GMOD/jbrowse2

JBrowse 2 development and support

Robin Haw

@hawrobin

just pay for the membership! usually with membership, the meeting is cheaper to attend! - assuming you can be reimbursed for the membership

Robin Haw

@hawrobin

Just read this on the poster submission page - Because some AACR Annual Meeting attendees and presenters may be restricted from traveling to New Orleans in April 2022, the AACR Annual Meeting 2022 will offer the following options for presenters of abstracts accepted for poster presentation:

In-Person Presentation with E-Poster—Presenters are strongly encouraged to travel to New Orleans to present their posters in person. However, all in-person presenters will also be required to submit a companion e-poster presentation to accommodate registered attendees who are unable to attend the meeting in person.
E-Poster Only—Presenters of accepted posters who are unable to travel to New Orleans will be required to submit an e-poster. These presenters will be expected to be available remotely during the dates of the poster sessions (April 10-13) to respond to any questions submitted through the e-poster platform.
PLEASE NOTE: E-poster presenters who do not attend the meeting in person are still required to register for the meeting.

Robin Haw

@hawrobin

I was able to create account and logged in. The submssion could be easy and then register later. Lincoln will probably be a member.

Robert Buels

@rbuels

Ok great. Do you think @scottcain and @hawrobin you guys could coordinate and submit something?

Robin Haw

@hawrobin

Yes, I can work on this tonight with @scottcain and try to submit tomorrow before 11:59pm. FYI, the deadline for late-breaking abstracts is 11:59 p.m. U.S. ET, Monday, January 10, 2022

I sent an email to Lincoln to see if he will sponsor one of us!

bbimber

@bbimber

We have an embedded ReactLinearGenomeView. The component has a menu in the upper-right, which can have items added to it. Is there a way to inject another item into the menu bar itself? Specifically, because we show this viewer full-screen, I want to put some kind of button/link that is very obviously has the text "Return to Site".

Robin Haw

@hawrobin

@scottcain I also took a look at the PAG abstract, made some suggestions

Colin Diesh

@cmdcolin

@bbimber if arbitrary header components want to be added to the react lgv we might be able to create an extra prop for that or similar

Colin Diesh

@cmdcolin

@bbimber possible helper here GMOD/jbrowse-components#2535

Garrett Stevens

@garrettjstevens

Another option could be to allow the user to specify their own ViewContainer, so they can e.g. match the styling on their page.

Colin Diesh

@cmdcolin

hmmm

could do that too

bbimber

@bbimber

Would customizing the ViewContainer allow us to increase the initial height? that's been a wish list item for us too

Colin Diesh

@cmdcolin

hmmm...maybe layout wise, but it might not have a bearing on the individual track heights

12 replies

Robin Haw

@hawrobin

@scottcain - i created an AACR 2022 folder in the Meetings folder on the Team drive

Robin Haw

@hawrobin

Lincoln is a member of AACR and I think he can be listed as a sponsor

bbimber

@bbimber

Another question: I see your docs on themes, which works well. However, are more public examples of specific color combinations people have figured out work well? For example, is there a stock jbrowse blue theme, red theme, etc? Or perhaps examples of what color sets people have used?

Colin Diesh

@cmdcolin

not too many examples of this yet i think, would be fun to make some more examples

Scott Cain

@scottcain

Category for JBrowse abstract. submit in which category? "Application of bioinformatics to cancer biology” or "New software tools for data analysis”? I feel like it should be the former, since it doesn’t really do “analysis”, it just helps users look at stuff to do their own analysis. Anybody want to disagree?

Also, sorry working on this so late: it’s been a busy day and I had to take the dog to the vet which has really messed up my schedule.

Colin Diesh

@cmdcolin

either probably fine

Scott Cain

@scottcain

I also have to pick keywords from a long, preexisting list. So far, the only one I’ve found that’s good is “genome"

Colin Diesh

@cmdcolin

such is the way when we step outside our normal conferences...

Scott Cain

@scottcain

yep

Robert Buels

@rbuels

@cmdcolin are you mostly out today with the moving?

Colin Diesh

@cmdcolin

yes

added to cal:)

Robert Buels

@rbuels

@peterkxie thoughts on #2541?

Shellfishgene

@Shellfishgene

Are csi indexes also supported for tabix (gff) files? I have a gff file that tabix won't do an tbi index for for some reason. When I use add-track with --indexFile=foo.gff.gz.csi it still tries to copy a (non existent) .tbi file.

Shellfishgene

@Shellfishgene

If I use inPlace and the csi index it works...

Colin Diesh

@cmdcolin

i think that add track works with indexFile and csi

$ jbrowse add-assembly test_data/volvox/volvox.fa --out t1 --load copy
Added assembly "volvox" to t1/config.json

$ jbrowse add-track test_data/volvox/volvox-sorted.bam --indexFile=test_data/volvox/volvox-sorted.bam.csi --out t1 --load copy
Added track "volvox-sorted" to t1/config.json

$ ls -1 t1
config.json
volvox.fa
volvox.fa.fai
volvox-sorted.bam
volvox-sorted.bam.csi

using jbrowse cli 1.5.1

Colin Diesh

@cmdcolin

some mega ucsc trackhubs/assembly hubs that could be cool to load

https://hgdownload.soe.ucsc.edu/hubs/birds/hub.txt

from https://genome-blog.soe.ucsc.edu/blog/2021/11/23/genark-hubs-part-1/

Shellfishgene

@Shellfishgene

Yes, it worked with my bam and cram files, but not with gff and csi.

Shellfishgene

@Shellfishgene

Maybe this line: https://github.com/GMOD/jbrowse-components/blob/24b45e29b681277e68ec088034f3ef25bb80c389/products/jbrowse-cli/src/commands/add-track.ts#L391 should be index: index || ${fileName}.bai instead, like the part for bam?

Colin Diesh

@cmdcolin

@Shellfishgene ah thanks much

this should get fixed

Colin Diesh

@cmdcolin

possible issue about estimating bytes downloaded, could be possibly a method for stats estimation GMOD/jbrowse-components#2251

Colin Diesh

@cmdcolin

Pangenome hackathon+talks Dec 9-10 https://twitter.com/erikgarrison/status/1465346595835326497?t=NnmbhvRONJYJoxYX16s9tg&s=19

Robert Buels

@rbuels

Oh that’s cool, you gonna go?

Colin Diesh

@cmdcolin

perhaps:)

it's free so why not

Robert Buels

@rbuels

Wonder if we can find some synergies between that working with crazy rearrangements

Colin Diesh

@cmdcolin

surely. even "non crazy"stuff benefits

bbimber

@bbimber

Hello - I'm hoping to get some advice. We're trying to make a plugin that filters variants in a VCF track based on whether specific samples are non-wild type. The logic is not hard (make sure the genotype of samples !== '"./." or "0/0"); however, has ~2500 samples. At least how we're doing this makes a very noticeable lag in loading. I experimented with pre-computing an array of the non-WT samples in the getFeatures() method of a custom VcfTabixAdapter; however, this code is called repeatedly whenever any rendering happens. Is there a place I could hook into the processing of VCF features that would let me efficiently pre-compute some information, and let that information persist? Alternately, is there another way I should think about approaching this problem?

Robert Buels

@rbuels

@bbimber I think a custom adapter is a good approach. What would probably help the performance of this a lot would be adding a cache of the features that your custom adapter is creating, so that the calls to getFeatures don't repeat the fetch/parse/filter steps

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