBrowse list

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

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

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...<mailto: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...<mailto:col...@gm...>>
Sent: Monday, December 11, 2023 4:40:06 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto:gmo...@li...> <gmo...@li...<mailto: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...<mailto: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<mailto:corepack@0.22.0>

└── npm@10.2.3<mailto: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...<mailto:col...@gm...>>
Sent: Friday, December 8, 2023 3:29 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto: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...<mailto: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...<mailto:van...@uc...>>
Sent: Monday, November 27, 2023 4:41 PM
To: Colin <col...@gm...<mailto:col...@gm...>>
Cc: gmo...@li...<mailto: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...<mailto:col...@gm...>>
Sent: Monday, November 27, 2023 3:43 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto: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...<mailto: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...<mailto:col...@gm...>>
Sent: Sunday, November 26, 2023 8:03 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto: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...<mailto:van...@uc...>> wrote:

Hi all,



I followed the same structure that was outlined in the docs section at jbrowse.org<http://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...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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

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

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
>
>

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

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

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...<mailto: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<mailto:corepack@0.22.0>

└── npm@10.2.3<mailto: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...<mailto:col...@gm...>>
Sent: Friday, December 8, 2023 3:29 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto: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...<mailto: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...<mailto:van...@uc...>>
Sent: Monday, November 27, 2023 4:41 PM
To: Colin <col...@gm...<mailto:col...@gm...>>
Cc: gmo...@li...<mailto: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...<mailto:col...@gm...>>
Sent: Monday, November 27, 2023 3:43 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto: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...<mailto: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...<mailto:col...@gm...>>
Sent: Sunday, November 26, 2023 8:03 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto: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...<mailto:van...@uc...>> wrote:

Hi all,



I followed the same structure that was outlined in the docs section at jbrowse.org<http://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...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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

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

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
>
>

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

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

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<mailto:corepack@0.22.0>
└── npm@10.2.3<mailto: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...<mailto: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...<mailto:van...@uc...>>
Sent: Monday, November 27, 2023 4:41 PM
To: Colin <col...@gm...<mailto:col...@gm...>>
Cc: gmo...@li...<mailto: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...<mailto:col...@gm...>>
Sent: Monday, November 27, 2023 3:43 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto: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...<mailto: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...<mailto:col...@gm...>>
Sent: Sunday, November 26, 2023 8:03 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto: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...<mailto:van...@uc...>> wrote:
Hi all,

I followed the same structure that was outlined in the docs section at jbrowse.org<http://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...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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

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

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
>
>

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

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

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...<mailto:col...@gm...>>
Sent: Monday, November 27, 2023 3:43 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto: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...<mailto: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...<mailto:col...@gm...>>
Sent: Sunday, November 26, 2023 8:03 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto: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...<mailto:van...@uc...>> wrote:
Hi all,

I followed the same structure that was outlined in the docs section at jbrowse.org<http://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...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] text-index problem

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

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] text-index problem

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

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] text-index problem

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

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
>

[Gmod-ajax] text-index problem

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

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

Re: [Gmod-ajax] JBrowse office hours and community meetings

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

Our first community meeting was great thanks to all who joined! We had a
total of 5 people including 3 of our core team!

Our next community meeting is today, 5pm Pacific time, Nov 28 (yes evening
time instead of morning time, we are alternating biweekly)

JBrowse 2 community meeting (Asia Pacific-friendly)
Tuesday, November 28 · 8:00 – 9:00pm
Time zone: America/New_York
Google Meet joining info
Video call link: https://meet.google.com/rnq-exdt-tuz

More info https://jbrowse.org/jb2/contact/ !

Hope to see you there,
-Colin



On Thu, Nov 16, 2023 at 9:34 AM Colin <col...@gm...> wrote:

