Gbgff

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FlyBase gene models displayed as remote tracks on Gbrowse, via gbgff

gbgff is a GFF3 dumper script that come packaged with GBrowse version 1.69 and later.  Its purpose is the export configured annotations from one instance of Gbrowse to another.

  • It is analogous to DAS, except that:
    • It supports both server and client-side configuration of glyph rendering
    • It supports 3-level gene models and other multi-level features made possible by GFF3

Installation

  • gbgff does not require an special set-up, it is installed with Gbrowse.
  • This application has only been tested with servers using a GFF-3 back-end with Bio::SeqFeature::Store

Configuration

Server-side

  • Tracks are configured as normal (see the Gbrowse tutorial and the Configure HOWTO for details)
  • The only thing to be aware of is that callbacks are disabled for security reasons
    • Any server-side options configured with callbacks will fall through to the [TRACK DEFAULTS] setting, if available
    • Note: server-side options will be overridden by client-side settings, so callbacks can still be used

Client-side

  • The GFF3 exported by gbgff can be used like a DAS source.

as a DAS-lite remote feature

  • to use the dumper as a DAS source, add the 'remote feature'

The URL format follows the same pattern as GBrowse: host/cgi-bin/gbgff/data_source?param=value;param2=value2

[mygene]
remote feature = http://remote.host/cgi-bin/gbgff/source?type=gene;ref=$ref;start=$start;end=$end
glyph          = gene
bgcolor        = blue
#etc...
  • Note that the $ref, $start, aand $end variables are interpolated to the current segment
    • These variables are a required part of the url

as a remote URL

as an uploaded file