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ยท 5 min read

We are pleased to release v1.6.6!

This contains several updated synteny features, including:

  • load .chain files from UCSC
  • load .delta files from mummer
  • load .anchors and .anchors.simple files from MCScan from the GUI
  • ability to "rectangularize" the dotplot view and improved dotplot view overviews (shows total bp of selected regions)

Screenshot showing updated import form with ability to load MCScan data

Screenshot showing multiple tracks open at once, with the .anchors (green, gene pairs) and .anchors.simple (black, larger synteny blocks) files from MCScan shown in the dotplot view

Note: MCScan functionality existed internally but was not easy to use. The configuration schema for MCScan anchors files changed also to load the .bed files at startup. See the config guide for details

We also have an updated configuration editor GUI with collapsible sections

Screenshot showing new collapsible (turquoise) sections in the config editor

A number of alignments track look and feel improvements were also added. The scale bar was made to just list the min and max values when the height is small, clip indicator position when horizontally flipped was fixed, and the headroom was removed making the snpcoverage take up the full height of the small area it uses.

There have also been some changes to how internet accounts work. If you use one of the built-in accounts like Google Drive or Dropbox, there's no need to change anything. If you've implemented your own internet account, though, see #2725 for more 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.

1.6.6 (2022-03-15)โ€‹

Packages in this release

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/development-toolshttps://www.npmjs.com/package/@jbrowse/development-tools
@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-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-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
    • #2796 Add collapsible accordion sections in configuration editor (@cmdcolin)
    • #2791 Add new coloring options for dotplot and ability to "rectangularize" dotplot view (@cmdcolin)
    • #2741 Allow ability to enter a space-separated locstring to open a list of regions (@cmdcolin)
    • #2725 Refactor InternetAccounts, add standard getFetcher (@garrettjstevens)
    • #2787 Display the total bp viewed in the header of the dotplot view (@cmdcolin)
    • #2767 Wiggle and SNPCoverage look and feel improvements (@cmdcolin)
    • #2746 Add .delta and .chain format adapters, fix ref name aliasing in synteny/dotplot views, and optimize very long CIGAR string in synteny view (@cmdcolin)
  • Other
    • #2799 Exit process after rendering to speed up jb2export (@cmdcolin)
    • #2793 Add abortcontroller polyfill to jbrowse-img to allow it to run under node 14 (@cmdcolin)
    • #2761 Add a --clean argument to jbrowse upgrade to clean up old files (@cmdcolin)
    • #2760 Make a configurable refNameColumn in RefNameAliasAdapter (@cmdcolin)

๐Ÿ› Bug Fixโ€‹

  • core
  • Other
    • #2797 Fix crash plotting methylation in sparse regions (@cmdcolin)
    • #2782 Fix display of cytobands when horizontally flipped (@cmdcolin)
    • #2678 Preserve double border line when using trackLabel offset and use smaller gap between snpcoverage and reads (@cmdcolin)
    • #2774 Fix overwriting broken symlink with --force in add-track CLI (@cmdcolin)
    • #2773 Fix using global stats autoscale on wiggle tracks (@cmdcolin)
    • #2766 Add a check for empty content blocks to fix rare empty stats estimation (@cmdcolin)

๐Ÿ“ Documentationโ€‹

๐Ÿ  Internalโ€‹

Committers: 2โ€‹

ยท 3 min read

We are pleased to announce v1.6.5!

This features some various bugfixes to the @jbrowse/cli tool, including better support for large config files with the admin-server, and renaming --out to --root for the admin-server.

It also includes two important fixes related to stats estimation in 1.6.4, one where tracks would display an error on sparse tracks and another where tracks would fail to perform stats estimation on BAM files due to a type confusion.

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.

1.6.5 (2022-02-18)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-dotplot-view
@jbrowse/plugin-hic
@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-sequencehttps://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-svghttps://www.npmjs.com/package/@jbrowse/plugin-svg
@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
    • #2758 Use VariantTrack for plaintext VCF type (@cmdcolin)
    • #2738 Add better catch for XS and TS tag detection from CRAM (@cmdcolin)
    • #2733 Use sparse array for alignments coverage to fix bug viewing large sparse regions (@cmdcolin)
    • #2734 Use node fetch instead of follow-redirects in cli (@cmdcolin)
    • #2726 Handle .bgz file extension for text-index (@cmdcolin)
    • #2727 Add engines 16 to @jbrowse/img (@cmdcolin)
    • #2723 Make jbrowse desktop more robust to errors when reading recent sessions file (@cmdcolin)
    • #2715 Change --target to --root for jbrowse CLI admin-server (@cmdcolin)
  • core
    • #2757 Fix type confusion with stats estimation causing BAM files to fail byte size calculation (@cmdcolin)
    • #2750 Add bezierCurveTo to offscreen canvas ponyfill to fix sashimi arcs rendering in alignments track in webkit and firefox (@cmdcolin)
    • #2719 Avoid uninitialized state during stats estimation (@cmdcolin)
    • #2707 Fix ability to use authenticated assembly files (@garrettjstevens)
    • #2695 Fix disabled state on the linear genome view track labels dropdown menu (@cmdcolin)

