JBrowse 2 linear genome view React component; bigwig tracks

[arpanda]

I was trying to visualize some data for phythopthora genomes using a react application. For that, I used the following two links as guide.

1. https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
2. https://github.com/GMOD/jbrowse-components/blob/HEAD/products/jbrowse-react-linear-genome-view/docs/example.md

Codes are available at https://github.com/computational-genomics-lab/eumicrobe-db-client/blob/master/src/jbrowse/jbrowse.js

Somehow, here the bigwig track code is not running and giving error, I had to comment that section of the code to run the script. Here is that section of the code.

{
    trackID: "SSR_phy",
    name: "SSR",
    assemblyNames:["Phyag_NZFS3770"],
    type: "QuantitativeTrack",
    adapter: {
            type: "BigWig",
            bigWigLocation: { uri: ssrbw },
    }
  },

I also tried the add track option to show the same bigwig file but failed.

The code are temporarily hosted at http://97.107.139.167:3000/jbrowse/jbrowse

Any suggestion to fix the issue.

[cmdcolin]

I also tried the add track option to show the same bigwig file but failed.

what is the error you see?

Also, it is somewhat unusual to be "importing" the fa, fai, and bigwig
like this

import fasta from '../genome_data/Phyag_NZFS3770.fna'

that behavior would be up to your particular build system how that is handled e.g. it would require an advanced "loader" system from webpack or similar, because by default you generally just import js files

it does seem to be working for you with the fa and fai file (maybe because they are plaintext ?) but then it is failing on the bigwig, possibly because it is a binary format (just a guess...)

in any case, it may be good to not rely on this ability to import random files: you may want to make these setup on a fileserver somewhere, and refer to them by URL (as it is done in the tutorial)

[arpanda]

This time, I added in the track config. The browser consol is not reporting any error but the page is loading phase only. Here is temporary link for setup . http://97.107.139.167:3000/jbrowse/jbrowse

[cmdcolin]

The config should be trackId not trackID

[cmdcolin]

adapter.type should also be BigWigAdapter not BigWig

[cmdcolin]

There is a certain danger to hand-editing configs, our config system is very strict and there can be trouble if the config fails to validate the schema. You can see at the link eventually the error prints out

`Uncaught Error: [mobx-state-tree] Error while converting  {"config":{"assembly":{"name":"GRCh38","sequence":{"type":"ReferenceSequenceTrack","trackId":"GRCh38-ReferenceSequenceTrack","adapter":{"type":"BgzipFastaAdapter","fastaLocation":{"uri":"https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz","locationTyp......}]}]}}}` to `ReactLinearGenomeView`

which indicates that track does not have the right config schema. fixing can be tricky so it is best to try to get it right the first time if possible, by using the jbrowse CLI or jbrowse admin-server to edit configs, even though these are not geared towards the embedded (@jbrowse/react-linear-genome-view) component currently.

[arpanda]

Got it. It's working now. Thanks Colin.