User talk:RobertBuels

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JBrowseDev/Installation

mostly out-of-data CPAN methods rendered unnecessary by setup.sh and bundling of cpanm

New JBrowse

Status

• Mature release
• Active development
• Active support

Resources

• Home Page
• Quickstart
• Blog
• Configuration
• Demo
• Mailing Lists

JBrowse is a genome browser with a fully dynamic AJAX interface. It is extremely fast, and very scalable for large datasets. JBrowse renders most tracks entirely within the user's web browser. JBrowse is being developed as the eventual official successor to GBrowse.

Demo

D. melanogaster

Quick Start: Tutorial

The Getting Started with JBrowse Tutorial provides a basic step-by-step recipe for quickly getting up and running with JBrowse.

Installation

1. Download JBrowse onto your web server 2. Unpack JBrowse into a directory that is served by your web browser. On many systems, this defaults to /var/www.

   cd /var/www
   tar -xzf jbrowse-*.tar.gz

3. Run the automated-setup script, which will attempt to install all of JBrowse's (modest) prerequisites for you. For the installation to completely succeed, including support for WIG and BAM data, your system must have:

• a working internet connection for downloading Perl modules from CPAN
• compilers for C and C++
• make
• the svn Subversion client (for fetching the samtools code, needed for BAM support)
• development libraries and header files (not just compiled shared objects) for:
  • libpng
  • Zlib
  • GD

For tips on installing these baseline libraries, see #Troubleshooting.

4. When you can see the included Volvox example data, you are ready to configure JBrowse to show your own data! Proceed to the JBrowse Configuration How-To.

Configuring JBrowse

• Configuration Guide
  • Formatting reference sequences (e.g. from FASTA files, or a Chado database)
  • Creating feature tracks (e.g. from BED or GFF files, a Chado database, or the UCSC genome browser)
  • Creating image tracks (e.g. from WIG files)
  • Making features searchable by name
  • Removing tracks

• Additional topics:
  • Using Configuration Files
  • Using a Database

Troubleshooting

Installing prerequisites under Linux - Ubuntu / Debian

Something like this should do the trick:

 sudo apt-get install libpng-dev zlib1g-dev libgd2-xpm-dev

Installing prerequisites under Mac OS X

Coming soon.

Contact

Please direct questions and inquiries regarding JBrowse to the mailing lists below.

In particular, requests for help should be directed to gmod-ajax@lists.sourceforge.net.

	Mailing List Link	Description	Archive(s)
JBrowse	gmod-ajax	JBrowse help and general questions.	Nabble (2010/05+), Sourceforge
	jbrowse-dev	JBrowse development discussions.	Nabble (2011/08+)

JBrowse Development

JBrowse is an open-source project, started and managed by the laboratory of Ian Holmes at the University of California, Berkeley.

The JBrowse source code repository is kept on GitHub. Please feel very free to fork the code on GitHub and make modifications and improvements, submitting pull requests. GitHub has a very nice tutorial on how to get started with this style of development.

As of January 2012, the lead developer of JBrowse is Robert Buels. Most of JBrowse was originally written by Mitch Skinner.

Developer Communication

There is a mailing list for developers, and there is usually a teleconference on the 3rd Monday of the month at 2pm Pacific US time. We welcome participation from Please contact Robert Buels if you would like to listen in or participate.

Presentations

Date	Presenter	Venue	Links
April 2012	Robert Buels	GMOD 2012 Community Meeting	PDF
January 2012	Robert Buels	Plant and Animal Genome (PAG) XX	PDF
April 2010	Mitch Skinner	UCSC genome browser group ("genecats") meeting	PDF
August 2009	Ian Holmes	GMOD Community Meeting	Talk summary | PDF
January 2009	Mitch Skinner	GMOD Community Meeting	Talk summary | PDF
July 2008	Ian Holmes	GMOD Community Meeting	Talk summary | PDF