๐Ÿ“ Documentationโ€‹

๐Ÿ  Internalโ€‹

Committers: 3โ€‹

ยท 3 min read

This release has a couple long awaited features!

There are also some improvements to synteny and dotplot views. The synteny view can now render curvy lines and "square" the views (so they each have the same zoom level), and have individual search panels in the synteny view. You can now also vertically resize the linear synteny view panel allowing for a taller or shorter view! The rendering has also been sped up in both linear synteny and dotplot views with certain code paths being up to 40x faster.

Also check out the recording and notes from our PAG 2022 tutorial session!

Screenshot showing the new curvy lines of the synteny view with the grape vs peach demo http://jbrowse.org/code/jb2/v1.6.4/?config=test_data%2Fconfig_synteny_grape_peach.json&session=share-EdWfJj5aIY&password=S8PGj

note that 1.6.0-1.6.3 were slightly buggy and collected into 1.6.4 here

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

๐Ÿš€ Enhancementโ€‹

๐Ÿ› Bug Fixโ€‹

๐Ÿ“ Documentationโ€‹

  • #2663 Add documentation for URL params and session spec (@cmdcolin)
  • #2655 Add link to PAG 2022 youtube tutorial on demos page and course archive (@cmdcolin)

๐Ÿ  Internalโ€‹

  • core
    • #2649 Add Cypress test of package that uses embedded components (@garrettjstevens)
    • #2648 Avoid console.warns in tests due to writing to MST nodes that are not alive (@cmdcolin)
  • Other
    • #2657 Fix hot reload using yarn resolution on react-error-overlay (@cmdcolin)

Committers: 3โ€‹

ยท One min read

This fixes a babel misconfiguration in v1.5.8 that prevented embedded packages from working

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.

1.5.9 (2022-01-13)โ€‹

Packages in this release

๐Ÿ› Bug Fixโ€‹

Committers: 1โ€‹

ยท 2 min read

This release fixes an important issue where @jbrowse/react-linear-genome-view and other embedded packages did not work with v1.5.5 due to a babel misconfiguration apologies to all affected!

Also we now can access the parent feature in jexl callbacks with parent(feature) or get(feature, 'parent') which is often needed when coloring subfeatures like exon/CDS features

This release also was made because v1.5.6 and v1.5.7 only were half-published to npm, so v1.5.8 fixes it here

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

๐Ÿš€ Enhancementโ€‹

  • core
    • #2629 Add ability to get parent feature in jexl syntax with either parent(feature) or get(feature,'parent') (@cmdcolin)
    • #2632 Add vertical resize handle to dotplot view (@cmdcolin)

Committers: 2โ€‹

ยท 2 min read

This release fixes an important bug for users of @jbrowse/react-linear-genome-view where some features would not be able to be clicked in v1.5.3 and v1.5.2.

It also adds some better layout in the feature details panel, improved typescript interfaces, and allows users to open multiple genome assemblies from the start screen in JBrowse Desktop

This release also supercedes v1.5.4 which failed to upload to npm properly

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

๐Ÿš€ Enhancementโ€‹

๐Ÿ› Bug Fixโ€‹

๐Ÿ  Internalโ€‹

Committers: 3โ€‹

ยท One min read

This release fixes @jbrowse/development-tools, which was broken in v1.5.2, and is otherwise identical to v1.5.2. See the v1.5.2 release announcement for details about that release.

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.

1.5.3 (2021-12-21)โ€‹

Packages in this release

PackageDownload
@jbrowse/development-toolshttps://www.npmjs.com/package/@jbrowse/development-tools

๐Ÿ› Bug Fixโ€‹

Committers: 1โ€‹

ยท 5 min read

We're excited to present some great new features and performance improvements in v1.5.2!

New arc display typeโ€‹

A new display type has been added for drawing arcs. The color, thickness, height, label, and caption of the arcs can be customized.

