Difference between revisions of "Gbgff"
From GMOD
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(→as a DAS-lite remote feature) |
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* The GFF3 exported by gbgff can be used like a DAS source. | * The GFF3 exported by gbgff can be used like a DAS source. | ||
===as a DAS-lite remote feature=== | ===as a DAS-lite remote feature=== | ||
| − | * to use the dumper as a DAS source, add the 'remote feature' | + | * to use the dumper as a DAS source, add the '''''remote feature''''' option |
The URL format follows the same pattern as GBrowse: '''<font color=red>host</font>/<font color=blue>cgi-bin/gbgff</font>/<font color=green>data_source</font>?type=type1+type2;ref=$ref;start=$start;end=$end''' | The URL format follows the same pattern as GBrowse: '''<font color=red>host</font>/<font color=blue>cgi-bin/gbgff</font>/<font color=green>data_source</font>?type=type1+type2;ref=$ref;start=$start;end=$end''' | ||
Revision as of 14:26, 19 March 2008
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 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
