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v1.7.10 Release

· 4 min read

We are pleased to present the latest JBrowse 2 release!

This has some great new features including

Feature detail formatter

Here is an example which adds a link to the "Name" panel in the feature details. It uses the jexl callback that returns an object with keys for each field to modify (e.g. the key name is used here). See

{
"type": "FeatureTrack",
"trackId": "ncbi_gff_hg19_2",
"name": "NCBI RefSeq",
"formatDetails": {
"feature": "jexl:{name:'<a href=https://google.com/?q='+feature.name+'>'+feature.name+'</a>'}"
},
"assemblyNames": ["hg19"],
"adapter": {
"type": "Gff3TabixAdapter",
"gffGzLocation": {
"uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz"
},
"index": {
"location": {
"uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz.tbi"
}
}
}
}

Example screenshot

See https://jbrowse.org/jb2/docs/config_guide/#customizing-feature-details-panels for more info

Clearer configuration panel with explicit "Add item" button with "OK"/"Cancel" to confirm

Large track menus no longer disappear off the screen

Before

After

See also the "Copy config" button to download the config

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.

1.7.10 (2022-06-13)

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-authentication
@jbrowse/plugin-breakpoint-split-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-linear-comparative-view
@jbrowse/plugin-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@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/imghttps://www.npmjs.com/package/@jbrowse/img
jbrowse-predefined-sessions
@jbrowse/react-circular-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

🚀 Enhancement

  • Other
    • #3025 Add dotplot session spec (@cmdcolin)
    • #2975 Add simplified URL format for loading synteny views (@cmdcolin)
    • #3023 Add error handling in case of invalid OAuth2 configuration used. (@andrzejgrzelak)
    • #3020 Allow choosing trackId when using text-index with --file with --fileId (@cmdcolin)
    • #3016 Allow whitespace separated refname,start,end type locstring (@cmdcolin)
    • #3006 Add string array configuration slot UI improvements (@cmdcolin)
    • #2998 Avoid rendering offscreen contents in pileup renderer (@cmdcolin)
    • #3000 Add reference base and correct percentage calculations to tooltip on SNPCoverage display (@cmdcolin)
  • core
    • #2981 Add simplified URL format for loading spreadsheet and SV inspector (@cmdcolin)
    • #2990 Use shortened megabases (M) display when zoomed out, and option to hide the "open track selector" button (@carolinebridge-oicr)
    • #3003 Add ability to run field formatters on the feature details panel (@cmdcolin)
    • #3017 Add button to copy track config in About track dialog (@cmdcolin)
    • #2999 Generate clickable links to track data in about track dialog (@cmdcolin)
  • __mocks__, core
    • #3005 Use cascading menu helper library for track menu to avoid menu going offscreen (@cmdcolin)

🐛 Bug Fix

Committers: 3