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  • Apr 11 17:46
    cmdcolin commented #1591
  • Apr 11 17:45
    cmdcolin commented #1594
  • Apr 11 11:35
    Gogis0 opened #1594
  • Apr 09 21:45
    scottcain closed #1593
  • Apr 09 21:45
    scottcain commented #1593
  • Apr 09 21:10
    cmdcolin commented #1593
  • Apr 09 19:17
    cmdcolin commented #1593
  • Apr 09 19:17
    cmdcolin commented #1593
  • Apr 09 18:51

    cmdcolin on v4.0.3

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  • Apr 09 18:50
    scottcain opened #1593
  • Apr 09 18:18

    cmdcolin on master

    Make sure version pushed on yar… (compare)

  • Apr 09 18:17

    cmdcolin on master

    v4.0.3 (compare)

  • Apr 08 21:55
    cmdcolin commented #52
  • Apr 08 18:41
    rbuels commented #52
  • Apr 08 17:39

    cmdcolin on clone_obj

    (compare)

  • Apr 08 17:38
    cmdcolin commented #63
  • Apr 08 16:54
    rbuels commented #63
  • Apr 08 16:52

    rbuels on yield_thread_time

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  • Apr 08 16:51

    rbuels on master

    Bump abortable-promise-cache to… Add yieldThreadTime for parsing… Add readme note and 1 more (compare)

  • Apr 08 16:51
    rbuels closed #72
Colin Diesh
@cmdcolin
jbrowse is unable to represent some exact coordinate ranges due to pixels and math and stuff. tries its best
Scott Cain
@scottcain
Oh, I get it. I didn’t think about that. Cool.
btski
@btski
@rbuels @cmdcolin I apologize for missing this earlier. Robert's fix for PR #1585 seems to have problems with loading the associated sequence. No errors were reported.
Screen Shot 2021-03-24 at 5.12.41 PM.png
Colin Diesh
@cmdcolin
ah gotcha. good catch
will need a little follow up then
Colin Diesh
@cmdcolin
went ahead and pushed a fix for that to our dev branch @btski
uploaded a built version to this branch in case it helps...sometimes hard to build custom releases GMOD/jbrowse#1585
btski
@btski
Tried copying files from commits GMOD/jbrowse@a372758 and GMOD/jbrowse@aeb0b02. Neither worked with forward slashes (did not test them without forward slash).
Also tried installing JBrowse-1.16.12-alpha.0.zip. Ran setup script. Fails to display sequences (both with and without forward slashes).
Screen Shot 2021-03-25 at 2.52.25 PM.png
Colin Diesh
@cmdcolin
@btski I made an update to the dev branch with a fix to that...don't have a build handy as a replacement but if you want to check out the dev branch can try that
btski
@btski
Didn't I apply the most recent dev branch commits? Sorry, not sure what I'm missing.
Colin Diesh
@cmdcolin
The replaceAll error shouldn't happen if aeb0b02 is applied
To create a custom build or setup from the dev branch u may need to use a GitHub clone
Basically can create a build from the dev branch like this; git clone https://github.com/GMOD/jbrowse; cd jbrowse-components; git checkout dev; ./setup.sh
Then setup.sh runs we pack and stuff (can use yarn build or yarn watch to just run we pack instead of setup.sh too)
Webpack*
btski
@btski
Sounds good. I'll try to clone dev from GitHub. I noticed that JBrowse-1.16.12-alpha.0.zip is missing directories. Doesn't have src/JBrowse so I can't patch src/JBrowse/Store/SeqFeature/SequenceChunks.js
Colin Diesh
@cmdcolin
And then maybe an un-noted bit of info is that you can then copy that whole GitHub clone directory wherever is needed, similar to however the zip file you downloaded from the pr. It takes a special setup to create the smaller bundles like I uploaded to the pr (have to run a makefile plus some perl stuff...can advise if that is needed too)
The built versions don't use sec/JBrowse it is all webpacked and minified
That's why basically ya need the whole GitHub repo just to make a patch. Kinda annoying but kinda just what the webpack world has brought on us
btski
@btski
Dev branch up and running. Works!
Scott Cain
@scottcain
🎉
Colin Diesh
@cmdcolin
excellent :)
bbimber
@bbimber
Hello, I am wondering if anyone has tried anything like the following. We have a VCF track, where the file has 1000s of samples and a lot of annotations. When rendering the browser view, most of that information and parsing is simply not used/needed. We only actually do anything with genotypes when the details view is opened. Further, when viewing a large region this track lags, which probably is related to a lot of download/parsing (but have not formally profiled this). I am considering making a plugin that would allow this track to query a slimmed down VCF (no genotypes, less INFO annotation) as the primary data source. The details view would need to be hooked into, and provide this with an alternate VCF URL. When a single variant is clicked, we'd query one position from this alternate VCF and parse/load that information. Has anyone attempted something like this before?
Colin Diesh
@cmdcolin
@bbimber i believe phytozome has this
which jbrowse version are you using?
bbimber
@bbimber
it will be JB2. we're using JB1 on our production servers now, but i want to migrate us
Colin Diesh
@cmdcolin
gotcha
jb1, in some cases, tries to not spend time parsing all the genotypes
in jb2 it actually parses all genotypes by default, which means in some cases it can actually be somewhat slower than jb1 for vcf with very long genotype lists
so it will actually benefit a lot from such a system
we have tested loading 1000 genomes type data in jb2 and its not too bad but something like you are proposing would be interesting
i actually made a fun silent movie browsing 1000 genome trio dataset here the other day :) https://www.youtube.com/watch?v=zy3nC4OfP2U
bbimber
@bbimber
maintaining the two VCFs is a little annoying, but not that cumbersome. the concept of separating the primary data URL and a 'details URL' might have general utility in other cases (like perhaps a database backing up the details view).
Colin Diesh
@cmdcolin
yep
if you have sample data you'd like us to look at we can check it out...see if this type of thing is needed
it may end up for that particular thing a custom detail panel that performs a fetch against a databse may be the best bet, as it may be hard to generalize
but we can surely find something to work :)
Scott Cain
@scottcain
Interesting buggy behavior; I'll file a bug report unless there is an obivous fix. When I load this link: https://wormbase.org/tools/genome/jbrowse-simple/?data=data%2Fc_elegans_PRJNA13758&loc=V%3A14373361..14373473&tracks=Curated_Genes%2CDNA&highlight= the refernce sequence is misaligned, as that gene glyph marks a start of translation, but the ATG isn’t aligning to the start of the glyph. If I close and reload the reference sequence track, it now shows the ATG start at the right place. Any idea what’s going on?
And, I should note, this behavior is reproducible on my Mac in Chrome, Firefox and Safari.
Colin Diesh
@cmdcolin
ooo
maybe make an issue for that..
Scott Cain
@scottcain
I should mention this is from the dev branch and is a few months old. I’ll rebuild to make sure it’s still doing it and then make the issue
Scott Cain
@scottcain
Yep, it still does it with a fresh build. I’ll write the issue.
Scott Cain
@scottcain
… Oh, I bet I know what the problem is. If it’s what I think, it’s embarassing.
Scott Cain
@scottcain
Yeah, there is more than one track in trackList.json with the key ""Reference sequence (DNA)”. The code that builds trackList is indiscriminately pulling in configs that start with “c_elegans” but because we have three assemblies, it’s pullng in the ref seq tracks for all three, so it appears to be a (so far predictable) crap shoot as to which ref seq you get. Lovely.
scottcain @scottcain goes off to rebuild, test, redeploy in shame.
Colin Diesh
@cmdcolin
nice:)