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

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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

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________________________________
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

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