> First community meeting in ~30min
>
>
> JBrowse 2 community meeting (Europe/North America-friendly)
> Thursday, November 16 · 10:00 – 11:00am
> Time zone: America/New_York
> Google Meet joining info
> Video call link: https://meet.google.com/uti-xsjf-xbu
>
>
> -Colin
>
> On Mon, Nov 13, 2023 at 2:04 PM Colin <col...@gm...> wrote:
>
>> Hello all,
>> We just recently started a new outreach effort to have open community
>> meetings that anyone can join, as well as "office hours" where you can
>> schedule 1-on-1 appointments with members of the JBrowse dev team.
>>
>> Link to our office hours scheduling calendar here:
>>  https://calendar.google.com/calendar/u/0/appointments/schedules/AcZssZ2WIB6bwPtShkYDn49c-ADXvpxfa6iyaEP453Uvy-e-RDZPZF5rsbTRbRlXrWelVpSicZJQsdn5
>> <https://calendar.google.com/calendar/u/0/appointments/schedules/AcZssZ2WIB6bwPtShkYDn49c-ADXvpxfa6iyaEP453Uvy-e-RDZPZF5rsbTRbRlXrWelVpSicZJQsdn5>
>>
>> Links for Google Meet for the community calls. The first community call
>> will be this week on Thursday:
>>
>>    - Monthly on the third Thursday, 10am EST (North America, Europe
>>    friendly) <https://meet.google.com/rnq-exdt-tuz>
>>    - Monthly on the last Tuesday, 8pm EST (Asia Pacific friendly)
>>    <https://meet.google.com/uti-xsjf-xbu>
>>
>> Google calendar link to add both community calls to your calendar:
>>
>>    - Add both events to your Google calendar
>>    <https://calendar.google.com/calendar/u/2?cid=ZDgxZmE0Yjk3YjdiZTAxYThjMDAzYzNkOThkMjUyOGQ1ZWM4YzNkMzRjNjgwMmQ3YjZhOWEwYmU4NDYxZDBiM0Bncm91cC5jYWxlbmRhci5nb29nbGUuY29t>
>>
>> Feel free to let us know if you have any questions, and feel free to
>> share this with anyone you think might be interested https://jbrowse.org/jb2/contact/
>> <https://jbrowse.org/jb2/contact/>
>>
>> -Colin
>>
>

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

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

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...<mailto:van...@uc...>> wrote:
Hi all,

I followed the same structure that was outlined in the docs section at jbrowse.org<http://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...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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

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

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
>
>

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

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

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...<mailto: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...<mailto:col...@gm...>>
Sent: Sunday, November 26, 2023 8:03 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto: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...<mailto:van...@uc...>> wrote:
Hi all,

I followed the same structure that was outlined in the docs section at jbrowse.org<http://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...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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

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

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
>

[Gmod-ajax] Callback function error with dbxrefs

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

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

Re: [Gmod-ajax] JBrowse office hours and community meetings

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

First community meeting in ~30min


JBrowse 2 community meeting (Europe/North America-friendly)
Thursday, November 16 · 10:00 – 11:00am
Time zone: America/New_York
Google Meet joining info
Video call link: https://meet.google.com/uti-xsjf-xbu


-Colin

On Mon, Nov 13, 2023 at 2:04 PM Colin <col...@gm...> wrote:

> Hello all,
> We just recently started a new outreach effort to have open community
> meetings that anyone can join, as well as "office hours" where you can
> schedule 1-on-1 appointments with members of the JBrowse dev team.
>
> Link to our office hours scheduling calendar here:
>  https://calendar.google.com/calendar/u/0/appointments/schedules/AcZssZ2WIB6bwPtShkYDn49c-ADXvpxfa6iyaEP453Uvy-e-RDZPZF5rsbTRbRlXrWelVpSicZJQsdn5
> <https://calendar.google.com/calendar/u/0/appointments/schedules/AcZssZ2WIB6bwPtShkYDn49c-ADXvpxfa6iyaEP453Uvy-e-RDZPZF5rsbTRbRlXrWelVpSicZJQsdn5>
>
> Links for Google Meet for the community calls. The first community call
> will be this week on Thursday:
>
>    - Monthly on the third Thursday, 10am EST (North America, Europe
>    friendly) <https://meet.google.com/rnq-exdt-tuz>
>    - Monthly on the last Tuesday, 8pm EST (Asia Pacific friendly)
>    <https://meet.google.com/uti-xsjf-xbu>
>
> Google calendar link to add both community calls to your calendar:
>
>    - Add both events to your Google calendar
>    <https://calendar.google.com/calendar/u/2?cid=ZDgxZmE0Yjk3YjdiZTAxYThjMDAzYzNkOThkMjUyOGQ1ZWM4YzNkMzRjNjgwMmQ3YjZhOWEwYmU4NDYxZDBiM0Bncm91cC5jYWxlbmRhci5nb29nbGUuY29t>
>
> Feel free to let us know if you have any questions, and feel free to share
> this with anyone you think might be interested https://jbrowse.org/jb2/contact/
> <https://jbrowse.org/jb2/contact/>
>
> -Colin
>

[Gmod-ajax] JBrowse office hours and community meetings

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

Hello all,
We just recently started a new outreach effort to have open community
meetings that anyone can join, as well as "office hours" where you can
schedule 1-on-1 appointments with members of the JBrowse dev team.

