JBrowse 1.2 released

New JBrowse release!  This is version 1.2, which makes the server-side scripts much more scalable, includes a script for importing UCSC database dumps into JBrowse, and integrates Juan Aguilar’s touch code for the iPad/iPhone.  Code is here:


Release Notes:

version 1.2, Febrary 2011

These notes document changes since release 1.1 in September 2010.
(Release Notes for 1.1 are here.)

Most of the work in this release went into making JBrowse handle large
amounts of feature data
better.  Before, the amount of memory used
when processing BAM files was more than 10 times the size of the file;
now, the amount of memory required is fixed.

Other new features in this release:

  • Import of UCSC database dumps. A ucsc-to-json.pl script is now provided for taking database dumps from UCSC and creating a JBrowse instance using them.  The “genePred” and “bed” track types are currently supported; “psl” tracks are not yet supported.
  • Touch. Juan Aguilar’s code for using JBrowse on an iOS device (iPhone, iPod touch, iPad) is now integrated.  As of the current release, users wanting to use JBrowse on those devices have to navigate to a separate HTML page (touch.html) rather than the default index.html; i.e. the code does not currently detect touchscreen devices automatically.
  • Bug fixes. A number of bugs have also been fixed, including one that restricted the placement of the “data” directory, and a bug in wiggle rendering that caused spurious peaks or troughs at tile boundaries.

Known issues/limitations with this release:

  • Some additional CPAN modules are now required:


  • No JSON-level backward compatibility. If you are upgrading from an older version of JBrowse, you will have to regenerate all the JSON files on your server. This means wiping your jbrowse/data directory and re-running all server scripts (flatfile-to-json, biodb-to-json, wig-to-json, etc.) to regenerate your data from the original FASTA/GFF/BED/WIG files. We apologize for the inconvenience of this, but it is inevitable sometimes; we do aim to minimize the number of releases which are backwardly-incompatible in this way.
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