Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • Dec 04 21:24
    dependabot[bot] labeled #77
  • Dec 04 21:24
    dependabot[bot] opened #77
  • Dec 04 21:24

    dependabot[bot] on npm_and_yarn

    Bump decode-uri-component from … (compare)

  • Dec 03 01:47
    codecov[bot] commented #68
  • Dec 03 01:44
    dependabot[bot] labeled #68
  • Dec 03 01:44
    dependabot[bot] opened #68
  • Dec 03 01:44

    dependabot[bot] on npm_and_yarn

    Bump decode-uri-component from … (compare)

  • Dec 03 00:31
    codecov[bot] commented #122
  • Dec 03 00:28
    dependabot[bot] labeled #122
  • Dec 03 00:28
    dependabot[bot] opened #122
  • Dec 03 00:28

    dependabot[bot] on npm_and_yarn

    Bump decode-uri-component from … (compare)

  • Dec 03 00:14
    dependabot[bot] labeled #59
  • Dec 03 00:14
    dependabot[bot] opened #59
  • Dec 03 00:14

    dependabot[bot] on npm_and_yarn

    Bump decode-uri-component from … (compare)

  • Nov 23 14:55

    cmdcolin on master

    Update CHANGELOG.md v5.0.9 (compare)

  • Nov 23 14:55

    cmdcolin on v5.0.9

    (compare)

  • Nov 23 14:54

    cmdcolin on fix_breakend_parsing_symbolic_alleles

    (compare)

  • Nov 23 14:54
    cmdcolin closed #97
  • Nov 23 14:54

    cmdcolin on master

    Fix erroneous parsing of symbol… (compare)

  • Nov 23 12:36
    codecov[bot] commented #94
David Pratella
@dprat
and here is the bed
Colin Diesh
@cmdcolin
but it's possible that this wont work with range requests (referencing https://github.com/GMOD/jbrowse-components/discussions/3172)
Robert Buels
@rbuels
Crazy that Django still doesn’t support range requests
Colin Diesh
@cmdcolin
ya, i just setup a django app for quick testing and the development server does not support it
i'm not sure i'm getting the same errors as @dprat is reporting though
this is what i'm seeing just for reference https://github.com/cmdcolin/django-jbrowse2-nonworking-example
Colin Diesh
@cmdcolin
if you have a different setup let me know @dprat
might be that using a apache server deployed in parallel with the django server or similar might be best for the situation https://docs.djangoproject.com/en/4.1/howto/static-files/deployment/#serving-static-files-in-production
David Pratella
@dprat
Capture d’écran 2022-09-08 à 19.15.33.png
this is what I get
Colin Diesh
@cmdcolin
@dprat i tested out a config pretty much the same as yours and the result probably comes back to the lack of range request in the django server
you are able to get past the screen i used because you use fasta index, which only needs a non-range-request to boot up (just requests the full fasta index .fai file with a http 200) and then you hit the range request issue which turning on the bedtabix file
actually, it is slightly different but related
it gives an internal error called (failed)net::ERR_CONTENT_DECODING_FAILED
and that is because it is applying Content-Encoding: gzip which jbrowse does not want to happen
if you renamed the .gz extension to .somethingelse
then it would get past that error but then give you 206 errors
i would consider hosting static files on a different server
David Pratella
@dprat
hmm fine if that's the way i'll do it like this !
Thx for your time and quick reply !
Colin Diesh
@cmdcolin
sure thing :) if you find a good workflow that works for you let us know, definitely have had a couple users interested in this type of setup
David Pratella
@dprat
ok i'll let you know !
David Pratella
@dprat
@cmdcolin do you think I would end with the same problem if I was using gff3 instead ?
Colin Diesh
@cmdcolin
if you are using only small files, you might be able to get it to work
that would mean using plaintext bed, plaintext gff
and we would need to create a plaintext fasta adapter (does not exist right now)
but it would not allow any indexed data files like BAM,CRAM,BigWig,Tabix (tabix can be used for VCF,GFF,BED,etc), etc. as these are large and use range requests
Sacha Laurent
@sachalau
Hi everyone, I haven't been here for a while but I have a question regarding the most efficient way to configure dynamically a large number of tracks, and periodically update the track list using jbrowse. I'm not sure it would be appropriate for an issue in GitHub so I thought I'd try here first.
Colin Diesh
@cmdcolin
@sachalau welcome back :)
are there any specific details about your setup e.g. the dynamic part?
most of the time, a "static file" with all the tracks is configured (e.g. trackList.json) in jb1 (config.json in jb2)
but you can certainly also write a REST API that generates that tracklist too
Robert Buels
@rbuels
@sachalau if it were me, i would write a web app in react that organizes all the tracks, and then I would use the JBrowse 2 react embedded linear view to display them
that would remove the need to write any configuration files to disk
and all of the changes would be instant
Sacha Laurent
@sachalau
Hi again, so when I was working on a diagnostic lab, I set up jb1 to visualize the outputs of our WES experiments. Each time a new batch of samples were processed, I would automatically generate a new trackList.json incorporating the new data. That way lab members could search directly in jbrowse any sample, and I could craft automatic url links to the data as well.
Now the problem is a bit different, because I'm starting again and could use jb2 directly, the data sits in S3 instead of our local compute disks, and the number of samples is in the (high) tens of thousands, instead of few thousands. I would like a jb2(/1?) instance from which I could directly visualize the CRAM files sitting in S3.
Sacha Laurent
@sachalau
So I do not want to display all the tracks at the same time but be able to load them into jb2 in the easiest way possible
Colin Diesh
@cmdcolin
@sachalau probably creating a rest api for the tracklist would be good
express.js can be a good way to make small REST API code
Sacha Laurent
@sachalau
Thanks Colin, I'll follow your advice and have a look at what I can do that way.
Colin Diesh
@cmdcolin
sure thing :) after the REST API is created, you can use e.g. with jb1 ?data=http://yourhost/path/to/your/restapi (similar idea with jb2)
li06889
@li06889:matrix.org
[m]
Hello I am working on a project where I need to be able to upload data files into Jb1 with just a link. Everytime I try to do this nothing happens. No error message but also nothing ever uploads. Wondering if anyone has had the same issue and been able to work around it somehow
Colin Diesh
@cmdcolin
@li06889:matrix.org hi there. technically there is no function in jb1 to truly 'upload' data files. it can 'open them' but that data stays in the web browser. if it is failing to open your files, there could be a bug perhaps. if you have any more detail, let us know
Malcolm Cook
@malcook

"The "name" field (column 4) of a BED file can contain GFF3 style key-value attribute tags by specifying "gffTags=on" on the track line. These attributes will be displayed in the mouse hover popup text." - I often use this capability (https://software.broadinstitute.org/software/igv/feature_track_options) happily in desktop IGV, and less happily in igv.js (https://github.com/igvteam/igv.js/issues/1550).

Is it reasonable to hope it might be (someday?) be supported in jbrowse?

Colin Diesh
@cmdcolin
any particular reason for using bed instead of gff at that point?
just a random note, we don't try to interpret "track" lines at all...wish bed format was better standardized in general
Malcolm Cook
@malcook

hi @cmdcolin - no particular reason - that's just what I have at the end of a particular pipeline.

That said, does jbrowse display GFF column 9 attributes on hover? Further, is there any possibility of controlling the label displayed on the glyph in the browser. I presume that by default it displays the value of the GFF name attribute, but is there any override of this default? FWIW - IGV provides for choosing alternate attribute to display as label.

Scott Cain
@scottcain
@malcook you can create a javascript callback that will display any information you want. For example, for several WormBase variant tracks (that should come from VCF but actually come from GFF). I pull a bunch of data from the GFF’s column 9. For example, see https://wormbase.org/tools/genome/jbrowse-simple/?data=data%2Fc_elegans_PRJNA13758&loc=III%3A1855046..1860848&tracks=Change-of-function%20alleles%2CChange-of-function%20polymorphisms%2CHigh-throughput%20alleles%2CMillion%20Mutation%20Project%2CPolymorphisms&highlight= and mouseover any features. The function that generates these hovers is variationsBalloon at https://github.com/WormBase/website-genome-browsers/blob/af7ed9a60061e8b0d241fe1cad480f1c8f7ec291/jbrowse/jbrowse/data/functions.conf#L368 and the config bit that makes it work looks like this onClick json: https://github.com/WormBase/website-genome-browsers/blob/af7ed9a60061e8b0d241fe1cad480f1c8f7ec291/jbrowse/jbrowse/data/c_elegans/includes/variations_million_mutation_project.json#L25-L30
Scott Cain
@scottcain
… And you can also choose anything you want as a label, again by providing a javascript callback (and I think it may be possible just to provide an attribute name in curly braces in the json config like ”label” : “{variantID}” but I’m not positive as I don’t do that)