Link to our office hours scheduling calendar here:
 https://calendar.google.com/calendar/u/0/appointments/schedules/AcZssZ2WIB6bwPtShkYDn49c-ADXvpxfa6iyaEP453Uvy-e-RDZPZF5rsbTRbRlXrWelVpSicZJQsdn5
<https://calendar.google.com/calendar/u/0/appointments/schedules/AcZssZ2WIB6bwPtShkYDn49c-ADXvpxfa6iyaEP453Uvy-e-RDZPZF5rsbTRbRlXrWelVpSicZJQsdn5>

Links for Google Meet for the community calls. The first community call
will be this week on Thursday:

   - Monthly on the third Thursday, 10am EST (North America, Europe
   friendly) <https://meet.google.com/rnq-exdt-tuz>
   - Monthly on the last Tuesday, 8pm EST (Asia Pacific friendly)
   <https://meet.google.com/uti-xsjf-xbu>

Google calendar link to add both community calls to your calendar:

   - Add both events to your Google calendar
   <https://calendar.google.com/calendar/u/2?cid=ZDgxZmE0Yjk3YjdiZTAxYThjMDAzYzNkOThkMjUyOGQ1ZWM4YzNkMzRjNjgwMmQ3YjZhOWEwYmU4NDYxZDBiM0Bncm91cC5jYWxlbmRhci5nb29nbGUuY29t>

Feel free to let us know if you have any questions, and feel free to share
this with anyone you think might be interested
https://jbrowse.org/jb2/contact/
<https://jbrowse.org/jb2/contact/>

-Colin

Re: [Gmod-ajax] JBrowse2 move track labels above tracks

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

v2.7.2 released now with the ability to configure the default track labels
setting. note that users are still allowed to change it for their
preference, so this config setting combines with a users current
localstorage preference, so if the config doesn't look like it is working
then try clearing localstorage and starting a new session

a config snippet in our volvox config shows how to use:

https://github.com/GMOD/jbrowse-components/blob/ab1d5d525d25841f1f057d762527646986836b77/test_data/volvox/config.json#L189-L192

basically, in your config.json:

{
  "configuration": {
    "LinearGenomeViewPlugin": {
      "trackLabels": "offset"
    }
}

-Colin

On Wed, Oct 25, 2023 at 8:38 PM David Goodstein <dmg...@lb...> wrote:

> We (Phytozome) second that request; extremely useful feature.
>
>
> -David
>
>
> David M. Goodstein, Ph.D.
> Phytozome & Plant Comparative Analysis Group
> Joint Genome Institute
> US Dept. of Energy - Lawrence Berkeley National Lab
> https://phytozome.jgi.doe.gov
>
>
>
>
> On Oct 25, 2023, at 3:59 PM, Colin <col...@gm...> wrote:
>
> Users can manually change the track labels setting in the UI, but it's not
> formally a config variable you can set, but you can make a config with a
> defaultSession that has this setting turned on though, and then that is a
> way of setting this via the config
>
>
> https://jbrowse.org/jb2/docs/user_guides/basic_usage/#track-label-positioning
>
> We can try to brainstorm a way to make this a single config slot though
>
> -Colin
>
> On Wed, Oct 25, 2023, 2:23 PM Vaneet Lotay <van...@uc...>
> wrote:
>
>> Hello,
>>
>>
>> In JBrowse1 there was a nice feature to prevent track labels from
>> blocking or overlapping with the track itself:
>>
>>
>>
>> trackLabels
>>
>>
>>
>> Set "trackLabels": "no-block" to enable the trackLabels to be out of the
>> way of the features. Added in 1.12.5
>>
>>
>>
>>
>>
>> I tried adding this to the global configuration section of config.json,
>> but that didn’t work.  Is this feature possible in JBrowse2?
>>
>>
>>
>> Tjamls.
>>
>>
>>
>> Vameet
>>
>>
>>
>> *Vaneet Lotay*
>>
>> *Xenbase Bioinformatician*
>>
>> *University of Calgary*
>>
>> *2500 University Drive NW*
>>
>> *Calgary, AB T2N 1N4*
>>
>> *CANADA*
>>
>>
>> _______________________________________________
>> 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] Question from CSHL course participant

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

Hi Gabriel,

I'm cc'ing the JBrowse mailing list in case anybody else from the community
wants to chime in. I'll try to address your questions inline below

On Wed, Oct 25, 2023 at 1:22 PM Barcia Durán, José Gabriel <
Gab...@ny...> wrote:

> Hi Scott,
>
>
> I'm an instructor at NYU Langone—the one who kept asking about JBrowse 2
> this afternoon. Thanks for your presentation; it was really useful.
>
>
> Thanks for saying so!


> I've been using IGV for years, so I'm quite please to learn there's a user
> friendly, more modern alternative.
>
>
> Would you mind clarifying a couple things for me?
>
>
> I'd use JBrowse 2 to visualize RNA-seq, ATAC-seq, ChIP-seq, and Hi-C data
> and produce figures for publication. It seems I'd only need to use the
> desktop tool—does that sound right?
>

Yes, anything that can be done in the web interface can be done with the
desktop tool as well, so if you're not interested in sharing the data on
the web (or not interested now--you can always decide to later!), the
desktop app should be fine. For RNA-seq, ATAC-seq and Chip-Seq, anything
that can be expressed either as a BAM/CRAM (for alignment) or as a BigWig
(for coverage, though the BAM/CRAM adapter can calculate coverage too) can
be displayed in JBrowse. I was about to write that Hi-C needed an external
plugin but I just checked one of my JBrowse instances and saw that it's
installed by default (I don't think it used to be). I don't have much
experience with that type of data, but there is a config guide for it on
the website:

  https://jbrowse.org/jb2/docs/config_guides/hic_track/

The "add track" dialog supports Hi-C data, so it should work in exactly the
same way as the example when I added a GFF file during the class.

>
> I am curious to be able to see the same genes in two species, with their
> associated data (e.g., RNA-seq), on different tracks but the same
> visualization. Would that be possible for human and mouse genes? Do I need
> a special config to be able to do this? I don't think I see the mouse
> genome come up in the available tracks on the right.
>

Yes, it is certainly possible. The JBrowse instance I'm creating for the
Alliance of Genome Resources will have that (ie, hg38 and mm39). You can
have multiple genomes displayed in a view. Not just with synteny views like
I showed in class, but two separate genomes can be displayed by using the
"Add" menu and selecting "Linear Genome View" which will give you a dialog
to pick another genome (or the same one, if you'd like to view to locations
of the same genome at once).  Here's an example from my dev JBrowse
instance--the only downside is that the mouse tracks are pretty barebones,
but you could always use the add tracks option to add your own :-)

https://stage.dgaayxgqoarxf.amplifyapp.com/?session=share-sZAZdFpp6d&password=fstZ2

Also, with the synteny view like this one:

https://stage.dgaayxgqoarxf.amplifyapp.com/?session=share-qiDQVIpEqW&password=iiukF

You can add any tracks you want to either the human or the mouse views, and
either ones that are provided with the browser or tracks of your own.
The glyph/button in the upper left corner that looks like three tiny
checkboxes with lines next to them will open the track selector for either
the upper or lower assembly.
The only caveat I have is that you might want to make sure you have a nice
tall browser because I have definitely turned my external monitor on its
side sometimes
to see all of the tracks I want to add :-)


> Lastly, I'm also interested in lncRNAs—is JBrowse a good tool to visualize
> those annotations? Would I be able to add my own annotations, in the event
> the transcripts I'm interested in are missing?
>

 As far as I know JBrowse is good a visualizing lncRNAs, but you tell me:

https://stage.dgaayxgqoarxf.amplifyapp.com/?session=share-IHNTRxxy_y&password=7Awgt

(I don't know a lot about lncRNAs either--to me it's just another gene type
with coordinates that I want to display. If there is something you think it
could do better to improve the expressiveness of the display, let me know!)

As for adding your own--it depends on what you mean and want to have
happen. If for example, you run an analysis or have predictions or the like
that indicate the presence of a lncRNA and you get those results in a
common format (GFF, Bed or GTF would be the most common examples), you can
use that to add a new track of "your" lncRNAs. If you want them displayed
in the same track as the annotations that come from the source (RGD for
human and MGI for mouse in the JBrowse links above), you would have to go
through a little more effort to merge the source GFF files and then
"re-add" them to JBrowse. Lastly, if you wanted to use a graphical editor
to create the gene annotations yourself, you'd have to go down the route of
getting Apollo, which is probably more work than you'd want to do depending
on the size of your project.

I hope this all at least makes some sense; please let us know if you have
more questions!

