Difference between revisions of "GBrowse"

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(Net-based Installer Script)
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The net installer script, called {{GitHub|GBrowse|master/bin/gbrowse_netinstall.pl|gbrowse_netinstall.pl at the GBrowse GitHub repository}} will automatically download and install GBrowse and its Perl libraries for you. See [[#Installation|Installation]] for details on using this script.
 
The net installer script, called {{GitHub|GBrowse|master/bin/gbrowse_netinstall.pl|gbrowse_netinstall.pl at the GBrowse GitHub repository}} will automatically download and install GBrowse and its Perl libraries for you. See [[#Installation|Installation]] for details on using this script.
  
=== SVN ===
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=== GitHub ===
  
There are often new features and bug fixes in the current development version which have not yet been released. To get the latest version, please use [[Subversion]] (SVN). The recommended branch to use is ''trunk'', which is usually stable:
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There are often new features and bug fixes in the current development version which have not yet been released. To get the latest version, please use [[GitHub]]. The recommended branch to use is ''master'', which is usually stable:
  
   svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/trunk Generic-Genome-Browser
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   git clone git://github.com/GMOD/GBrowse.git
  
Once you have successfully checked out the Generic-Genome-Browser distribution, fetch recent changes by executing <code>svn update</code> inside the <code>Generic-Genome-Browser</code> directory.
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Once you have successfully checked out the GBrowse repository, fetch recent changes by executing <code>git pull</code> inside the <code>GBrowse</code> directory.
  
You can also browse the {{SF_SVN|Generic-Genome-Browser|GBrowse SVN}}.
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You can also browse the [http://github.com/GMOD/GBrowse GBrowse GitHub repository].
  
 
==== 1.x Development Version ====
 
==== 1.x Development Version ====
  
The link above will get you to the GBrowse2 development version.  To get to the GBrowse 1.x development branch, use stable:
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{{NeedsEditing}}
  
   svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/branches/stable Generic-Genome-Browser
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The link above will get you to the GBrowse2 development version.  To get to the GBrowse 1.x development branch, use the stable branch:
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 +
   Something like this--how do you get a branch in git?
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  git clone git://github.com/GMOD/GBrowse.git
  
 
== About Databases ==
 
== About Databases ==

Revision as of 20:13, 19 May 2011

http://gmod.org/wiki/GBrowse#Logo}}

__NOTITLE__

The Generic Genome Browser (GBrowse) is a genome viewer and is GMOD's most popular component. For a demo of its features, see WormBase, FlyBase, or Human Genome Segmental Duplication Database and others.

Description

GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Some of its features include:

  • Simultaneous bird's eye and detailed views of the genome.
  • Scroll, zoom, center.
  • Use a variety of premade glyphs or create your own.
  • Attach arbitrary URLs to any annotation.
  • Order and appearance of tracks are customizable by administrator and end-user.
  • Search by annotation ID, name, or comment.
  • Supports third party annotation using GFF formats.
  • Settings persist across sessions.
  • DNA and GFF dumps.
  • Connectivity to different databases, including BioSQL and Chado.
  • Multi-language support.
  • Third-party feature loading.
  • Customizable plug-in architecture (e.g. run BLAST, dump & import many formats, find oligonucleotides, design primers, create restriction maps, edit features)

GBrowse Versions

GBrowse 1.X (currently 1.70) is the older series that has been in use since 2002. It is recommended for applications which use a single database only and which must support legacy browsers.

GBrowse 2.0 is a rewrite of the original GBrowse to add dynamic updating via AJAX and a smoother user experience. In addition, it provides administrators with the ability to attach a different genome database to each GBrowse track, making it much easier to manage and update tracks. It also provides a distributed backend system of "slave" renderers, allowing each track to be rendered in parallel on a different machine and significantly increasing performance. GBrowse 2.0 is considered stable,but does not have full internationalization support. In addition, there may be issues with older browsers that do not support newer JavaScript features.

Installation

GBrowse is Perl-based. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. See the step-by-step instructions below for detailed instructions:

Documentation

On-line documentation

GBrowse 1.x GBrowse 2.0
Usage OpenHelix Tutorial
Install Wiki Wiki
Configure Wiki / Tutorial Wiki / Tutorial


POD documentation

There are many useful POD documents included with the distribution. These are converted to HTML files when you install the package, and can be found in /gbrowse/docs/pod:

Since these are in Perl POD format these files may contain formatting code when viewed in a Web browser.

