-
Notifications
You must be signed in to change notification settings - Fork 63
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
3 changed files
with
146 additions
and
1 deletion.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,93 @@ | ||
--- | ||
title: v2.8.0 Release | ||
date: 2023-11-09 16:18:56 | ||
tags: ['release', 'jbrowse 2'] | ||
--- | ||
|
||
This release improves support for BEDPE and arc rendering of structural | ||
variants. | ||
|
||
It also adds a new CLI command called `jbrowse sort-gff` that intends to help | ||
simplify the loading of GFF tabix tracks. | ||
|
||
Usage: | ||
|
||
``` | ||
jbrowse sort-gff yourfile.gff | bgzip > yourfile.sorted.gff.gz | ||
tabix yourfile.sorted.gff.gz | ||
jbrowse add-track yourfile.sorted.gff.gz --load copy --out /var/www/html/jbrowse2 | ||
``` | ||
|
||
The jbrowse CLI tool can load BEDPE files with simply | ||
`jbrowse add-track yourfile.bedpe` (or, optionally gzipped e.g. | ||
yourfile.bedpe.gz) | ||
|
||
![](https://user-images.githubusercontent.com/6511937/281789167-aef6ccd2-c7e4-444e-b213-f3876fedabf9.png) | ||
|
||
Screenshot showing the same data rendered as both a BEDPE file and VCF file with | ||
different variant types (`<DUP>, <DEL>, <INV>, <TRA>`). Notably, this arc | ||
rendering can render 'cross-region' or 'inter-chromosomal' arcs. | ||
|
||
Also, if you haven't seen it, check out our new office hours and community call | ||
schedule! See https://jbrowse.org/jb2/blog/2023/11/03/office-hours/ | ||
|
||
## Downloads | ||
|
||
- [v2.8.0](https://github.com/GMOD/jbrowse-components/releases/tag/v2.8.0) | ||
|
||
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](https://jbrowse.org/jb2/docs/quickstart_web) for more | ||
details. | ||
|
||
yarn run v1.22.19 $ lerna-changelog --silent --next-version 2.8.0 | ||
|
||
## 2.8.0 (2023-11-09) | ||
|
||
#### :rocket: Enhancement | ||
|
||
- Other | ||
- [#4045](https://github.com/GMOD/jbrowse-components/pull/4045) Create | ||
multi-region arc display type for variant tracks | ||
([@cmdcolin](https://github.com/cmdcolin)) | ||
- [#4050](https://github.com/GMOD/jbrowse-components/pull/4050) Allow | ||
specifying alternative config.json path via global variable | ||
([@cmdcolin](https://github.com/cmdcolin)) | ||
- [#4046](https://github.com/GMOD/jbrowse-components/pull/4046) Show last | ||
autosave on jbrowse-web start screen | ||
([@cmdcolin](https://github.com/cmdcolin)) | ||
- [#4044](https://github.com/GMOD/jbrowse-components/pull/4044) Speed up | ||
"multi-region" navigation in search box | ||
([@cmdcolin](https://github.com/cmdcolin)) | ||
- [#4032](https://github.com/GMOD/jbrowse-components/pull/4032) Add | ||
`jbrowse sort-gff` subcommand ([@cmdcolin](https://github.com/cmdcolin)) | ||
- `product-core` | ||
- [#4040](https://github.com/GMOD/jbrowse-components/pull/4040) Strip baseUri | ||
in 'About track' copy config ([@cmdcolin](https://github.com/cmdcolin)) | ||
- `core` | ||
- [#4035](https://github.com/GMOD/jbrowse-components/pull/4035) Prompt to | ||
horizontally flip view when launching linear synteny view on inverted | ||
feature ([@cmdcolin](https://github.com/cmdcolin)) | ||
- `app-core` | ||
- [#4024](https://github.com/GMOD/jbrowse-components/pull/4024) Add | ||
right-handed arrow to view title to emphasize the focused view | ||
([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) | ||
|
||
#### :bug: Bug Fix | ||
|
||
- [#4052](https://github.com/GMOD/jbrowse-components/pull/4052) Fix browser back | ||
button behavior in jbrowse-web ([@cmdcolin](https://github.com/cmdcolin)) | ||
- [#4043](https://github.com/GMOD/jbrowse-components/pull/4043) Fix crash in | ||
"Open session" widget for sessions that have 'track-less views' | ||
([@cmdcolin](https://github.com/cmdcolin)) | ||
|
||
#### :memo: Documentation | ||
|
||
- [#4027](https://github.com/GMOD/jbrowse-components/pull/4027) Add office hours | ||
and community meetings ([@cmdcolin](https://github.com/cmdcolin)) | ||
|
||
#### Committers: 2 | ||
|
||
- Caroline Bridge | ||
([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) | ||
- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 2.23s. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters