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  • 16:16
    alexjacobsCDS opened #3126
  • 16:16
    alexjacobsCDS labeled #3126
  • Aug 05 20:51
    codecov[bot] commented #2929
  • Aug 05 20:50
    carolinebridge-oicr synchronize #2929
  • Aug 05 20:50

    carolinebridge-oicr on multilevel-linear-view

    lint (compare)

  • Aug 05 20:47
    codecov[bot] commented #2929
  • Aug 05 20:46
    carolinebridge-oicr synchronize #2929
  • Aug 05 20:46

    carolinebridge-oicr on multilevel-linear-view

    package test update (compare)

  • Aug 05 20:19
    codecov[bot] commented #2929
  • Aug 05 20:19
    carolinebridge-oicr synchronize #2929
  • Aug 05 20:19

    carolinebridge-oicr on multilevel-linear-view

    lint (compare)

  • Aug 05 20:08
    codecov[bot] commented #2929
  • Aug 05 20:08
    carolinebridge-oicr synchronize #2929
  • Aug 05 20:08

    carolinebridge-oicr on multilevel-linear-view

    bug with ascending limits add view above anchor bug (compare)

  • Aug 04 22:22
    garrettjstevens opened #3123
  • Aug 04 22:22
    garrettjstevens labeled #3123
  • Aug 04 22:17
    garrettjstevens labeled #3122
  • Aug 04 22:17
    garrettjstevens opened #3122
  • Aug 04 00:47
    garrettjstevens commented #3112
  • Aug 03 14:24
    Averstic commented #3094
Scott Cain
@scottcain
If I knew even a little bit about pop gen...
fromconfigadapter might not be insane—if generating the output isn’t too hard, I don’t care to much about the size of the output (I think—as long as it doesn’t crash the browser)
Scott Cain
@scottcain
Well, that didn’t take long: I installed anaconda on my M1 mac and then followed the install directions for jbrowse-jupyter and on the first attempted to actually do something, I did python browser.py and got the error message (in its entirety): Illegal instruction: 4, which is a very helpful message. It turns out this is a known thing in python/Mac circles, but I haven’t yet found a solution.
Colin Diesh
@cmdcolin
Scott Cain
@scottcain
Does anybody happen to know if there is a pythonish way to get sequence via an http range request from indexed fasta? I expected biopython to provide an API but it doesn’t look like it.
googling “indexed fasta http range python” returns very little (though a link to JBrowse is in the results)
Colin Diesh
@cmdcolin
run samtools faidx via a shell exec maybe
Scott Cain
@scottcain
I was hoping to do it in a notebook :-/
Colin Diesh
@cmdcolin
if it's for a demo, can use a smaller genome, and download it into the session
Scott Cain
@scottcain
Yep, that’s what I think I’ll have to do. Maybe “volvox"
Colin Diesh
@cmdcolin
many or most bacteria have an interesting statistic called gc skew that is fun to plot
Scott Cain
@scottcain
That’s a good idea; I’ll look at that
Colin Diesh
@cmdcolin
can see all the genes change orientation
Alexey Mukhin
@AcaDemIQ
After update JBrowse to 2.0.1 I've got several warnings. Is it normal?)

`` WARNING in ../../packages/core/pluggableElementTypes/renderers/ServerSideRendererType.tsx:4:32 TS7016: Could not find a declaration file for module 'canvas-sequencer'. '/home/mukhin/jbrowse-components/node_modules/canvas-sequencer/dist/index.js' implicitly has an 'any' type. Trynpm i --save-dev @types/canvas-sequencerif it exists or add a new declaration (.d.ts) file containingdeclare module 'canvas-sequencer';`
2 | import { DeprecatedThemeOptions } from '@mui/material'
3 | import { ThemeProvider } from '@mui/material/styles'

4 | import { CanvasSequence } from 'canvas-sequencer'
| ^^^^^^^^^^^^^^^^^^
5 | import { renderToString } from 'react-dom/server'
6 |
7 | import {

WARNING in ../../packages/core/pluggableElementTypes/renderers/ServerSideRendererType.tsx:182:32
TS7016: Could not find a declaration file for module 'canvas2svg'. '/home/mukhin/jbrowse-components/node_modules/canvas2svg/canvas2svg.js' implicitly has an 'any' type.
Try npm i --save-dev @types/canvas2svg if it exists or add a new declaration (.d.ts) file containing declare module 'canvas2svg';
180 | const { width, height, canvasRecordedData } = results
181 |

182 | const C2S = await import('canvas2svg')
| ^^^^^^^^^^^^
183 | const ctx = new C2S.default(width, height)
184 | const seq = new CanvasSequence(canvasRecordedData)
185 | seq.execute(ctx)

WARNING in ../../packages/core/PluginLoader.ts:1:27
TS7016: Could not find a declaration file for module 'load-script2'. '/home/mukhin/jbrowse-components/node_modules/load-script2/index.js' implicitly has an 'any' type.
Try npm i --save-dev @types/load-script2 if it exists or add a new declaration (.d.ts) file containing declare module 'load-script2';

1 | import domLoadScript from 'load-script2'
| ^^^^^^^^^^^^^^
2 |
3 | import { PluginConstructor } from './Plugin'
4 | import { ConfigurationSchema } from './configuration'

WARNING in ../../packages/core/rpc/WebWorkerRpcDriver.ts:60:40
TS2554: Expected 0 arguments, but got 1.
58 | const instance = this.makeWorkerInstance()
59 |

60 | const worker = new WebWorkerHandle({ workers: [instance] })
| ^^^^^^^^^^^^^^^^^^^^^^^
61 |
62 | // send the worker its boot configuration using info from the pluginManager
63 | const p = new Promise((resolve: (w: WebWorkerHandle) => void, reject) => {

WARNING in ../../packages/core/rpc/WebWorkerRpcDriver.ts:64:37
TS7006: Parameter 'e' implicitly has an 'any' type.
62 | // send the worker its boot configuration using info from the pluginManager
63 | const p = new Promise((resolve: (w: WebWorkerHandle) => void, reject) => {

64 | worker.workers[0].onmessage = e => {
| ^
65 | if (e.data === 'ready') {
66 | resolve(worker)
67 | } else if (e.data === 'readyForConfig') {

WARNING in ../../packages/core/util/offscreenCanvasPonyfill.tsx:5:32
TS7016: Could not find a declaration file for module 'canvas-sequencer'. '/home/mukhin/jbrowse-components/node_modules/canvas-sequencer/dist/index.js' implicitly has an 'any' type.
Try npm i --save-dev @types/canvas-sequencer if it exists or add a new declaration (.d.ts) file containing declare module 'canvas-sequencer';
3 | import isNode from 'detect-node'
4 |

5 | import { CanvasSequence } from 'canvas-sequencer'
| ^^^^^^^^^^^^^^^^^^
6 |
7 | // eslint-disable-next-line @typescript-eslint/no-explicit-any
8 | type AbstractCanvas = any

WARNING in ../../packages/core/util/offscreenCanvasUtils.tsx:3:32
.... ```

Colin Diesh
@cmdcolin
@AcaDemIQ this is basically expected, i see this also using yarn start
in the jbrowse-web folder
it's just the typechecking that 'create-react-app' seems to try to do is not recognizing the 'declare module' statements we already have for these modules
users of embedded or users that download the release from github/jbrowse cli tool wont see this though
its just a dev version of jbrowse web
also, fun news, gonna try our biorxiv submission!
Colin Diesh
@cmdcolin
alrighty, it is submitted
Teresa Martinez
@teresam856
🥳🎉
Scott Cain
@scottcain
Looking at this https://github.com/GMOD/jbrowse-jupyter/blob/865fdef07c1316f6057fc24db5003f4d83a62049/jbrowse_jupyter/jbrowse_config.py#L26-L37 makes me think it’s not currently possible to use assemblies other than hg19 or hg38 in jupyter. Am I missing something?
Colin Diesh
@cmdcolin
not sure but there is a set_assembly param here https://gmod.github.io/jbrowse-jupyter/docs/html/jbrowse_jupyter.html
Colin Diesh
@cmdcolin
might run a v2.1.0 release!
Colin Diesh
@cmdcolin
wooo
it's out now
Scott Cain
@scottcain
:tada:
Scott Cain
@scottcain
I think I found a bug in jbrowse-jupyter, but as I’m a bit of a python newb I thought I’d ask for a second opinion. In this notebook: https://colab.research.google.com/drive/1Bq19-i4FNKVqfrMiTxgunYFZuMrmP-ql (which I think I set the permissions correctly for y’all to open), there is a call to add_df_trackthat is failing because the code is checking that it’s a linear genome view by looking for “LGV” in a view attribute. This fails because (I think) there is no mention of “LGV” anywhere in the config that’s been created. The closest thing is in defaultSession.view.type, which is “LinearGenomeView”. The problem is, I don’t see a way of setting the view type anywhere else, either when the config is created or after with a “set_view_type” or similar method.
…I just remembered in Teresa’s demo there is a call to that method, so I need to go back to it to figure out what’s different.
Robert Buels
@rbuels
@cmdcolin @scottcain outreach call?
Scott Cain
@scottcain
Oh, I totally forgot
Sure we can chat
Robert Buels
@rbuels
come on in
Robert Buels
@rbuels
@teresam856 hey would you be willing to have a meeting with @scottcain to set him up with a development environment for jbrowse-jupyter and go over the release process?
Scott Cain
@scottcain
Oh, this notebook is soooo close to working: there are a few hacks I had to do to make it get to this point but those seem ok. It is now failing when trying to open jbrowse, where it spews MANY error messages to the console. :-/ I have no idea what’s wrong at this point https://colab.research.google.com/drive/1Bq19-i4FNKVqfrMiTxgunYFZuMrmP-ql
Teresa Martinez
@teresam856
Of course, I don’t have access to my computer today because I’m out of town but @scottcain we can definitely set up a time to pair of you would like me to help out with the dev env. You can also send me a link to your notebook and I can take a look in the meantime
Oh I’ll check out the colab notebook and see what may be going on
Teresa Martinez
@teresam856
I ran the notebook and seemed to work all the way until I hit the human demo, and that’s because hg38 was not defined. Not sure if any changes were done to the notebook but I will take a better look once I get access to my computer.
Scott Cain
@scottcain
@teresam856 thanks, that would be great; let’s chat some time next week if you’re around.
Teresa Martinez
@teresam856
Awesome. I will be free all next week so feel free to send me an invite with whichever time may work best for you. @scottcain
Ian Holmes
@ihh
I predict a lot of requests for better documentation/ easier install/ other support
Garrett Stevens
@garrettjstevens
@carolinebridge-oicr is working on a refresh of the documentation, probably good timing for that
Caroline Bridge
@carolinebridge-oicr
monthly meeting today? so I can give lincoln ample notice
Robert Buels
@rbuels
Not today, no