Difference between revisions of "News/GBrowse 2.13 Release"

Latest revision as of 23:10, 9 October 2012

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:

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.

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.

Posted to the GMOD News on 2010/07/13

Revision as of 23:11, 24 January 2011 (view source) Clements (Talk \| contribs) (Created when GMOD News was moved from old, fragile, high-maintenance unified page system to a less fragile, one news item per page method.)		Latest revision as of 23:10, 9 October 2012 (view source) Girlwithglasses (Talk \| contribs) m (Text replace - "\{\{ImageRight\\|(.+)\\|(.+)\\|(.+)\\|(.+)\}\}" to "$2")
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	[[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:		[[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: