Difference between revisions of "Gbgff"
From GMOD
(→as a DAS-lite remote feature) |
(→as a DAS-lite remote feature) |
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* to use the dumper as a DAS source, add the 'remote feature' | * to use the dumper as a DAS source, add the 'remote feature' | ||
| + | # URL format: host/cgi-bin/gbgff/data_source?param=value;param2=value2 | ||
<pre> | <pre> | ||
[mygene] | [mygene] | ||
| − | remote feature = http://remote.host/cgi-bin/gbgff? | + | remote feature = http://remote.host/cgi-bin/gbgff/source?type=gene;ref=$ref;start=$start;end=$end |
glyph = gene | glyph = gene | ||
| + | bgcolor = blue | ||
#etc... | #etc... | ||
</pre> | </pre> | ||
| + | |||
| + | *Note that the $ref, $start, aand $end variables are interpolated to the current segment | ||
| + | **These variables are a required part of the url | ||
===as a remote URL=== | ===as a remote URL=== | ||
===as an uploaded file=== | ===as an uploaded file=== | ||
Revision as of 14:12, 19 March 2008
gbgff is a GFF3 dumper script that come packaged with GBrowse version 1.69 and later. Its purpose is the export configured annotations from one instance of Gbrowse to another.
- It is analogous to DAS, except that:
- It supports both server and client-side configuration of glyph rendering
- It supports 3-level gene models and other multi-level features made possible by GFF3
Installation
- gbgff does not require an special set-up, it is installed with Gbrowse.
- This application has only been tested with servers using a GFF-3 back-end with Bio::SeqFeature::Store
Configuration
Server-side
- Tracks are configured as normal (see the Gbrowse tutorial and the Configure HOWTO for details)
- The only thing to be aware of is that callbacks are disabled for security reasons
- Any server-side options configured with callbacks will fall through to the [TRACK DEFAULTS] setting, if available
- Note: server-side options will be overridden by client-side settings, so callbacks can still be used
Client-side
- The GFF3 exported by gbgff can be used like a DAS source.
as a DAS-lite remote feature
- to use the dumper as a DAS source, add the 'remote feature'
- URL format: host/cgi-bin/gbgff/data_source?param=value;param2=value2
[mygene] remote feature = http://remote.host/cgi-bin/gbgff/source?type=gene;ref=$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
