Integrated Genome Browser /

Filename Size Date modified Message
core
developmentPlugins
distribution
doc
galaxy
main
optionalPlugins
plugins
tools/LuceneIndexing
4.4 KB
IGBF-1347: Added other Developers' Names
13.7 KB
global application of formatting
3.5 KB
updated NOTICES.txt to give credit to install4j
2.9 KB
Remove link to developer's guide (needs work)
10.9 KB
IGBF-1463:changing to 9.1.0
2.0 KB
updated gradle for new build server config
1.1 KB
added parallel builds for the maven build
1.4 KB
added parallel builds for the maven build
2.0 KB
added parallel builds for the maven build
57.0 KB
IGBF-1463:changing to 9.1.0
361 B
work
179 B
updated launch scripts to remove max heap argument
1.9 KB
updated launch scripts to remove max heap argument
1.8 KB
updated launch scripts to remove max heap argument
26 B
added gradle settings file

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.

See:


Command-line quick start

To build and run from the command line:

  1. Clone the team repository to your desktop.
  2. Inside the local copy, check out the branch you wish to build. Review branch names to identify currently released version of IGB.
  3. Build IGB using maven. Skip tests to save time.
  4. Run IGB using the run_igb script for your platform.

Note: Instructions above assume you have Java installed on your computer. See Download section for platform-specific installers, which come with IGB and Java together.

Ex)

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, including third party libraries, required to run IGB.
  • Copy IGB jar files (artifacts) to your local maven cache, useful you are developing IGB Apps.
  • Run IGB

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 Developer alumni, see:


To contribute

Use fork-and-branch workflow:

  1. Fork the team repository.
  2. Create branches specific to the changes you want to make, push to your fork.
  3. Issue pull requests to the team repository's master branch from the branch on your fork.