Difference between revisions of "Gbgff"
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− | '''''gbgff''''' is a GFF3 dumper script that | + | '''''gbgff''''' is a [[GFF3]] dumper script that comes packaged with [[GBrowse]] version 1.69 and later. Its purpose is to export configured annotations from one instance of GBrowse to another. |
− | *It is analogous to DAS, except that: | + | *It is analogous to [[:Category:DAS|DAS]], except that: |
**It supports both server and client-side configuration of glyph rendering | **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 | **It supports 3-level gene models and other multi-level features made possible by GFF3 | ||
</big> | </big> | ||
=Installation= | =Installation= | ||
− | *gbgff does not require | + | *gbgff does not require any special set-up - it is installed with GBrowse. |
− | *This application has only been tested with servers using a | + | *This application has only been tested with servers using a GFF3 back-end with [http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/SeqFeature/Store.html Bio::SeqFeature::Store] |
=Configuration= | =Configuration= | ||
==Server-side== | ==Server-side== | ||
− | * Tracks are configured as normal (see the | + | * Tracks are configured as normal (see the {{GBrowseAdminTutorialLink|GBrowse Administration 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 | * 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 | ** Any server-side options configured with callbacks will fall through to the [TRACK DEFAULTS] setting, if available | ||
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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>? | + | 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=$end''' |
<pre> | <pre> | ||
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</pre> | </pre> | ||
− | * | + | *Note1: that the '''''$ref, $start'',''' and '''''$end''''' variables are interpolated to the current segment |
**These variables are a required part of the url | **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=== | ===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 | ||
+ | [[image:gff_remote_url.png]] | ||
− | + | *which will yield a new track: | |
+ | [[image:gff_remote_track]] | ||
+ | |||
+ | [[Category:GMOD Components]] | ||
+ | [[Category:GBrowse]] | ||
+ | [[Category:HOWTO]] |
Latest revision as of 15:52, 25 September 2009
gbgff is a GFF3 dumper script that comes packaged with GBrowse version 1.69 and later. Its purpose is to 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 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
Configuration
Server-side
- 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
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
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: