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v1.0.1 Release

· 4 min read

This release of JBrowse Web includes several improvements and bug fixes, including:

  • A new sequence track renderer that includes translation frames
  • The addition of session connections
  • A new track selector icon
  • Improvements to feature details widgets
  • And more! See details below.

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.

v1.0.1 (2020-11-25)​

🚀 Enhancement​

🐛 Bug Fix​

  • core
    • #1491 Fix ability to add a PAF synteny track with add-track (@cmdcolin)
    • #1470 Avoid rendering the literal string 'null' in the feature details (@cmdcolin)
  • Other
    • #1489 Fix long read vs ref CIGAR rendering for horizontally flipped synteny view (@cmdcolin)
    • #1460 Add support for more bigBed subtypes and fallback for unsupported types (@peterkxie)
    • #1472 Wait on assemblies that are being tracked by the assemblyManager only (@cmdcolin)
    • #1466 Avoid rendering the display and renderer settings in the about this track dialog (@cmdcolin)
    • #1461 Fix usage of jbrowse-cli on node 10.9 related to fs.promises (@cmdcolin)
    • #1452 Bug: search box disappears from LGV header on smaller widths (@teresam856)
    • #1432 Make global variables window.JBrowseSession and window.JBrowseRootModel available in jbrowse-web (@teresam856)
    • #1431 Fix connection tracks not showing up in track selector (@garrettjstevens)
    • #1428 Fix the listVersions behavior of the jbrowse-cli returning duplicate entries (@cmdcolin)
    • #1422 Fix crash from empty ALT field in VCF (@cmdcolin)
    • #1413 Fix ability to add CRAM tracks using the web based add-track GUI (@cmdcolin)

📝 Documentation​

🏠 Internal​

Committers: 5​

v1.0.0 Release

· 2 min read

I am pleased to announce the first stable release of JBrowse 2!

This release includes our new "display modes" concept which allows the same track to be displayed in different view types. For example, the same synteny track can be used in both a dotplot or a linear synteny view. Similarly, a SV VCF with breakends can be used in the circular view or a linear genome view.

This has been a massive effort by the team to get us to this 1.0.0 release, and we greatly thank all the beta users who have helped us with testing.

Changes

  • fixed bug with reference sequences that don't use the alias system
  • fixed bug with SV inspector having a disabled state stuck on the buttons
  • added documentation for the jbrowse admin-server command
  • added display modes, a giant effort to make the same track visible in multiple contexts
  • added a splash screen when no default session is in the config file
  • changed error state of spreadsheet to a volatile
  • fixed loading state of the RefNameAutocomplete
  • fixed spreadsheet import of VCF with no FORMAT column
  • made a small bundle-size improvement from removing unused crypto-js resources
  • removed savedSessions from config schema
  • fixed deleting a track when a closed widget references it
  • fixed crash when live editing an assembly in the assembly manager
  • added a simple PAF import form in the DotplotView and LinearSyntenyView import forms
  • updated @mui/material version
  • clearer output printed when using admin-server

Enjoy!

To install, you can download the link above, or you can use the jbrowse CLI tool to automatically download the latest version. See the jbrowse 2 quick-start guide for more info

v0.0.1-beta.28 Release

· 2 min read

This is the next round in our beta testing on the way to a stable release

New features include

  • added an assembly manager
  • added a bugfix for refname mapping that caused slowness
  • updated colors tied to the theme
  • fixed side scrolling on OSX triggering the back button
  • created shorter share URLs
  • fixed for VCF track set
  • created a default title on views that corresponds to the assembly name being viewed if relevant
  • better autoinference on add track
  • slower update frequency for the header bar, allowing faster scroll
  • hide callbacks on irrelevant config slots
  • disable opening local URLs in the add track workflows currently
  • created a --indexFile flag for the add-track CLI for adding BAI, CRAI, TBI, CSI index, etc. if it isn't automatically inferred
  • created a --out flag for the add-track CLI
  • improve behavior when running the CLI outside of the config directory
  • add ability to use the admin-server and the normal localhost:3000 webpack-dev-server in parallel

Enjoy!

To install, you can download the link above, or you can use the jbrowse CLI tool to automatically download the latest version. See the jbrowse 2 quick-start guide for more info

v0.0.1-beta.27 Release

· One min read

Hello all,

This is the first automated release of JBrowse 2 beta! This includes many exciting features including a new session sharing system. There are a whole host of other changes that have not been tracked CHANGELOGs yet but we will be reporting more granular updates with our later releases!

To install, you can download the link above, or you can use the jbrowse CLI tool to automatically download the latest version. See the jbrowse 2 quick-start guide for more info

JBrowse 2 launch!

· One min read
Colin Diesh

We are happy to now announce the release of JBrowse 2 public beta

JBrowse 2 has been in development for almost 2 years at this point, and it has now developed features that offer compelling new functionality

Now, it is finally getting more stable, and we invite interested users to try it out!

To get started

  • Download a release
  • Set it up
  • Try it with your own data
  • Tell us about your experience!

We are excited to get you involved, and this website will evolve here soon