Setup Guide

If you only want to run ChiBE, then please use the install files at the main page. This page describes how to run ChiBE from the latest sources.

Before starting, please make sure that you have JDK, Mercurial, and Maven 3 in your system.

Download sources

Pull:

git clone https://github.com/PathwayCommons/chibe.git

This will create a directory named chibe, containing all the sources.

Compile

Go into the project directory, and tell maven to compile the project.

cd chibe
mvn clean compile

Prepare Jar

mvn assembly:single

This will create ChiBE.jar under the target folder in the project directory.

Run ChiBE

Run ChiBE with the following command.

If using Mac (it should be version 10.6 or higher):

java -d32 -XstartOnFirstThread -jar target/ChiBE.jar

For other platforms:

java -jar target/ChiBE.jar

If you plan to load very large graphs, or load expression datasets, then increase the maximum memory as needed.

java -Xmx4G -jar target/ChiBE.jar

Contributing

You can commit your changes, while in the project directory (chibe), with:

git commit

This will let you write a commit message, and will commit your changes to your local repository.

If you are a committer to the project, you can push your committed changes to Google repository with:

git push