Fwd: [Gmod-ajax] JBrowse 1.12.3 Released

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Fwd: [Gmod-ajax] JBrowse 1.12.3 Released

nathandunn

JBrowse released a new version. 

If you need this version (you probably don’t) in Apollo in a released version of apollo, you change your config to point the tag instead of the commit hash as below and rebuild using ./apollo clean-all && ./apollo deploy :

jbrowse {
git {
url= "https://github.com/gmod/jbrowse"
tag = 1.12.3-release
// . . . .
I’ve made the change in master, but we also haven’t tested it in production yet either.    However, I wanted to make sure users could take advantage of some of these great new features and bug fixes if they were effecting you.

Cheers,

The Apolloo Team

Begin forwarded message:

From: Eric Yao <[hidden email]>
Subject: [Gmod-ajax] JBrowse 1.12.3 Released
Date: May 3, 2017 at 4:07:13 PM PDT
To: JBrowse List <[hidden email]>

We are happy to announce JBrowse 1.12.3 release!  


This release includes a lot of improvements and bugfixes and we thank the community for the support. Some great new features include parsers for new file formats including 2bit format, which can be loaded via prepare-refseqs.pl. There are also new parsers for tabix BED files, tabix GFF and IonTorrent BAM files. Some other improvements include a new `noFill` option to display BigWig tracks as a scatter plot, the `cacheMismatches` option that improves performance for BAM files with long reads, and many other small improvements and fixes. Enjoy!

Minor improvements

  • Upgraded build system to install dependencies with bower and
    updated to dojo 1.9.8 (issue #718).
  • Added the ability to load tabix indexed GFF and BED files.
    Thanks to Colin Diesh and @zhjilin for contributing (issue #670).
  • Added ability to open BED files in the “Open track” user interface
    (issue #729).
  • Added ability to access SPARQL and other jbrowse data stores via CORS. Thanks to the WebApollo hackathon and Eric Rasche for contributing (issue #679).
  • Added extra coloring schemes for the Sequence track when using
    protein residues. Thanks to Eric Rasche for the idea and
    implementation (issue #673).
  • Added ability to specify custom exporter classes for the “Save
    track data” option, for example, adding exporter code in plugins
    (issue #682).
  • Added ability to specify custom name store classes via plugins,
    which allows plugins to implement their own search functionality
    (issue #732).
  • Added a timeout for the track feature density calculations which
    can aid problems like consistent chunkSizeLimit issues
    (issue #540issue #730).
  • Added an option to specify multiple highlights, or bookmarks,
    using the config file, a remote service, or the URL bar
    (issue #668).
  • Added support for parsing BAM files from IonTorrent (issue #782issue #568).
  • Added support for native file access to .2bit files (issue #759).
  • Added list of plugins in about box (issue #848).
  • Added cacheMismatches option to improve performance when viewing long-read alignments (issue #860).
  • Added subfeatureDetailLevel config item to make View details box only load subfeatures on demand (issue #861).
  • Added ability to draw scatter plot from BigWig tracks. Thanks to
    Keiran Raine for the contribution (issue #741).
  • Added a fullviewlink option for the URL bar to disable “View full
    link” attribute in embedded JBrowse. Thanks to Vivek Krishnakumar for contributing (issue #813).
  • Added URL parameter &tracklabels=0 and config parameter to hide track labels (issue #869).
  • Added renderAlignment option which creates a per-base alignment view of the read versus the reference (issue #795).
  • Added inferCdsParts option which creates CDS subfeatures from a continuous CDS region for CanvasFeatures glyphs. Thanks to
    Vivek Krishnakumar for the contribution (issue #872).
  • Added events tracks/focus, tracks/unfocus, allowing for context
    switching based on selected track.

Bug fixes

  • Made the menu bar widgets centered again (issue #680).
  • Fixed error where the sequence track would not load after “Open
    sequence file” (issue #831).
  • Fixed problem with persistant “Error reading from name store”
    message. Thanks to Anthony Bretaudeau for contributing the fix!
    (issue #820).
  • Reverted to standard eukaryotic codon set.
  • Fixed issue where saving session in JBrowse Desktop where plugins were not saved with session.
  • Fixed an error if there were numerical values being used as label
    or description for the CanvasFeatures type tracks. Thanks to
    Eric Rasche for reporting (issue #673).
  • Fixed some issues where the Gene glyph would not layout some
    features correctly. Thanks to Eric Rasche for reporting
    (issue #686).
  • Fixed an issue with JBrowse Desktop where saving session would not save the tracks that were not visible.
  • Added fix when using indexed fasta from prepare-refseqs.pl.
    Thanks to @billzt for the report (issue #719).
  • Added a fix for an issue where editing the configuration of files
    that were opened by a user didn’t work. Thanks to @lpryszcz for
    the report (issue #569).
  • Fixed some inconsistencies where “Open sequence” on file with a
    .fasta file extension failed (issue #696).
  • Fixed issue where track labels would re-appear during scroll
    (issue #793).
  • Added handler for click scrolling in genome view. Thanks to
    @exogenesys for fixing (issue #709).
  • Fixed a rare error that only affected some versions of Chrome
    (issue #758).
  • Removed linear gradients from some NeatFeatures tracks
    (issue #721).
  • Fixed issue where saving GFF3 would fail if the source data
    was in VCF format (issue #800).
  • Fixed issue where there was a mix of plugin declarations
    (issue #866).
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