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

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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
>
>
>
>
>
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