Scott


> Thanks again,
>
>
> Gabriel
>


-- 
------------------------------------------------------------------------
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 move track labels above tracks

[David G. <dmg...@lb...>]

We (Phytozome) second that request; extremely useful feature.


-David


David M. Goodstein, Ph.D.
Phytozome & Plant Comparative Analysis Group
Joint Genome Institute
US Dept. of Energy - Lawrence Berkeley National Lab
https://phytozome.jgi.doe.gov




> On Oct 25, 2023, at 3:59 PM, Colin <col...@gm...> wrote:
> 
> Users can manually change the track labels setting in the UI, but it's not formally a config variable you can set, but you can make a config with a defaultSession that has this setting turned on though, and then that is a way of setting this via the config
> 
> https://jbrowse.org/jb2/docs/user_guides/basic_usage/#track-label-positioning
> 
> We can try to brainstorm a way to make this a single config slot though
> 
> -Colin
> 
> On Wed, Oct 25, 2023, 2:23 PM Vaneet Lotay <van...@uc... <mailto:van...@uc...>> wrote:
>> Hello,
>> 
>> 
>> In JBrowse1 there was a nice feature to prevent track labels from blocking or overlapping with the track itself:
>> 
>>  
>> 
>> trackLabels
>> 
>>  
>> 
>> Set "trackLabels": "no-block" to enable the trackLabels to be out of the way of the features. Added in 1.12.5
>> 
>>  
>> 
>>  
>> 
>> I tried adding this to the global configuration section of config.json, but that didn’t work.  Is this feature possible in JBrowse2?
>> 
>>  
>> 
>> Tjamls.
>> 
>>  
>> 
>> Vameet
>> 
>>  
>> 
>> Vaneet Lotay
>> 
>> Xenbase Bioinformatician
>> 
>> University of Calgary
>> 
>> 2500 University Drive NW
>> 
>> Calgary, AB T2N 1N4
>> 
>> CANADA
>> 
>>  
>> 
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li... <mailto: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 move track labels above tracks

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

Users can manually change the track labels setting in the UI, but it's not
formally a config variable you can set, but you can make a config with a
defaultSession that has this setting turned on though, and then that is a
way of setting this via the config

https://jbrowse.org/jb2/docs/user_guides/basic_usage/#track-label-positioning

We can try to brainstorm a way to make this a single config slot though

-Colin

On Wed, Oct 25, 2023, 2:23 PM Vaneet Lotay <van...@uc...> wrote:

> Hello,
>
>
> In JBrowse1 there was a nice feature to prevent track labels from blocking
> or overlapping with the track itself:
>
>
>
> trackLabels
>
>
>
> Set "trackLabels": "no-block" to enable the trackLabels to be out of the
> way of the features. Added in 1.12.5
>
>
>
>
>
> I tried adding this to the global configuration section of config.json,
> but that didn’t work.  Is this feature possible in JBrowse2?
>
>
>
> Tjamls.
>
>
>
> Vameet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse2 move track labels above tracks

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

Hello,

In JBrowse1 there was a nice feature to prevent track labels from blocking or overlapping with the track itself:

trackLabels

Set "trackLabels": "no-block" to enable the trackLabels to be out of the way of the features. Added in 1.12.5


I tried adding this to the global configuration section of config.json, but that didn't work.  Is this feature possible in JBrowse2?

Tjamls.

Vameet

Vaneet Lotay
Xenbase Bioinformatician
University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

Re: [Gmod-ajax] [apollo] Translation of JBrowse1 REST API to JBrowse2

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

Hi Michael
Sorry for delay in reply, definitely feel free to let us know if you have
any updates or questions. Regarding docs, main portal is here
https://jbrowse.org/jb2/docs

Developer docs related to things like plugins are here, for example,
creating an adapter which can be used for adapting to a REST APIs
https://jbrowse.org/jb2/docs/developer_guides/creating_adapter/ and then
our embedded components that you refer to have links to 'storybook demos'
and other docs here https://jbrowse.org/jb2/docs/embedded_components/


If you are accustomed to JBrowse 1 terminology, here is a rough mapping

JBrowse 1->JBrowse 2
storeClass->adapter (there is no more urlTemplate, you look at the config
docs https://jbrowse.org/jb2/docs/config_guides/alignments_track/ or
"auto-generated config docs" for each little schema type
https://jbrowse.org/jb2/docs/config/bamadapter/ and you will see that there
is instead things like bamLocation, gffGzLocation, etc. sort of different
for each track type)
trackList->track label->config.json track trackId
trackList track key->config.json track name
bin/prepare-refseqs.pl->jbrowse add-assembly (assemblies have a special
area of the config that provides a ReferenceSequenceTrack)
bin/flatfile-to-json.pl->jbrowse add-track

