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路 3 min read

We're excited to announce the v1.4.4 release! Some highlights of this release include:

Text searching#

Finally, we have added the ability to search by gene name!

Users will now be able to create their own text indexes with the jbrowse text-index command, which creates an index for searching by gene names, identifiers and descriptions.

searching in lgv

GIF showing the process of searching via the location search box of the Linear Genome View. Try it out yourself here, type your favorite gene name e.g. HER2, PTEN, or others in the search box https://jbrowse.org/code/jb2/v1.4.4/?config=test_data%2Fconfig_demo.json&session=share-H3vwqh1BKa&password=xYz9Z

For a quick introduction and a tutorial on how to add this feature to your JBrowse instance, check out this quick start

Like most parts of JBrowse, the text searching system is pluggable. Plugin developers can add new text index adapters to connect JBrowse to other types of text search services, indexes, or databases.

Users of the @jbrowse/react-linear-genome-view can also enable text searching functionality, see https://jbrowse.org/storybook/lgv/v1.4.0/?path=/story/text-searching--page

Note that 1.4.0-1.4.3 had issues during publish, so we moved all release notes for them to here. Thanks to @bbimber for letting us know about these issues.

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.

1.4.4 (2021-09-14)#

Packages in this release

PackageDownload
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-trixhttps://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variantshttps://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/desktop
@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

馃殌 Enhancement#

  • Other
    • #2287 Use react-popper to reduce tooltip lag on pages with many elements (@cmdcolin)
    • #2294 Don't rely on SVTYPE=BND for breakend split view options and thicker mouseover chords on circular views (@cmdcolin)
    • #2272 Auto adjust box RefNameAutocomplete width based on refName length (@cmdcolin)
    • #2243 Import bookmarks functionality for grid bookmark widget (@cmdcolin)
  • core
    • #2247 New jbrowse-desktop start screen design (@cmdcolin)
    • #2254 Better error reporting from web worker and chrom sizes adapter errors (@cmdcolin)
    • #1881 Add new text searching functionality to core, with jbrowse text-index CLI command to generate trix index (@teresam856)

馃悰 Bug Fix#

  • core
    • #2320 Fix issue where add track widget doesn't infer adapters on second usage (@cmdcolin)
    • #2250 Prevent the ToggleButton for the FileSelector toggling to local file when only URL should be available (@cmdcolin)
  • Other
    • #2309 Fix mouseover selection appearing across unrelated blocks (@cmdcolin)
    • #2283 Fix ability for the variant detail panel to create breakpoint split view for \<TRA> elements (@cmdcolin)
    • #2268 Fix autocomplete height on small displays (@cmdcolin)

馃摑 Documentation#

  • #2300 Release announcement draft v1.4.0 (@teresam856)
  • #2310 Add cancer demos to the demos page on website (@cmdcolin)
  • #2253 Add note about legacy-peer-deps to embedded component readme (@cmdcolin)
  • #2262 Add more MDX documentation pages to @jbrowse/react-linear-genome-view storybooks (@cmdcolin)

馃彔 Internal#

Committers: 3#

路 4 min read

We're excited to announce the v1.3.5 release of JBrowse! Some highlights of this release include:

New embedding build of @jbrowse/react-linear-genome-view#

This release adds a new UMD build of our @jbrowse/react-linear-genome-view React component. This build will allow users to use our React Linear Genome View in a website that doesn't otherwise use React. See a tutorial for how to get started using this build:

A preliminary beta version of this build was used in a tutorial at BOSC2020, and that tutorial was also on our website. If you've used that version, the interface has changed somewhat, so come check out the new tutorial for the official released version!

Bookmark widget#

A new widget has been added that is accessible from the Linear Genome View view menu or when you click and drag over a region in the header (a.k.a rubber band selection). This view keeps a list of bookmarked regions, which you can add custom labels to, and also which you can use to navigate back to that region. The bookmarks can also be exported.

Bookmark widget in use

Note to plugin developers#

If your plugin adds menu items or context menu items to a track, or customizes renderProps, there may be some changes that affect how those menu items work, particularly in #2226 and #2229. Also see an updated example of context menu items here.

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.

1.3.5 (2021-08-23)#

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-data-managementhttps://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-grid-bookmarkhttps://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-hic
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@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/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

馃殌 Enhancement#

馃悰 Bug Fix#

馃摑 Documentation#

馃彔 Internal#

  • core
    • #2057 Use idMaker for dataAdapterCache key for faster FromConfigAdapter performance (@cmdcolin)
    • #2231 Export offscreenCanvasUtils (@cmdcolin)
    • #2226 Use superRenderProps and superTrackMenuItems for better simulated inheritance model (@cmdcolin)
    • #1874 Add aborting to CoreGetFeatures rpcManager call (@cmdcolin)
  • Other

Committers: 4#

路 3 min read

This is a small bugfix release that includes notable fixes for the methylation/modifications drawing (the negative strand reads displayed the data incorrectly) and the reference name selector

Please check the release notes for more details!

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.

1.3.3 (2021-08-02)#

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-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-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-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

馃殌 Enhancement#

馃悰 Bug Fix#

  • Other
    • #2159 Stop local storage quota-exceeded errors preventing the app from starting (@cmdcolin)
    • #2161 Remove outline from clicking on SVG chord tracks (@cmdcolin)
    • #2157 Fix rendering of negative strand alignment modifications/methylation (@cmdcolin)
    • #2131 Fix mouseovers/click handlers after "force load" button pressed (@cmdcolin)
    • #2128 Fix using the "Color by modifications" setting on files that need ref renaming (@cmdcolin)
    • #2115 Fix bug where sometimes plugin could not be removed from UI (@garrettjstevens)
    • #2119 Fix loading indicator on the reference sequence selector getting stuck (@cmdcolin)
  • core
    • #2101 Fix behavior of the end-of-list indicator in refNameAutocomplete to always display as a disabled item (@teresam856)

馃彔 Internal#

Committers: 3#

路 2 min read

This is a hotfix release that fixes a bug that prevented the @jbrowse/react-linear-genome-view component from being used in v1.3.1

It also contains a couple other small improvements

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.

1.3.2 (2021-07-07)#

Packages in this release

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-circular-viewhttps://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svghttps://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-variantshttps://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/desktop
@jbrowse/react-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

馃殌 Enhancement#

馃悰 Bug Fix#

  • #2109 Make sure to wait for assembly to load before downloading canonical refnames in SV inspector (@cmdcolin)
  • #2111 Fix "Can't resolve '@jbrowse/plugin-legacy-jbrowse'" in @jbrowse/react-linear-genome-view (@garrettjstevens)

Committers: 2#

路 3 min read

Hello everyone! This release offers a couple important bug fixes.

For users of @jbrowse/react-linear-genome-view, we have fixes that improve speed, CSS style consistency, and theming. We also have another speed improvement for users with many scaffolds or contigs. Please see the release notes below for more details!

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.

1.3.1 (2021-07-06)#

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-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-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-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

馃殌 Enhancement#

馃悰 Bug Fix#

  • Other
    • #2097 Improve speed for laying out features for embedded/mainthreadrpc scenarios (@cmdcolin)
    • #2096 Fix issue with page reload after editing session title (@cmdcolin)
    • #2074 Fix support for opening local files in spreadsheet/SV inspector (@cmdcolin)
    • #2061 Fix issue with using --force error when no track was previously loaded (@cmdcolin)
    • #2024 Flip drawing of negative strand PAF features in linear synteny and dotplot views (@cmdcolin)
    • #2023 Fix infinite loop in adding some plugins on desktop (@cmdcolin)
    • #2019 Fix session import to use blob map for opening local files (@cmdcolin)
  • core
    • #2071 Add indicator to the end of ref name dropdown to suggest user to type the searchbox for more (@teresam856)
    • #2056 Fix infinite recursion in FromConfigAdaptor by avoiding mutating the passed in data when using SimpleFeature (@cmdcolin)
    • #2018 Fix 3'UTR in sequence detail panels when no UTRs are in gff (@cmdcolin)

馃彔 Internal#

Committers: 5#

路 4 min read

We're excited to announce the v1.3.0 release of JBrowse Web! Some highlights of this release include:

In-app plugin store#

Building on the plugin store on our website in the last release, we're now excited to announce that plugins can be installed from within JBrowse Web! Plugins from our plugin store can now be installed with the click of a button.

Screenshot of plugin store with MsaView plugin installed and open

Open local files#

JBrowse Web now has the ability for tracks to use files on your local hard drive. This is a great option if you want to visualize files you have locally without uploading them to a server. These files will need to be re-opened each time the app is opened or refreshed, but more robust handling of local files will be available when we release JBrowse Desktop.

Screenshot of selector in URL and File states

Color by MM and MP/ML tags in BAM/CRAM#

The MM and MP/ML tags can be used to color alignments tracks by either base modifications or by methylation. The modifications mode is exciting because it can show arbitrary DNA/RNA modifications, and the methylation mode uses specific CpG context to show both modified and unmodified CpGs.

Screenshot of alignments tracks colored by methylation and base modification

In this screenshot, the top alignments track is colored by methylation and the bottom alignments track is colored by base modification.

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.

1.3.0 (2021-05-24)#

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-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

馃殌 Enhancement#

  • Other
    • #2001 Make tracks added using the add track widget a session track if not in adminMode (@cmdcolin)
    • #1980 Add popup confirmation dialog for unknown session plugins, and use plugins.json as a whitelist (@cmdcolin)
    • #1977 Upgrade @material-ui/data-grid (@cmdcolin)
  • core
    • #1982 Allow manually specifying adapter type if filename does not match expected pattern (@cmdcolin)
    • #1975 Allow local files on the users computer to be opened as tracks in jbrowse-web (@cmdcolin)
    • #1865 Show modified bases using MM and MP/ML tags in BAM/CRAM (@cmdcolin)
    • #1984 Better feature details when there are short arrays of json supplied as feature data (@cmdcolin)
    • #1931 Create in app graphical plugin store (@elliothershberg)

馃悰 Bug Fix#

  • core
    • #1985 Avoid error calculating UTR on features that have no exon subfeatures (@cmdcolin)
    • #1954 Add more environments to configSchema create calls to fix ability to use custom jexl commands with main thread rendering (@cmdcolin)
    • #1963 Fix ability to use DialogComponent (used for svg export, pileup sort, etc) on embedded components (@cmdcolin)
    • #1945 Fix hic not being able to render due to incorrect lazy loading (@cmdcolin)
  • Other

馃摑 Documentation#

  • #2002 Add @jbrowse/img to homepage (@cmdcolin)
  • #2007 Update docs for modifications/methylation coloring, plugin store, and the sequence panel in feature details (@cmdcolin)
  • #1976 reorganize the demo page to emphasize the cancer sv demo more (@rbuels)
  • #1952 Add demo for 1000 genomes extended trio dataset to website (@cmdcolin)
  • #1862 Add example for using a build-time included plugin to storybook (@cmdcolin)

馃彔 Internal#

  • Other
    • #2003 Make SNPCoverage independently generate the modifications tag-color mapping (@cmdcolin)
  • core, development-tools

Committers: 4#