Skip to main content

v1.2.0 Release

We're excited to announce the v1.2.0 release of JBrowse Web!

New plugin store added to website#

One of the core aspects of JBrowse 2 is that it is an extensible platform for biological visualization that can be extended with plugins. We are excited to introduce the first version of our plugin store, where we list the current external plugins that are available. Check it out here. In the coming weeks, we will also be bringing this plugin store directly into the application, allowing plugin installation with the click of a button. Stay tuned!

SVG export#

We're excited to introduce a new feature to JBrowse Web: built-in SVG export of track visualizations! This feature currently supports the linear genome view, and will be extended to more views in future releases.

With the addition of this feature, it is now even easier to create publication-ready screenshots of JBrowse views.

Virtualized track lists#

An important consideration for genomics software is scaling to very large datasets. We have implemented a virtualization of our hierarchical track selector, enabling it to support arbitrarily large track lists.

Lazy loading#

We have expanded our use of lazy loading, which optimizes app performance and improves load times.

Downloads#

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.

See "Packages in this release" in the changelog for links to packages published on NPM.

1.2.0 (2021-05-03)#

Packages in this release

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignmentshttps://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-bedhttps://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-viewhttps://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-confighttps://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-managementhttps://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-filtering
@jbrowse/plugin-gff3https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequencehttps://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svghttps://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-variantshttps://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wigglehttps://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/clihttps://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/react-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

๐Ÿš€ Enhancement#

  • core
    • #1125 Export SVG (@cmdcolin)
    • #1867 Virtualized tree for tracklist to support having thousands of tracks (@cmdcolin)
    • #1660 Allow connections to have multiple assemblies (@garrettjstevens)
    • #1864 Add Material UI's DataGrid to re-exports (@garrettjstevens)
    • #1875 Make drawer widget titles stay visible when scrolling inside the widget (@cmdcolin)
    • #1877 Add ability to copy the text produced by the feature details sequence panel to MS Word/Google Docs and preserve styling (@cmdcolin)
    • #1854 Make "About track" dialog available from tracklist and for non-LGV tracks (@cmdcolin)
    • #1853 Add mouseovers in feature details that show field descriptions for VCF fields (@cmdcolin)
  • Other
    • #1892 Create new JB2 plugin store (@elliothershberg)
    • #1901 Make using --out for add-assembly create output directory if it does not exist and fix outputting to symlink (@cmdcolin)
    • #1850 Add true breakend ALT strings to the feature details panel (@cmdcolin)
    • #1878 Add --delete to set-default-session, fix --session (@garrettjstevens)
    • #1861 Change Alignments track "Fade mismatches by quality" setting to a separate config param and made it less strict (@cmdcolin)

๐Ÿ› Bug Fix#

  • core
    • #1924 Fix import of BED and navToLocString from spreadsheet views (@cmdcolin)
    • #1918 Fix issue with some falsy values being hidden in feature details (@cmdcolin)
    • #1911 Fix breakpoint split view visualizations for files that need ref renaming (e.g. chr1 vs 1) (@cmdcolin)
    • #1904 Fix issue with synteny polygons displaying slightly offset (@cmdcolin)
    • #1884 Fix rIC ponyfill for use on Safari (@cmdcolin)
  • Other
    • #1912 Fix reloading of local sessions when using React.StrictMode (@cmdcolin)
    • #1900 Make clicking away from autocomplete popup on track container work (@cmdcolin)
    • #1878 Add --delete to set-default-session, fix --session (@garrettjstevens)
    • #1871 Fix crash on dotplot/linear synteny import form and when closing linear synteny track (@cmdcolin)
    • #1860 Fix alignments read filter jexl syntax (@cmdcolin)

๐Ÿ“ Documentation#

  • #1914 Use MDX to add proper image captions in web and pdf documentation (@cmdcolin)
  • #1855 Add download page in website header and new super-quick-start guide (@cmdcolin)

๐Ÿ  Internal#

Committers: 4#