Releases: GMOD/jbrowse-components
Release v1.4.0
Release superceded by v1.4.4
Release v1.3.5
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.
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.
1.3.5 (2021-08-23)
Packages in this release
🚀 Enhancement
- Other
- #2163 Add new embeddable React Circular Genome View (@garrettjstevens)
- #2229 Use extendPluggableElement for context menu items (@garrettjstevens)
- #2233 Add optional chromSizes config slot to TwoBitAdapter to speed up loading of TwoBit files with many refseqs (@cmdcolin)
- #2199 Make the BED parser not interpret general tab delimited data as BED12 (@cmdcolin)
- #2241 Restore previous window location when re-opening on desktop (@garrettjstevens)
- #2203 Add a helpful message if there is a 404 on config.json error (@cmdcolin)
- #2204 Hide reads with unmapped flag by default in alignments tracks (@cmdcolin)
- #2198 Add better inversion visualization to read vs reference visualizations (@cmdcolin)
- #2154 Add UMD build of react-linear-genome-view for plain-js use (@garrettjstevens)
core- #2236 Detect assembly loading error and encapsulate error instead of failing at app level (@cmdcolin)
- #2029 Polish desktop builds (@elliothershberg)
- #2140 New core plugin that adds a "bookmarked regions" list widget, new extension points system (@elliothershberg)
🐛 Bug Fix
core- #2245 Fix missing regenerator runtime dependency in core (@garrettjstevens)
- #2202 Fixed a crash when an incompatible adapter is selected for provided data in 'open track' (@carolinebridge-oicr)
- #2197 Fix handle leak for killed worker checker (@cmdcolin)
- Other
📝 Documentation
- #2192 Update Linear Genome View embedding docs (@garrettjstevens)
🏠 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
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- Elliot Hershberg (@elliothershberg)
- Garrett Stevens (@garrettjstevens)
Release v1.3.4
Release superceded by v1.3.5
Release desktop v1.3.3-beta.0
This is the initial beta release of the JBrowse 2 desktop app! 🎉
As the JBrowse developer team prepares for the 1.0.0 desktop release, we would greatly appreciate user feedback at this stage. Applications for MacOS, Linux, and Windows are now available for download.
Note: As this is a beta release, aspects of the app interface are subject to change since the desktop product is still under very active development at this stage.
Release v1.3.3
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!
1.3.3 (2021-08-02)
Packages in this release
🚀 Enhancement
- Other
core
🐛 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)
🏠 Internal
- Other
- #2152 Remove storybook symlink workaround (@garrettjstevens)
core
Committers: 3
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- Teresa Martinez (@teresam856)
Release v1.3.2
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
1.3.2 (2021-07-07)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view |
| @jbrowse/plugin-spreadsheet-view | |
| @jbrowse/plugin-sv-inspector | |
| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg |
| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants |
| @jbrowse/desktop | |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
🚀 Enhancement
- Other
core
🐛 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
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Release v1.3.1
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!
1.3.1 (2021-07-06)
Packages in this release
🚀 Enhancement
core- #2094 More usage of typography to improve consistent text styling (@cmdcolin)
- #2068 Add non-indexed and plaintext VCF Adapter to variants plugin (@carolinebridge-oicr)
- #2067 Better error message if a file location has an empty string (@garrettjstevens)
- #2064 Export offscreenCanvasPonyfil from core/util (@garrettjstevens)
- #2060 Improve performance with large numbers of reference sequences by using MST volatiles (@cmdcolin)
- #2050 Configurable app logo for web (@elliothershberg)
- Other
- #2104 Use ScopedCssBaseline to help style the embedded component (@cmdcolin)
- #2015 Deprecate ThemeProvider in
@jbrowse/react-linear-genome-view(@garrettjstevens)
🐛 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)
🏠 Internal
core- #1967 Omit configurationSchema snapshot when it matches the default (@garrettjstevens)
- #2078 Restore eslint rule for no-unused-vars (@cmdcolin)
- #2051 Add missing named exports to shared core modules (@garrettjstevens)
- #2045 Add basic architecture for text searching (@teresam856)
- Other
Committers: 5
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- Elliot Hershberg (@elliothershberg)
- Garrett Stevens (@garrettjstevens)
- Teresa Martinez (@teresam856)
Release v1.3.0
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.
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.
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.
In this screenshot, the top alignments track is colored by methylation and the
bottom alignments track is colored by base modification.
1.3.0 (2021-05-24)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools |
| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments |
| @jbrowse/plugin-breakpoint-split-view | |
| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view |
| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config |
| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management |
| @jbrowse/plugin-dotplot-view | |
| @jbrowse/plugin-filtering | |
| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 |
| @jbrowse/plugin-hic | |
| @jbrowse/plugin-legacy-jbrowse | |
| @jbrowse/plugin-linear-comparative-view | |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/plugin-lollipop | |
| @jbrowse/plugin-menus | |
| @jbrowse/plugin-protein | |
| @jbrowse/plugin-rdf | |
| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence |
| @jbrowse/plugin-spreadsheet-view | |
| @jbrowse/plugin-sv-inspector | |
| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg |
| @jbrowse/plugin-trackhub-registry | |
| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants |
| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle |
| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli |
| @jbrowse/desktop | |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
🚀 Enhancement
- Other
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)
🐛 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
📝 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)
🏠 Internal
- Other
core,development-tools
Committers: 4
- Colin Diesh (@cmdcolin)
- Elliot Hershberg (@elliothershberg)
- Garrett Stevens (@garrettjstevens)
- Robert Buels (@rbuels)
Release v1.2.0
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.
1.2.0 (2021-05-03)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments |
| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed |
| @jbrowse/plugin-breakpoint-split-view | |
| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view |
| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config |
| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management |
| @jbrowse/plugin-dotplot-view | |
| @jbrowse/plugin-filtering | |
| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 |
| @jbrowse/plugin-hic | |
| @jbrowse/plugin-legacy-jbrowse | |
| @jbrowse/plugin-linear-comparative-view | |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/plugin-lollipop | |
| @jbrowse/plugin-menus | |
| @jbrowse/plugin-protein | |
| @jbrowse/plugin-rdf | |
| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence |
| @jbrowse/plugin-spreadsheet-view | |
| @jbrowse/plugin-sv-inspector | |
| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg |
| @jbrowse/plugin-trackhub-registry | |
| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants |
| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle |
| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli |
| @jbrowse/desktop | |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
🚀 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)
🐛 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)
📝 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)
🏠 Internal
core- #1932 Update analytics and share API URLs to refer to more stable locations (@peterkxie)
- #1888 More lazy loading of react components to reduce bundle size ([@cmdcolin](https:...
Release v1.1.0
We're pleased to announce a new release of JBrowse Web!
Changed callbacks language from JavaScript to Jexl
To allow users to safely and seamlessly share advanced configurations in sessions, we now use Jexl to express configuration callbacks. Note that this is a breaking change, function()-style callbacks will no longer work.
For details, see the callbacks section of our configuration guide.
Fetch intron and upstream/downstream sequences
We also have several other improvements including the ability to get intron and
upstream/downstream sequence in the feature details
Interactive documentation using Storybook
Another new update is the first release of our interactive Storybook docs for the embeddable React Linear Genome View.
The docs contain live examples of how the LGV component can be used, along with source-code examples.
The site can be found here.
Enhanced navigation to drawer widget stack
We have added a dropdown to enhance navigation between stack of active widgets. The update also adds a minimize button to allow quick access to full screen JBrowse web.
🚀 Enhancement
core- #1846 Improve copy+paste in the data grids for feature details (@cmdcolin)
- #1814 Add ability to get promoter sequence and intron sequence for genes from the feature details panel (@cmdcolin)
- #1816 Remove some animation effects (@cmdcolin)
- #1778 Adds dropdown to show drawer widget stack (@teresam856)
- #1685 Change callbacks language from JavaScript to Jexl (@peterkxie)
- Other
- #1831 Add dialog for launching breakpoint split view from variant feature details (@cmdcolin)
- #1803 Transcript and gene glyphs can now display implied UTRs, active by default (@cmdcolin)
- #1808 Add another heuristic for returning gene features from BigBed (@cmdcolin)
- #1774 Add warning dialog in LGV before returning to import form to prevent accidentally losing the current view (@cmdcolin)
🐛 Bug Fix
core- #1811 Check for existence of window more robustly to allow in SSR or node applications (@elliothershberg)
- #1793 Fix dotplot rendering outside it's allowed bounds (@cmdcolin)
- #1783 Add hic aborting and fix remoteAbort signal propagation (@cmdcolin)
- #1723 A few bugfixes (@garrettjstevens)
- Other
📝 Documentation
- #1824 Add storybook docs page for nextjs usage (@elliothershberg)
- #1770 1469 storybook deploy (@elliothershberg)
- #1807 Update developer guide to cover displays, and highlight working external plugins (@cmdcolin)
- #1779 Collaborative release announcement editing (@rbuels)
- #1791 Add a couple more demos for our live version with MDX (@cmdcolin)
🏠 Internal
- Other
- #1820 Create v1.1.0.md, draft of release announcements (@garrettjstevens)
- #1823 Add note about previewing changelog to CONTRIBUTING.md (@garrettjstevens)
core