Hi all, This quick release fixes issues with opening local files on JBrowse Desktop
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.
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.6.3
Done in 0.81s.
Hello all,
This release includes a relatively large refactoring of the CLI to use built-in node.js arg parsing, but other than that, these are just small bugfixes and usability improvements. Please see release notes for more info
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.
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.6.2
core
core
Hi all, This has a number of small bugfixes and features. Here are a couple highlights
In previous releases, the dropdown submenus would close the instant your mouse left their boundaries, but now, they stay open until you select a menu item or click away. This can be very useful when accessing nested submenus
We added the ability for plugins to add new entries to the root configuration. This now makes it possible to add easy-to-access configuration for your plugin. Example:
export default class MsaViewPlugin extends Plugin {
name = 'MyPlugin'
install(pluginManager: PluginManager) {}
configure(pluginManager: PluginManager) {}
rootConfigurationSchema(pluginManager: PluginManager) {
return {
mything: ConfigurationSchema('MyConfig', {
greetings: {
type: 'string',
defaultValue: 'hello world',
},
}),
}
}
}
A user could then customize their greeting in a new way like
{
"assemblies": [...],
"tracks": [...],
"plugins": [...],
"mything": {
"greetings": "hello jbrowsers"
}
}
This can then be used in your code by
readConfObject(session.jbrowse, ['mything','greetings'])
Here is an example used by the MSA view plugin https://github.com/GMOD/jbrowse-plugin-msaview/blob/7027f01abe2b4253fd2a250021d2b13a1b4f2fce/src/index.ts#L37-L59
We anticipate that this will enable new and easier plugin customizations
See the release notes below for more info
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.
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.5.1
app-core, core, embedded-core
core
app-core, core
core
core
The synteny view can display long alignments, including insertions and deletions. However, particularly in chain files, the specific "insertion/deletion" markers are less meaningful as a large insertion+deletion pair is often used to connect more high-scoring alignments across large distances
Screenshot before/after toggling the setting to show only matches
This release removes the "start screen" from jbrowse-web. Instead of showing the start screen, users are just dropped straight into the main jbrowse 2 interface. This will hopefully "drop users into the action" faster.
Some notable bug fixes include
bigtools (a newer Rust-based bigwig
toolkit)Feel free to let us know if you have any feedback
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.
yarn run v1.22.18 $ lerna-changelog --silent --silent --next-version 3.5.0
core
core
Hello all, this release adds a small set of features and bugfixes
We added a fuzzy finder library (uFuzzy) that helps prioritize the results returned by our text search (e.g. trix), so gene name searching should provide much more relevant results
We updated gallery (https://jbrowse.org/jb2/gallery/) with new screenshots and live links, and are rolling out updated screenshots throughout the docs pages to be more up to date and high quality
We also fixed a bug in methylation/modifications rendering that caused crashes in v3.2.0-v3.3.0 and updated Electron to v36 (which now uses GTK4 on linux)
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.
yarn run v1.22.18 $ lerna-changelog --silent --silent --next-version 3.4.0
core
core
addToExtensionPoint example in docs
(@garrettjstevens)core, product-core
core
Hello all,
This release adds a significant update to the multi-variant renderer that allows it to be used for visualizing structural variants Previously, all variants >10bp were filtered out, with the idea that overlapping variants are too difficult to interpret
This PR now allows drawing large structural variants in the multi-sample variant display type. It will actually draw long, even overlapping, structural variants!
Figure: Screenshot showing many SV calls over a 5Mbp+ region from the 3,202 human samples from the 1000 genomes project, with a large "inversion" variant showing the shaded triangles. The right side panel shows the feature details for this inversion variant showing the new genotype frequency panel, indicating about 47% of samples have a 'heterozygous' inversion call here
Loading a random track, and turning on the arc display, there are indications of a large variant for a random sample here (green and navy arcs indicate discordant read pairing associated with inversion)
We hope that you enjoy these new features! The visualizations may be visually complex but we hope it can be a magnifying glass to reveal important patterns of your datasets! Feel free to let us know if you have any feedback
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.
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.3.0
core
app-core, core, embedded-core, product-core, sv-core, web-core
core
core
Hello all,
This release includes a new ability to provide simplified snapshots to the linear genome view, a new built-in clustering method for genotypes, and more
In recent versions, we provided the ability to cluster genotype and multi-wiggle tracks, however we provided an R script for users to perform clustering externally and import the results
With this release, we have added a basic in-app clustering workflow, greatly improving the ease-of-use of this feature
Screenshot of the in-app clustering user interface
We have renamed our embedded packages
Motivation: our vanillajs builds, which people often pointed to the "latest" release on from CDN networks, were no longer able to be updated in a backwards compatible way.
Therefore, we have renamed the packages, and updated tutorials.
This allows us to continue updating the package without any breakage for existing users. Please let us know if you run into any issues!
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.
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.2.0
core
app-core, core, product-core, web-core
This release adds several interesting features including
We created a new UI where the "view header" stays visible even when scrolling the page.
We also added the ability to "pin" tracks in the linear genome view, which also stay visible when scrolling the page.
Motivated by the clustering workflow in the Multi-variant viewer, a similar feature was added to the multi-quantitative track
To do this, we sample the data according to the current zoom level (otherwise, it would create very large matrices at per-base resolution) and then provide an R script the user can run to cluster the data
Before clustering
After clustering
The configuration system has a lot of complex substructure, but in this release we created the ability to supply a simplified config, and the results will be auto-determined
For example
{
"type": "AlignmentsTrack",
"trackId": "volvox_alignments",
"name": "volvox-sorted.bam",
"assemblyNames": ["volvox"],
"adapter": {
"type": "BedGraphTabixAdapter",
"bedGraphGzLocation": {
"uri": "file.bed.gz"
},
"index": {
"location": {
"uri": "file.bed.gz.tbi"
}
}
}
}
after
{
"type": "AlignmentsTrack",
"trackId": "volvox_alignments",
"name": "volvox-sorted.bam",
"assemblyNames": ["volvox"],
"adapter": {
"type": "BedGraphTabixAdapter",
"uri": "file.bed.gz"
}
}
The CLI tools and other systems will continue to output the verbose version for the time being, but this simplified system will be handy to anyone who does hand-coding of the configuration
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.
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.1.0
core
app-core, core, product-core
core
Fixes bug with trix searching that has existed since v3.0.0. Thanks to @abjanssen for reporting
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.
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.5
New release
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.
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.4
core
core