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GMOD/jbrowse2

JBrowse 2 development and support

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May 21 02:11

adamjohnwright commented #2968
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May 20 23:22

cmdcolin on main

[update docs] Add screenshot to… (compare)
May 20 21:30

cmdcolin commented #2949
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cmdcolin on mui5

Allow getting clip indicator af… Re-enable eslint autofix for pr… Support in-memory GFF3 and GTF … and 16 more (compare)
May 20 19:50

cmdcolin on main

[update docs] Bump demos (compare)
May 20 19:01

cmdcolin on v1.7.8

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May 20 19:01

cmdcolin on main

Prepare for v1.7.8 release [update docs] v1.7.8 (compare)
May 20 18:47

cmdcolin on v1.7.8_announce

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Add v1.7.8 announcement (#2966)… (compare)
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cmdcolin on v1.7.8_announce

[skip ci] highlights (compare)

bbimber

@bbimber

Another possibly dumb question: when making a plugin/widget, the component is rendered as a modal. Can I call something to close that window? if the user clicks off the modal it closes, but I dont see how to close it with code

Colin Diesh

@cmdcolin

possibly something like getSession(widgetModel).hideWidget(widgetModel.id)

bbimber

@bbimber

hideWidget(model) works, rather than model.id

Scott Cain

@scottcain

@rbuels @hawrobin @cmdcolin : outreach call? I’m in google hangout

Robert Buels

@rbuels

yep coming

Robin Haw

@hawrobin

Sorry I have a clash today!

Scott Cain

@scottcain

@rbuels @cmdcolin are we really having an outreach call Monday at 9:00am? It’s in my calendar, but I am doubting it.

Robert Buels

@rbuels

Hmm no I don’t know how that got on there

I’ll delete it

Scott Cain

@scottcain

👍

Colin Diesh

@cmdcolin

spotted a jb2 svg export in the wild https://twitter.com/ilyavkirov/status/1467854553563512847

and a embedded instance here http://portugalfishomics.ciimar.up.pt/app/scombercolias/

(from https://www.biorxiv.org/content/10.1101/2021.11.19.468211v1.full.pdf)

bbimber

@bbimber

Hey - i have a question on plugin config. We have a plugin that lets a user choose a custom coloring scheme. This include a custom renderer. By default, renders support the property 'color1', which can be JEXL to set feature color. Our custom renderer has another simple string property called 'palette'. If palette is non-null, we run code that takes that string, builds a JEXL expression, and then sets color1. This works fine if the user picks that interactively. However, I'd like to hook into somewhere such that if the initial rendererConfig JSON has 'palette', we execute code to set color1 right away. Is there a point where I can hook to add this kind of code?

4 replies

bbimber

@bbimber

Is there a way to remove a default menu item from a VCF track? we are currently adding menu items by overriding trackMenuItems() in a custom VariantDisplay class, but it's not clear whether i can remove default items

7 replies

Another question: our user base seems to have a hard time recognizing the track selector icon (we're using ReactLinearGenomeView). Has anyone encountered this and/or looked into more obvious ways to signal to users what to do? In our case, we load with one track pre-displayed, so there isnt the central 'Open Track Selector' button. For comparison, in JBrowse 1 the side panel was considerably more obvious

3 replies

Teresa Martinez

@teresam856

For anyone interested, here is a link to the jbrowse-jupyter https://github.com/GMOD/jbrowse-jupyter/tree/docs. All feedback is welcomed.

Junjun Zhang

@junjun-zhang

nice!

Robin Haw

@hawrobin

@scottcain @rbuels - do we want to do an ISMB 2022 tutorial? The deadline is monday.

Colin Diesh

@cmdcolin

rob is out on vacay right now just fyi

also, the tutorial for ismb says it's not generally used for presenting a specific software https://www.iscb.org/ismb2022-submissions/tutorials

Robin Haw

@hawrobin

opps, thx @cmdcolin. You are correct, it would be from a data viz or workflow persective. I was just looking over the tutorials from last year and they did not reflect a software demo style.

i was also surprised too see a relatively shortlist of tutorials! In previous years, their had been more.

Colin Diesh

@cmdcolin

i suppose if we want to focus more on jbrowse, probably go for a technology track like the link says

1 reply

Junjun Zhang

@junjun-zhang

anyone knows why we use a particular version of the mst library: "mobx-state-tree": "3.14.1", latest release is 5.1.0

Garrett Stevens

@garrettjstevens

I think it's because we use mobx v5, and mobx-state-tree >=v4 requires mobx v6. There are some breaking changes in mobx v6 and we haven't made it a priority to get things working with that version.

Also, we re-export mobx, mobx-state-tree, react, material-ui, and others for plugins to use, so if we upgrade them we risk breaking plugins. Those breaking changes may have to happen someday, but we'll have to plan for it.

Junjun Zhang

@junjun-zhang

thanks @garrettjstevens in terms of plugin, in the isoform inspector I am trying to use the same major versions of the main libraries as you listed, but still try to make sure it works with newer ones

Colin Diesh

@cmdcolin

docs for the d4 format now say it has some support for static http requests https://github.com/38/d4-format#reading-d4-file-served-by-static-http-server

Robin Haw

@hawrobin

@scottcain @cmdcolin - in view of rob being away, are we still meeting at 1?

Colin Diesh

@cmdcolin

hmm

i do want to try to make more progress on the pag workshop if possible. i dunno

Scott Cain

@scottcain

I’ve had no time this week to work on it unfortunately. AGR and WormBase releases have soaked up all my time, so I’d vote for putting it off

bbimber

@bbimber

Hey - I wanted to re-ask a question from earlier: does anyone have suggestions on coaxing an embedded LGV to make itself full page height? This would both be aesthetically preferable to us (otherwise we just have this white space), and at least in our hands it doesnt reliably auto-expand itself. The user can manually drag to open it, but that's not ideal here. Thanks for any ideas.

Colin Diesh

@cmdcolin

@scottcain @hawrobin ok. i suppose we can skip

@bbimber if you have a link that shows what you mean by not autoexpanding it may be useful

11 replies

bbimber

@bbimber

That screenshot is related to the thread above about autoexpanding LGV

Robin Haw

@hawrobin

@cmdcolin @scottcain can we meet sometime later next week?

Colin Diesh

@cmdcolin

@hawrobin we have a meeting scheduled again dec 17 if that helps

Colin Diesh

@cmdcolin

since christmas and new years will basically prevent us from meeting for awhile, would be good if we can flesh out that google doc before that dec 17 meeting

@scottcain @hawrobin maybe we can assign ourselves to one or more of the todo items here https://docs.google.com/document/d/11sEGtgM3pUjJJz0te_IhijbdVjHK_KWVOK2-z9eAMZk/edit#heading=h.7vukgf527z6j

Robin Haw

@hawrobin

sounds good!

Garrett Stevens

@garrettjstevens