Revision as of 11:52, 25 September 2009 by Clements
- 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
- gbgff does not require any special set-up - it is installed with GBrowse.
- This application has only been tested with servers using a GFF3 back-end with Bio::SeqFeature::Store
- Tracks are configured as normal (see the GBrowse2 Admin Tutorial and the GBrowse Configuration HOWTO for details)
- The config stanza for each feature type is dumped with the GFF3
- 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
- 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 option
The URL format follows the same pattern as GBrowse: host/cgi-bin/gbgff/data_source?type=type1+type2;ref=$ref;start=$start;end=$end
[mygene] remote feature = http://remote.host/cgi-bin/gbgff/source?type=gene;ref=$ref;start=$start;end=$end glyph = gene bgcolor = blue #etc...
- Note1: that the $ref, $start, and $end variables are interpolated to the current segment
- These variables are a required part of the url
- Note2: any options specified in the client-side config file will override remote options specified on the server
as a remote URL
- To use as a remote uploaded URL, enter a URL with the same structure as above into the "remote URL" box on the GBrowse display
- which will yield a new track: