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ยท One min read

This release fixes the UMD builds for the react components which failed to upload to npm in 2.1.3

Downloadsโ€‹

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.

2.1.4 (2022-09-16)โ€‹

Packages in this release

๐Ÿ› Bug Fixโ€‹

Committers: 1โ€‹

ยท 3 min read

This release includes a quality-of-life improvement for users plotting synteny with CIGAR strings. Before this version, the x-axis in the dotplot was assumed to be target sequence (and similarly, the top row in the linear synteny view was assumed to be the target sequence). But now, target can be either x- or y-axis in dotplot, and top or bottom in linear synteny views, removing the need for the user to care as much about query-vs-target ordering.

This release also includes several fixes for the the behavior of text searching in the linear genome view, a new button to open a .jbrowse file directly from the start screen on jbrowse-desktop, and an important bugfix to plotting inverted alignments on dotplots that affected versions v2.1.0-v2.1.2.

Screenshot showing the latest jbrowse desktop start screen, with a button to open .jbrowse sessions

Screenshot showing both X/Y orientations of two yeast genomes on the dotplot view, focusing on the deletions and insertions.

Enjoy!

Downloadsโ€‹

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.

2.1.3 (2022-09-15)โ€‹

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-comparative-adapters
@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-sequencehttps://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@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/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

๐Ÿš€ Enhancementโ€‹

  • Other
    • #3188 Add 'Open saved session' button to start screen on desktop (@cmdcolin)
    • #3187 Add mouseover tooltip descriptions to the header of the VariantFeatureDetails sample/genotype table (@cmdcolin)
    • #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
    • #3178 Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target (@cmdcolin)
    • #3173 Add ability for CLI to recognize plaintext BED files (@cmdcolin)
    • #3162 Add about dialog with version number for embedded components (@cmdcolin)
    • #3163 Note for user to wait before re-launching app on desktop update (@cmdcolin)
  • core

๐Ÿ› Bug Fixโ€‹

  • core
    • #3168 Fix search behavior when there are multiple matches in LGV header and when feature description matched in import form (@cmdcolin)
    • #3182 Fix "dead state tree node" error by creating snapshots of parent region for block calculations (@cmdcolin)
  • Other

๐Ÿ“ Documentationโ€‹

๐Ÿ  Internalโ€‹

Committers: 4โ€‹

ยท 3 min read

Hello all, we are pleased to announce v2.1.2!

This release includes a number of small bugfixes to the multi-wiggle track type, and a new feature for performing small sequence searches/motifs in the visible region.

Screenshot of the sequence search feature. It is available from the "view menu" on the linear genome view

Also, we just recently published the pre-print for our JBrowse 2 paper on bioRxiv! https://www.biorxiv.org/content/10.1101/2022.07.28.501447v1

This is a tour de force describing the basic ideas behind JBrowse 2 as an app. We are really pleased with how users and developers have helped to contribute to JBrowse 2 thus far, and look forward to many more years!

Downloadsโ€‹

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.

Packages in this release

PackageDownload
@jbrowse/plugin-alignmentshttps://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@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-comparative-adapters
@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-gff3https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmarkhttps://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtfhttps://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowsehttps://www.npmjs.com/package/@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-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trixhttps://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variantshttps://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wigglehttps://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/desktop
@jbrowse/imghttps://www.npmjs.com/package/@jbrowse/img
@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

๐Ÿš€ Enhancementโ€‹

๐Ÿ› Bug Fixโ€‹

  • Other
    • #3157 Support the "name" field on multi-wiggle adapter subadapters instead of source (@cmdcolin)
    • #3154 Use the union of all the subadapter refNames for the MultiWiggleAdapter getRefNames (@cmdcolin)
    • #3156 Fix for mouseover/mouse click on wiggle/multi-wiggle causing errors in embedded mode (@cmdcolin)
    • #3151 Fix ability to click and drag overview scale bar dragging right to left (@cmdcolin)
    • #3133 Update the ref name box when assembly is changed in LGV import form (@garrettjstevens)
    • #3131 Use "code" instead of "key" for undo/redo keyboard event, fixes shift+ctrl+z redo (@garrettjstevens)
    • #3119 Use es2015 setting for commonjs builds of packages to fix @jbrowse/img (@cmdcolin)
    • #3142 Fix unicode arrow icon not rendering with some fonts in configuration editor (@garrettjstevens)
  • core
    • #3120 Fix menu items for changing display type from track menu (@cmdcolin)

