Difference between revisions of "JBrowse"

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==JBrowse Development==
 
==JBrowse Development==

Revision as of 19:22, 24 August 2012

__NOTITLE__

JBrowse logo
Status
  • mature release
  • active development
  • active support
Resources
Events

2012 GMOD Summer School

About JBrowse

JBrowse is a genome browser with a fully dynamic AJAX interface, being developed as the eventual successor to GBrowse. It is very fast and scales well to large datasets. JBrowse does almost all of its work directly in the user's web browser, with minimal requirements for the server.

Visit the JBrowse website.

Downloads

Download JBrowse: http://jbrowse.org/install/

The source code for JBrowse can be downloaded from http://github.com/GMOD/jbrowse.

Using JBrowse

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

System Requirements

For a full JBrowse installation, 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 JBrowse Troubleshooting.

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

Make sure you have permissions to write to the contents of the jbrowse/ directory you have just created.

3. Run the automated-setup script, ./setup.sh, which will attempt to install all of JBrowse's (modest) prerequisites for you in the jbrowse/ directory itself. setup.sh does not need to be run as root or with sudo.

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

Configuration

See the JBrowse Configuration Guide for information on:

Additional topics:

Documentation

For data format specifications, developer information, and so forth, see JBrowse Advanced Topics.

Publications, Tutorials, and Presentations

Presentations

  • April 2012 - GMOD 2012 Community Meeting, Robert Buels: PDF
  • January 2012 - Plant and Animal Genome (PAG) XX: PDF
  • April 2010 - UCSC genome browser group ("genecats") meeting: PDF
  • August 2009 - GMOD Community Meeting: Talk summary

Contacts and Mailing Lists

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

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.

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 anyone and everyone. Please contact Robert Buels if you would like to listen in or participate.



More on JBrowse

See Category:JBrowse