Example of new arc track

New plugin build systemโ€‹

We've re-worked the system used by developers to build external plugins for more stability and flexibility. The current plugin build system will continue to work, but if you want to check out how the new template works, check out the JBrowse Plugin Template.

Storybook docs added for Circular Genome View React componentโ€‹

Find them linked under @jbrowse/react-circular-genome-view here.

Performance improvementsโ€‹

The alignments track now has 25% faster speed on most datasets and particularly on deep short read sequencing, it can be up to 10x faster.

Check out the release notes for more!

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.

1.5.2 (2021-12-20)โ€‹

Packages in this release

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/development-toolshttps://www.npmjs.com/package/@jbrowse/development-tools
@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-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-gtfhttps://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@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-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/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
    • #2579 Add help text and help dialog for the RefNameAutocomplete (@cmdcolin)
    • #2553 Add sashimi-style arcs for RNA-seq type skips on SNPCoverage display (@cmdcolin)
    • #2552 Change border on non-cytoband OverviewScaleBar visible region back to blue and cytoband OverviewScaleBar to a little lighter fill (@cmdcolin)
    • #2509 Implement prop interface for providing arbitrary user-defined glyphs to SvgFeatureRenderer (@hextraza)
    • #2485 Only use one button, "Go", in text search ambiguous results dialog (@cmdcolin)
    • #2501 Add a tooltip to desktop session path so you can see the full path if it's cut off (@garrettjstevens)
  • core
  • core, development-tools
    • #2487 Add support for additional types of plugin formats (commonjs, esm) to allow access to node modules on jbrowse desktop (@garrettjstevens)

๐Ÿ› Bug Fixโ€‹

  • Other
    • #2594 Fix infinite loop bug while searching certain strings and handle multi-word searches better (@cmdcolin)
    • #2589 Fix occasional failures observed from running text-index command (@cmdcolin)
    • #2583 Fix for alignments track base modifications display regarding skipped bases on Mm tag (@cmdcolin)
    • #2556 Fix ability to access BigWig tracks on http basic auth for some cases (@cmdcolin)
    • #2577 Fix ability to use --indexFile on VCF/GFF tabix and CRAM files and add plaintext VCF, GFF, GTF support to add-track CLI (@cmdcolin)
    • #2521 Fix ability to search for tracks with parentheses in tracklist (@cmdcolin)
    • #2512 Fix [object Window] issue in alignment read vs reference dialog (@cmdcolin)
    • #2499 Add missing dependency to CLI (@garrettjstevens)
  • core
    • #2585 Fix ability to use "Color by methylation" on files that require refname renaming (@cmdcolin)
    • #2517 Remove aborting on adapter loading process to fix some tracks getting stuck in infinite loading state (@cmdcolin)
    • #2564 Start looking for parents with parent, not self in findParentThat (@garrettjstevens)
    • #2563 Restore ability to load plugins from relative URL (@garrettjstevens)
    • #2533 Fix drawer widget minimized button being unclickable when overlapping with a view (@cmdcolin)

๐Ÿ“ Documentationโ€‹

๐Ÿ  Internalโ€‹

  • core

Committers: 6โ€‹

ยท 4 min read

This is the release of v1.5.1 with a bunch of small improvements and bugfixes, including...

Cytoband overviewโ€‹

We can now display the cytoband data for your genome assembly in the linear genome view overview, and this will now be available for hg19 and hg38 assembly configs on JBrowse Desktop

This can also appear in SVG exports

Plugins can integrate with "Add track" workflow betterโ€‹

Plugins that register new adapter types can integrate with the "Add track" workflow by registering themselves for a particular file type or file extension with the Core-guessAdapterForLocation

Open plaintext FASTA file on JBrowse desktopโ€‹

Users can now open a plain FASTA instead of an indexed FASTA on JBrowse desktop, and it will create a .fai index on the fly

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.