For custom sequence fetching and feature fetching, may require hand-editing
the config.json. The config.json you linked uses the "biothings" plugin to
fetch from mygene.info and myvariant.info. Example code for that here
https://github.com/cmdcolin/jbrowse-plugin-biothings-api/blob/master/src/MyGeneAdapter.ts.
Can add more info about plugins if interested


-Colin



On Thu, Oct 12, 2023 at 9:52 PM Michael Thang <m....@qf...> wrote:

> Hi Colin,
> Thank you for speedy reply and clarification ! I can relate the REST API
> (aka mygene.info) to a project I am working on and using this Django
> framework to embed jbrowse into it (machado
> <https://machado.readthedocs.io/en/latest/jbrowse.html>). I am keen to
> use Jbrowse2 but the main issue is how to translate the trackList.json to
> config.json for my project. As you mentioned above, most of the Jbrowse1
> options are dropped for Jbrowse2. I guess I need to investigate a bit more
> to see how much work I need to use Jbrowse2 for my project. The good news
> is the Machado Framework does come with API
> <https://www.machado.cnptia.embrapa.br/demo_machado/api/> setup and I am
> trying to understand how to combine the API and the Jbrowse2 in the
> config.json (Jbrowse2) based on the trackList.json
> <https://github.com/lmb-embrapa/machado/blob/master/extras/trackList.json.sample>
> (Jbrowse1) format.
>
> I think this is the config.json
> <https://github.com/cmdcolin/jbrowse-plugin-biothings-api/blob/master/config.json>
> you use to retrieve reference genome and tracks using API call. For me, it
> is a bit difficult to understand the options you use in the config.json. I
> believe there must be a documentation somewhere . can you please point me
> to the documentation if available?
>
> To date, I managed to setup the Jbrowse2 running on my apache server
> without any problems. What I want to explore next is to work on the REST
> API call to query and show the tracks/assemblies of interest on an embedded
> Jbrowse2. However, I am kind of stuck at the moment.
>
> Best
>
> On Friday, October 13, 2023 at 11:16:28 AM UTC+10 Colin wrote:
>
>> Hi Michael,
>>
>> Many of the JBrowse 1 options do not automatically apply to JBrowse 2
>> because the config.json format is quite a bit different from trackList.json.
>>
>>
>> I also see that your trackList.json refers to a "REST" data adapter from
>> JBrowse 1 (JBrowse/Store/SeqFeature/REST) but this data adapter type was
>> not added to JBrowse 2. We did not add this to JBrowse 2 because it is hard
>> or awkward to design a "blessed"  or "recommended" REST API format that we
>> want users to implement.  If you do want to make an adapter for your REST
>> API, you can write a custom plugin to do so. I may be biased because I
>> wrote a lot of data adapters for various REST APIs on the web as plugins (
>> mygene.info adapter, UCSC rest api adapter, etc) but my feeling is that
>> it  is relatively little code (100-200 lines for example) and it can
>> actually be useful, as a developer, to be in control of the client code
>> that is accessing your particular REST API.
>>
>> If your main concerns are getting a JBrowse 1 REST API working with
>> JBrowse 2 I can elaborate, or I can help with any of the other JBrowse 2
>> upgrade steps too :)
>>
>>
>> -Colin
>>
>> On Thu, Oct 12, 2023 at 11:42 AM Nathan Dunn <ndu...@gmail.com> wrote:
>>
>>>
>>>
>>> On Oct 11, 2023, at 11:40 PM, Michael Thang <m.t...@qfab.org> wrote:
>>>
>>> Hi Apollo Team,
>>> I would like to find out how to translate this Jbrowse1 trackList.json
>>> <https://github.com/hexylena/JBrowse-REST-API-Example/blob/master/data/trackList.json>
>>> to Jbrowse2. I just borrowed the trackList.json online, but I am running
>>> into the same situation where I have my Jbrowse1 configured to run API. I
>>> am exploring the posssiblity to use the same trackList.json format for
>>> Jbrowse2. However, the Jbrowse2 is using config.json instead and the json
>>> looks different. Therefore, I dont know if all these options
>>> <https://jbrowse.org/docs/global_options.html> are still applicable for
>>> Jbrowse2.
>>>
>>>
>>>
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