Integrated Genome Browser
The Integrated Genome Browser (IGB, pronounced ig-bee) is a fast, free, and highly interactive desktop genome browser ideal for exploring and understanding large-scale data sets from genomics. Originally developed at Affymetrix, IGB is now open source software.
IGB is also an extensible visual analytics platform. Developers can use IGB to create new interactive visualizations and visual analysis functions called IGB Apps.
To get IGB, clone this repository or download an IGB installer for your platform.
- BioViz Web site with platform-specific installers
- Searchable on-line User's Guide
- Developers Guide explains IGB development and IGB Apps
- IGB programming on-line class
- IGB Channel on YouTube with video tutorials and demos
- IGB Jira Issue Tracker site describes development plans
- Article describing Integrated Genome Browser: Visual analytics platform for genomics
Command-line quick start
To build and run from the command line:
- Clone the team repository to your desktop.
- Inside the local copy, check out the branch you wish to build. Check out release_candidate to get the released (or soon to be released) version of IGB.
- Build IGB using maven. Skip tests to save time.
- Run IGB using the run_igb script for your platform.
git clone https://bitbucket.org/lorainelab/integrated-genome-browser cd integrated-genome-browser mvn clean install -DskipTests=true run_igb.sh
The preceding commands:
- Create IGB executable igb_exe.jar, used by the run scripts to run IGB. Contains all dependencies required to run IGB.
- Copy IGB jar files (artifacts) to your local maven cache, useful you are developing IGB Apps.
IGB and IGB Apps use semantic versioning.
Note that IGB runs as modular OSGi bundles within an OSGi container. When IGB launches, the OSGi container may load these bundles to a local bundle cache directory named for the IGB version. To ensure that only the newest, most recently built code is used, delete the bundle cache directory for the version you want to run. See .igb in your user home directory.
To get help
Visit the Bioviz help page
Developing IGB Apps
IGB runs in an OSGi container, which supports adding and removing pluggable Apps while IGB is running. For OSGi tutorials written by IGB Developers, see:
- Stackleader.com blog posts on OSGI
Use fork-and-branch workflow:
- Fork the team repository.
- Create branches specific to the changes you want to make, push to your fork.
- Issue pull requests to the team repository's master branch.