Self-hosted Genome Browser

[haxiomic]

• [x] Refactor viewer component into separate lib
  • [x] Initial refactoring separation, see branch
  • [x] Genome browser API entry point
  • [x] Replace sirius dependency with configurable API
  • [x] Handle addTrack button in TrackViewer
  • [ ] Remove material-ui dependency
• [x] Merge refactor into master
• [ ] Develop initial pre-processing script
  • [ ] Explore tabix and how we can make use of it
  • Support processing:
    • [x] FASTA
    • [x] GFF3
    • [ ] BED
    • [ ] VCF
    • bigwig bigwig works well enough on it's own, we can develop a better format later
• [x] Develop app manifest file – the index file that describes the available resources
• [x] Demo self-hosted repo (currently in Genome-Browser/examples)
• [x] Explore FTP: what can we display given the existing plain-old FTP links Many existing services support
• [ ] UI for adding tracks and data sources
• [x] Embedding API wrapper (how should the browser work from an self-hoster's point of view)
• [x] API for custom track visualizations
• [ ] Source code examples and documentation
• [ ] Publish on NPM
  • [ ] Publish main repo
  • [ ] Publish dependencies: lib/GPUText, lib/gff3

[saliksyed]

@haxiomic This looks great ... I added bigwig as a format. Bigwig natively supports downsampling so we may be able to use it directly.

One task that I would add that is pretty important is generating a few really high quality source code examples. I think it would be amazing if people start adding new track visualization types -- this is where we can really establish a stronghold because of the WebGL based architecture that enables completely new capabilities.

[saliksyed]

Another point we'll want to take a look at is building a very simple UX for when you click elements. The browser should basically just display a data table with all the key value pairs, and optionally raw data of the JSON blob associated with the annotation.

[haxiomic]

Thanks for your feedback @saliksyed, I've added tasks for a custom visualizations API and source code examples

I like the idea of a minimal UX for basic interactions. I think we should make this easy to override so the embedder can implement their own