News/GBrowse 2.13 Release

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GBrowse 2.13 Released

GBrowse version 2.13 has been released. 2.13 is a maintenance update to 2.12. GBrowse 2.13 and 2.12 include these changes:

New features & enhancements
  • The DAS server and client are now functional. You will need Bio::Das version 1.17 and Bio::Graphics version 2.11 for best results.
  • The "import track" function now allows you to specify the URL of either a BAM or a BigWig file. The track will be displayed without physically copying the file onto the GBrowse server. You will need Bio::DB::Sam and Bio::DB::BigWig for these features to work.
  • Uploading a Wig file now generates a BigWig database for improved performance and scalability. This requires Bio::DB::BigWig to be installed.
  • There is now a Get chromosome sizes entry in the File menu.
  • Calling GBrowse with the CGI argument action=scan will generate a quick summary of track contents.
  • Improved performance when working with truly huge (>1000 track definition) configuration files.
  • Fasta, GFF3, SAM and wiggle dumps now include the genome build ID if that information is provided in the data source "metadata" configuration variable.
Bug fixes
  • When MySQL is used as the back end for user uploads, it will no longer fail on long filenames.
  • Fixed the "eurl" CGI parameter for importing data sets by their URLs.
  • Fasta and GFF3 dumps are now working when invoked from the File menu.
  • Fixed SAM file processing so as not to die when presented with a SAM @SQ header. This requires Bio::DB::Sam 1.20 to work properly.
  • Fixed upload listing table so as not to duplicate track labels.
  • Fixed track importation via the eurl parameter so that it works when the user's uploadid is empty (due to clearing cache of cookies).
  • Fixed DAS server handling of the link option.

Please use the GMOD bug tracking system to report bugs or feature requests.

Lincoln Stein

Posted to the GMOD News on 2010/07/13