1.5.1 (2021-11-04)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-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-gff3https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-gtfhttps://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@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-rdf
@jbrowse/plugin-sequencehttps://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@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
    • #2488 Improve usability of the search result autocomplete when typing in via keyboard (@cmdcolin)
    • #2267 Add cytoband to overview scale bar in LGV (@cmdcolin)
    • #2447 Drawer widget tooltips and use position: fixed on fab (@cmdcolin)
    • #2299 Add new pluggable element type and properties to adapter type for registering adapter association with 'add track' workflow (@carolinebridge-oicr)
  • Other

๐Ÿ› Bug Fixโ€‹

  • Other
    • #2494 Add polyfill for text-index compatibility with node 10 (@cmdcolin)
    • #2492 Fix ability to open breakpoint split view from a BEDPE row in SV inspector (@cmdcolin)
    • #2480 Fix refName renaming on VcfAdapter for files that don't have ##contig lines (@cmdcolin)
    • #2469 Fix embedded crash when opening dialogs (@garrettjstevens)
    • #2451 Fix issue with intermittent text-index failures and improve speed (@cmdcolin)
    • #2439 Fix adding plugins on desktop (@cmdcolin)
    • #2426 Fix CLI create/upgrade failing to find the latest release (@cmdcolin)
  • core
    • #2457 Fix linear synteny view import form failure (@cmdcolin)
    • #2444 Fix crash when chromSizesLocation not specified when loading TwoBitAdapter in GUI (@cmdcolin)

๐Ÿ“ Documentationโ€‹

๐Ÿ  Internalโ€‹

Committers: 4โ€‹

ยท 5 min read

We are pleased to present the release of v1.5.0! We have some major new features to announce with this version!

JBrowse Desktopโ€‹

JBrowse Desktop is our fully featured desktop application available for Mac, Windows, and Linux.

Everything you can do with JBrowse Web, you can do with JBrowse Desktop! In fact, because it runs as a desktop app, JBrowse Desktop can do things that the web can't like saving sessions to a file on your computer to revisit later.

JBrowse Desktop session

JBrowse Desktop features a new landing page designed to help you manage your work. Here's a few things you can do with it:

  • re-visit saved sessions using the recent session panel
  • launch new sessions easily from the quick start panel (e.g. hg19 and hg38 are built-in)
  • create a new entries in the quick start panel (e.g. quick launch your favorite organism)
  • quickly rename or delete sessions from the landing page

JBrowse Desktop landing page

With JBrowse Desktop, your genome browser and your web browser can finally live in harmony on your taskbar! โค๏ธ

Access authenticated resourcesโ€‹

This release also contains the ability to access authenticated resources. For JBrowse Desktop, the ability to open files from Google Drive and Dropbox share links is built in. For JBrowse Web, administrators can add some extra configuration to set these up.

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.

1.5.0 (2021-10-18)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-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-gff3https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmarkhttps://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-hic
@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-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-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
    • #2413 Bundle size savings (@cmdcolin)
    • #2390 Support plain text (non-tabix'ed) GFF files with new Gff3Adapter (@teresam856)
    • #2384 Allow docking the drawer on the left side of the screen (@cmdcolin)
    • #2387 Add bulk delete of sessions on jbrowse-desktop (@cmdcolin)
    • #2279 Add ability to access authenticated resources using pluggable internet accounts framework (@peterkxie)
  • Other
    • #2388 Create "quickstart list" on jbrowse-desktop which users can add to (@cmdcolin)
    • #2385 Ensure all dependencies are properly specified in package.json files using eslint-plugin-import (@cmdcolin)
    • #2373 Add auto update functionality for jbrowse-desktop (@cmdcolin)
    • #2369 Add tooltip with track description to track selector (@garrettjstevens)
    • #2258 Update admin-server to accept value from ?config= so that multiple configs could be edited (@cmdcolin)
    • #2321 Add show descriptions toggle box to most feature tracks (@cmdcolin)

๐Ÿ› Bug Fixโ€‹

  • Other
    • #2355 Allow prefix and exact matches jb1 text search (@cmdcolin)
    • #2348 Fix ability to use JB1 backcompat text search adapter (@teresam856)
    • #2322 Fix install plugin workflow and error handling on desktop, update to electron 15 (@cmdcolin)
    • #2329 Fix bugs preventing embedded circular genome view from rendering in some circumstances (@garrettjstevens)
  • core
    • #2352 Better keyboard navigations on text search autocomplete component (@cmdcolin)
    • #2332 Fix ability to use LocalFile on nodejs-based apps e.g. @jbrowse/img (@cmdcolin)

๐Ÿ“ Documentationโ€‹

๐Ÿ  Internalโ€‹

  • Other
  • core
    • #2379 Bump typescript to 4.4.3 (@cmdcolin)
    • #2363 Add some typescripting of some MST models and components (@cmdcolin)
    • #2351 Use main "module" field instead of "browser" from dependency package json files electron builds (@cmdcolin)
    • #2323 Remove session related menu items from jbrowse-desktop (@cmdcolin)

Committers: 6โ€‹