Downloads

Source Code Download (tar.gz file)

Download the source from the SourceForge download page.

Net-based Installer Script

The net installer script, called gbrowse_netinstall.pl at the GBrowse GitHub repository will automatically download and install GBrowse and its Perl libraries for you. See Installation for details on using this script.

GitHub

There are often new features and bug fixes in the current development version which have not yet been released. To get the latest version, please use GitHub. The recommended branch to use is master, which is usually stable:

 git clone git://github.com/GMOD/GBrowse.git

Once you have successfully checked out the GBrowse repository, fetch recent changes by executing git pull inside the GBrowse directory.

You can also browse the GBrowse GitHub repository.

1.x Development Version

This page or section needs to be edited. Please help by editing this page to add your revisions or additions.

The link above will get you to the GBrowse2 development version. To get to the GBrowse 1.x development branch, use the stable branch:

 Something like this--how do you get a branch in git?
 git clone git://github.com/GMOD/GBrowse.git

About Databases

GBrowse has a flexible adaptor (yes, it is spelled that way and is not "adapter") system for running off various types of databases/sources. A common question is "which adaptor should I be using?" This attempts to answer that question.

Adaptor Other required software Roughly how many users Pros Cons
Bio::DB::SeqFeature::Store (use bp_seqfeature_load.pl) MySQL, PostgreSQL, SQLite, BerkeleyDB Many and growing fast. Roughly 4X faster than Bio::DB::GFF for the same data; designed to work with GFF3 Developed for use with GFF3; about 2X slower than Bio::DB::GFF to load a database
Bio::DB::GFF (use bp_load_gff.pl, bp_bulk_load_gff.pl, bp_fast_load_gff.pl) A relational database server: MySQL, PostgreSQL, Oracle, or BerkeleyDB Lots! (Especially MySQL) Quite fast; large user base; Have to use this if your data is in the (now deprecated) GFF2 format. Does not work well with GFF3 formatted data
Bio::DB::Sam (available from CPAN) SAMtools Growing (particularly with GBrowse2) Very fast access to NextGen sequencing data Difficult to use with GBrowse 1.70
Bio::DB::BigWig and Bio::DB::BigWigSet (available from CPAN) UCSC Formats Growing (particularly with GBrowse2) Very fast access to data in bigWig format Difficult to use with GBrowse 1.70
Bio::DB::BigBed (available from CPAN) UCSC Formats Growing (particularly with GBrowse2) Very fast access to data in bigBed format Difficult to use with GBrowse 1.70
Bio::DB::Das::Chado (available from CPAN) PostgreSQL and a Chado schema Relatively few due to the specialized nature of Chado Allows 'live' viewing of the features in a Chado database Slow compared to Bio::DB::GFF
Bio::DB::Das::BioSQL (available from CPAN) MySQL and a BioSQL schema Relatively few due to the small number of BioSQL users Allows 'live' viewing of the features in a BioSQL database Slow compared to Bio::DB::GFF
Memory (ie, flat file database using either Bio::DB::GFF or SeqFeature::Store) None For real servers, none Easy for rapid development and testing Very slow for more than a few thousand features
LuceGene Lucene (searches indexed flat files) Relatively few

Email Threads

There have been some useful email threads on adaptor choices and tradeoffs.

Contacts

Please report bugs to the SourceForge Bug Tracker (select 'Category: Gbrowse').

Mailing List Link Description Archive(s)
GBrowse & GBrowse_syn gmod-gbrowse GBrowse and GBrowse_syn users and developers. Gmane, Nabble (2010/05+), Sourceforge
gmod-gbrowse-cmts Code updates. Sourceforge

The GBrowse logo was created by Alex Read, a participant in the Spring 2010 Logo Program, while a design student at Linn-Benton Community College.

References

See Also

Installation and Setup

GBrowse 2.0 Install HOWTOAdvancedInstall PathsCygwinGentooMac OS XUbuntuWindowsMigrating from GBrowse 1.X to 2.XGBrowse 1.X Install HOWTO

Configuration

GBrowse 2.0 HOWTOGBrowse Configuration HOWTOAuthenticationBalloonsDASFeature Frequency HistogramsGlyphsI18nImagesURL schemaSubtracksGBrowse AdaptorsGBrowse Backends

Development

GBrowse Persistent Variables

Other

Balloon TipsGBrowse imgRubber Band SelectionGlyphs and Glyph OptionsGbrowse BenchmarkingGBrowse User UploadsGBrowse FAQ

See also Category:GBrowse