JBrowse 1.11.4 released

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JBrowse 1.11.4 released

Diesh, Colin M.
Hello everyone,

I am happy to announce the release of JBrowse 1.11.4. This release represents they great community effort to keep things going after Rob’s leave. This version has some exciting new developments, such as high-resolution rendering of canvas-based tracks and a basic GTF file parser. There are also several important bug fixes, including an update to the setup.sh script in order to maintain compatibility with the latest BioPerl.

The release can be downloaded from http://jbrowse.org/jbrowse-1-11-4.

Full release notes:

## Minor improvements

 * Added high-resolution rendering for CanvasFeatures, SNPCoverage,
   BigWig tracks, and histograms. This allows rendering for canvas-
   based tracks to look much sharper on high-resolution displays and
   can even look sharper when zooming. The high-resolution rendering
   is disabled by default to avoid conflicts with existing instances,
   but feel free to test it out by setting "highResolutionMode" in
   jbrowse.conf. Thanks to Colin Diesh for the idea and implementation
   (issue #456)

 * Added the ability to run jbrowse scripts outside of the JBrowse
   root directory. Thanks to Chien-Chi Lo for the patch (issue #465).

 * Added basic GTF parser that can open files from the File->Open
   menu or by using the in-memory adaptor. Big thanks to Andrew Warren
   for the contribution (issue #453).

 * Added a change to the highlight button to allow the user to more 
   easily clear highlights. Thanks to Paul Hale for the suggestion
   and Colin Diesh for the fix (issue #445).

## Bug fixes

 * Fixed help page icons not loading since JBrowse 1.11.2. Thanks to
   Colin Diesh for catching the bug and fixing it (issue #460).

 * Fixed updating of the y-axis scale when using the resize
   quantitative tracks feature. Thanks again to Evan Briones for the
   original implementation and Colin Diesh for the fix (issue #461).

 * Changed the CanvasFeatures 'View details' pages to display the name
   and description of features in the dialog box. Thanks to Colin 
   Diesh for the fix (issue #463).

 * Added a bugfix for non-compliant servers that add a trailing slash
   to the URL. Thanks to Colin Diesh for the fix (issue #462).

 * Fixed a broken link in the documentation for biodb-to-json.

 * Updated setup.sh to maintain compatibility with the latest BioPerl.
   Thanks to Thomas Sibley and Scott Cain for helping with this issue
   (issue #468).

 * Fixed a long standing bug with the coloring of nucleotides on the
   SNPCoverage/Alignments2 track. Thanks to Long Le for reporting this
   on the mailing list.

 * Fixed a long standing bug with the scrollbar in the dialog box on
   Chrome and Safari browsers. Thanks to the #dojo irc channel and
   and Colin Diesh for helping fix this problem (issue #386).

 * Fix a small rendering problem that causes one pixel gap to appear
   on Safari due to subpixel rendering issues. Thanks to Colin Diesh
   for the preliminary fix (issue #341).

 * Fix a bug with CanvasFeatures based tracks loading huge amounts
   of data to generate histograms instead of using pre-generated
   histograms. Also lowered the maxScreenFeatureDensity default on
   the CanvasFeatures tracks so that histograms can be displayed more
   readily. Thanks to Daniel Troesser for reporting this issue on the
   mailing list and Colin Diesh for the fix (issue #475).


Happy browsing!!


Colin Diesh
Research Analyst
Elsik Lab
University of Missouri, Columbia