Difference between revisions of "Gbgff"

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<big>
 
<big>
'''''gbgff''''' is a GFF3 dumper script that come packaged with GBrowse version 1.69 and later. &nbsp;Its purpose is the export configured annotations from one instance of Gbrowse to another.
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'''''gbgff''''' is a [[GFF3]] dumper script that comes packaged with [[GBrowse]] version 1.69 and later. &nbsp;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 an special set-up, it is installed with Gbrowse.
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*gbgff does not require any special set-up - it is installed with GBrowse.
*This application has only been tested with servers using a GFF-3 back-end with [http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/SeqFeature/Store.html Bio::SeqFeature::Store]
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*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==
* No special configuration is required.
+
* Tracks are configured as normal (see the {{GBrowseAdminTutorialLink|GBrowse Administration Tutorial}} and the [[GBrowse Configuration HOWTO]] for details)
* Tracks are configures as normal (see the Gbrowse tutorial and the Configure HOWTO for details)
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* 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==
 
==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: '''<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>
# Dirt simple GFF3 dumper, suitable for a lightweight replacement to DAS.
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[mygene]
# Call this way:
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remote feature = http://remote.host/cgi-bin/gbgff/source?type=gene;ref=$ref;start=$start;end=$end
#    http://my.host/cgi-bin/gbgff/volvox?q=ctgA:1..2000;t=Genes+ExampleFeatures
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glyph          = gene
#
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bgcolor        = blue
# From within the "Add Remote Annotations" section, you can say:
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#etc...
#     http://my.host/cgi-bin/gbgff/volvox?q=$segment;t=Genes+ExampleFeatures
+
 
</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
 +
*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
 +
[[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

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

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

Gff remote url.png

  • which will yield a new track:

Gff remote track