Committers: 2โ€‹

ยท 3 min read

We are pleased to present 2.1.0! This release adds some significant new features including:

  • Multi-wiggle tracks - This allows, for example, multiple bigwig files to be displayed in a single track with synchronized scalebar settings. See multi-wiggle docs for more info.
  • Undo and redo functionality, let's you undo an operation in the UI e.g. closing a view, closing a track can be recovered
  • An alert when the dotplot view renders features that go beyond the bounds of the selected region. This is often an indication that the wrong assembly is being used or the query and target are backwards

Example links for multi-bigwig sessions

Multi-row plot showing 21 ENCODE bigWig tracks

Overlapping "xyplot" rendering multiwiggle rendering mode with "emphasised" points showing tumor vs normal coverage

Dotplot view showing warnings from rendering dotplot, generally due to the wrong assemblies being compared. Screenshot also shows the dropdown menu to choose whether mouse click-and-drag pans the view or selects a region

Undo and redo buttons in the Tools menu, also accessible from keyboard shortcuts ctrl+z/ctrl+y and cmd+z/cmd+shift+z. The Undo/Redo function is available in jbrowse-web and jbrowse-desktop currently

Downloadsโ€‹

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.

2.1.0 (2022-07-28)โ€‹

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-bedhttps://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-comparative-adapters
@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-hic
@jbrowse/plugin-legacy-jbrowsehttps://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-menus
@jbrowse/plugin-sequencehttps://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-svghttps://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trixhttps://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variantshttps://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wigglehttps://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/desktop
@jbrowse/imghttps://www.npmjs.com/package/@jbrowse/img
@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

๐Ÿš€ Enhancementโ€‹

  • core
    • #3111 Create undo manager in jbrowse-web and jbrowse-desktop (@cmdcolin)
    • #3115 Add warning when dotplot renders outside of it's boundaries, and create click-and-drag panning of dotplot view (@cmdcolin)
    • #3102 Allow creating alternative "add track workflows" from within the "Add track" widget (@cmdcolin)
    • #3043 Create MultiWiggle track type, adapter, and renderers (@cmdcolin)
  • Other
    • #3113 Improve SVG performance by avoiding re-render when feature is clicked (@cmdcolin)
    • #3110 Remove TSDX from plugin development tools (@garrettjstevens)
    • #3106 Add "emphasis" mode for no fill/scatterplot mode in XYPlot type renderings (@cmdcolin)

๐Ÿ› Bug Fixโ€‹

  • Other
    • #3109 Better support for developing plugins from within yarn 2+ workspaces (include __virtual folder in build) (@garrettjstevens)
  • core

๐Ÿ“ Documentationโ€‹

Committers: 2โ€‹

ยท 3 min read

We are pleased to announce 2.0.1

This release features the ability to mouseover and click synteny alignments on the linear synteny view

If there are base level alignments, either from the read vs ref view or e.g. a PAF file generated with minimap -c (outputs CIGAR), then you can also mouse over to get information about the particular part of that alignment e.g. the CIGAR string

Figure showing a mouseover inside a deletion in the read vs ref view

This release also has some other small fixes and improvements, see release notes!

Downloadsโ€‹

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.

2.0.1 (2022-07-13)โ€‹

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-arc
@jbrowse/plugin-authentication
@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-comparative-adapters
@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-gff3https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmarkhttps://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtfhttps://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowsehttps://www.npmjs.com/package/@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-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trixhttps://www.npmjs.com/package/@jbrowse/plugin-trix
@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/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

๐Ÿš€ Enhancementโ€‹

๐Ÿ› Bug Fixโ€‹

  • Other
    • #3088 Fix labels being cut-off in SVG features by rendering feature labels on main thread (@cmdcolin)
    • #3085 Fix zoom to behavior being inaccurate with many displayed regions visible (@cmdcolin)
    • #3082 Fix negative strand CIGAR renderings on linear synteny view (@cmdcolin)
    • #3077 Fix crash opening multiple synteny track selectors launched from dotplot view (@cmdcolin)
  • core
    • #3086 Fix pxToBp and bpToPx calculations when there are many displayed regions (@cmdcolin)

Committers: 2โ€‹

ยท 3 min read

We are pleased to release v2.0.0! This is a major version milestone, but it does not have a huge number of changes. Instead, the major change that resulted in becoming v2.0.0 was the upgrade of many of our dependencies including

  • material-ui v4 -> v5
  • mobx-state-tree v3.14.1 -> v5
  • mobx-react v6 -> v7
  • mobx v5 -> v6

Therefore, to help users that may have been relying on library versions like this, it is safer to make the version a major bump. If you run into any issues with this upgrade, let us know and we can help

Some notable improvements:

  • This release improves bundle sizes for users of embedded components, by adding ESM builds to NPM. This can reduce the initial load of a webpage using e.g. @jbrowse/react-linear-genome-view by about 55% (1.4MB gzipped js->770kb gzipped js)

Downloadsโ€‹

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.

2.0.0 (2022-07-07)โ€‹

Packages in this release

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignmentshttps://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@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-comparative-adapters
@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-gff3https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmarkhttps://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtfhttps://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowsehttps://www.npmjs.com/package/@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-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trixhttps://www.npmjs.com/package/@jbrowse/plugin-trix
@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/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

๐Ÿš€ Enhancementโ€‹

  • Other
    • #3001 Draw SNPs in modifications/methylation views (@cmdcolin)
    • #3068 Allow HTML in feature tooltips, remove react-simple-code-editor (@cmdcolin)
    • #3065 Allow changing between xyplot,line,density for linear wiggle tracks and other small fixes (@cmdcolin)
  • text-indexing
    • #3058 Improve bundle size and code splitting on embedded builds (v2) (@cmdcolin)
  • __mocks__, core, text-indexing
    • #2949 Upgrade to MUI v5, mobx-state-tree v5, mobx-react v6, mobx-react v7 (@cmdcolin)

๐Ÿ› Bug Fixโ€‹

  • Other
    • #3072 Fix the display of inversions for MCScan alignments (@cmdcolin)
    • #3074 Fix the display of deletions vs insertions being backwards in synteny view with CIGAR strings (@cmdcolin)
    • #3057 Fix export SVG crash on some BigWig tracks (@cmdcolin)
    • #3052 Fix negative value quantitative display in svg exports (@cmdcolin)
  • core
    • #3064 Fix opening link in new tab by default in feature details (@cmdcolin)
    • #3053 Avoid displaying [object Object] on deeply nested data in base feature details (@cmdcolin)

๐Ÿ  Internalโ€‹

Committers: 2โ€‹

ยท 3 min read

We are excited to announce v1.7.11!

This release has some relatively small fixes to the UI, docs, and examples. For developers, they may notice that we have removed node-canvas due to it's need for having extra system dependencies, and becuase it only really was needed in niche circumstances. This will improve the ease of installing packages like @jbrowse/react-linear-genome-view.

Downloadsโ€‹

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.

1.7.11 (2022-06-22)โ€‹

Packages in this release

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignmentshttps://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@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-comparative-adapters
@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-gff3https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmarkhttps://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtfhttps://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowsehttps://www.npmjs.com/package/@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-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trixhttps://www.npmjs.com/package/@jbrowse/plugin-trix
@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

๐Ÿš€ Enhancementโ€‹

  • core
    • #3044 Remove node-canvas from @jbrowse/core dependencies (@cmdcolin)
    • #3041 Fix ability to search and load data files using lower case refName aliases (@cmdcolin)
  • Other

๐Ÿ› Bug Fixโ€‹

  • #3049 Fix ability to use callbacks for the linear arc renderer (@cmdcolin)

๐Ÿ“ Documentationโ€‹

๐Ÿ  Internalโ€‹

  • core

Committers: 1โ€‹

ยท 4 min read

We are pleased to present the latest JBrowse 2 release!

This has some great new features including

Feature detail formatterโ€‹

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 confirmโ€‹

Large track menus no longer disappear off the screenโ€‹

Before

After

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

Downloadsโ€‹

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)โ€‹

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

๐Ÿš€ Enhancementโ€‹

  • 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)

๐Ÿ› Bug Fixโ€‹

Committers: 3โ€‹

ยท 2 min read

We are pleased to present v1.7.9!

This release features several bugfixes and improvements submitted by community members, including a CLI fix when specifying --indexFile with CSI files, and a new feature to get FASTA metadata from an external file.

Additionally, we have switched to canvas2svg for SVG exports, which can now handle more sophisticated operations like bezierCurves (used for sashimi-style arc in RNA-seq data), and circles (used by jbrowse-plugin-gwas)

Before (note bad intron and lack of arcs rendered on bottom track)

After (fixed intron rendering and arcs)

Downloadsโ€‹

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.

1.7.9 (2022-06-02)โ€‹

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-comparative-adapters
@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-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequencehttps://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-variantshttps://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/clihttps://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/imghttps://www.npmjs.com/package/@jbrowse/img
@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

๐Ÿš€ Enhancementโ€‹

  • core
    • #2991 Use canvas2svg for SVG export, fixes non-rasterized usage of bezier, arcs, and more (@cmdcolin)
    • #2483 Add setting to color by query score per alignment for dotplot, support HTML in config slot descriptions (@cmdcolin)
    • #2983 Set target=_blank by default in user HTML links (@cmdcolin)
  • Other

๐Ÿ› Bug Fixโ€‹

๐Ÿ  Internalโ€‹

Committers: 4โ€‹

ยท 2 min read

We are happy to announce v1.7.8

Some highlights include

  • ~20% speed improvement for CRAM data
  • bugfix for filter-by being broken on alignments tracks in v1.7.0-v1.7.7
  • bugfix for certain methylation/modifications being drawn incorrectly on alignments tracks
  • bugfix for the "Open" button not navigating to the correct location on the LGV import form
  • improved visualization of indels in methylation/modifications mode on alignments tracks
  • skip text index query if the input is a loc string, resulting in quicker navigation

Screenshots showing the new viewing of indels when viewing methylation

Before

After

See the release notes for details

Downloadsโ€‹

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.

1.7.8 (2022-05-20)โ€‹

Packages in this release

PackageDownload
@jbrowse/plugin-alignmentshttps://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-confighttps://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-legacy-jbrowsehttps://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/desktop
@jbrowse/imghttps://www.npmjs.com/package/@jbrowse/img
@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

๐Ÿš€ Enhancementโ€‹

๐Ÿ› Bug Fixโ€‹

  • #2969 Fix link on yeast synteny demo and fix CIGAR rendering on dotplot (@cmdcolin)
  • #2964 Fix crash displaying modifications called on softclipped regions of reads (@cmdcolin)
  • #2965 Fix filter functionality on pileup tracks (@cmdcolin)
  • #2953 Fix "Open" button on LGV ImportForm (@cmdcolin)
  • #2952 Fix read vs ref not finding primary alignment on certain CRAM files (@cmdcolin)
  • #2951 Fix viewing soft/hardclip indicator in some regions (@cmdcolin)

๐Ÿ“ Documentationโ€‹

๐Ÿ  Internalโ€‹

Committers: 2โ€‹