v2.1.6 Release

We are happy to release v2.1.6

This has several important fixes and improvements

• Tracks no longer hang in "Loading..." state under Safari and Webkit based browsers, a bug with starting the webworker was fixed
• There is now an option to use the WebWorkerRpc on the @jbrowse/react-linear-genome-view. This is a great improvement because the WebWorkerRpc dramatically reduces the "stalling" of the main thread when large datasets like BAM/CRAM are being loaded. See https://jbrowse.org/storybook/lgv/main/?path=/story/using-webworker-rpc--page for more info!
• All feature types, not just gene features, can obtain the underlying feature sequence with upstream/downstream options
• The ability to refer to plugins in a path relative to your data directory has been fixed, so you can easily refer to plugins in your config file with e.g. "plugins":[{"name":"MyPlugin","umdLoc":{"uri":"myplugin.js"}}] (umdLoc resolves the uri relative to the config.json file that it is in use). There is also umdUrl which can be used in place of umdLoc which can be used like this "plugins":[{"name":"MyPlugin","umdUrl":"myplugin.js"}] and this will resolve relative to the jbrowse root directory e.g. where the index.html is. We recommend using UMD for now, as ESM modules do not have full browser support e.g. in firefox yet, but this will likely be changing soon and we will update tutorials when this occurs!

See our volvox example for a simple no-build plugin https://github.com/GMOD/jbrowse-components/blob/main/test_data/volvox/umd_plugin.js along with it's config https://github.com/GMOD/jbrowse-components/blob/main/test_data/volvox/config.json and see our no-build plugin tutorial! https://jbrowse.org/jb2/docs/tutorials/no_build_plugin_tutorial/

Screenshot of the feature sequence panel showing on a SNP, allowing you to get upstream and downstream sequence of the SNP

Downloads

• v2.1.6

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

2.1.6 (2022-10-19)

Package	Download
@jbrowse/core	https://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignments	https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bed	https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view	https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config	https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management	https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3	https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark	https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf	https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowse	https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view	https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence	https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg	https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trix	https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants	https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle	https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli	https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img	https://www.npmjs.com/package/@jbrowse/img
jbrowse-predefined-sessions
@jbrowse/react-circular-genome-view	https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view	https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

🚀 Enhancement

• Other
  • #3272 Disable resolution of Derives_from fields in GFF3 parsing, fixes TAIR gff (@cmdcolin)
  • #3254 Use tick labels that correspond to the overview's larger zoom level (@cmdcolin)
• core
  • #3230 Add ability to customize About dialog with callbacks and optionally hide links to data (@cmdcolin)
  • #3275 Add help dialog for feature sequence panel (@cmdcolin)
  • #3250 Handle alternate line endings (@garrettjstevens)
  • #3252 Fix gene sequence fetching in embedded, and allow fetching genomic sequence for other feature types (@cmdcolin)
• core, text-indexing
  • #3276 Allow using web worker RPC on embedded LGV (@cmdcolin)

🐛 Bug Fix

• core
  • #3266 Fix relative path loading of plugins (@cmdcolin)
  • #3269 Fix ability to rename session in web/desktop (@cmdcolin)
  • #3256 Fix tracks hanging in safari and polyfill for bigwig tracks (@cmdcolin)
• Other
  • #3274 Update bbi-js for bugfix on webpack 4 (@cmdcolin)
  • #3259 Fix issue with breakpoint split view using view before initialized (@cmdcolin)

📝 Documentation

• #3255 Add more docs about color callbacks (@cmdcolin)

🏠 Internal

• core
  • #3261 Fix for flaky test (@cmdcolin)

Committers: 3

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Scott Cain (@scottcain)