University of Cambridge The Gurdon Institute


BEADS: Bias Elimination Algorithm for Deep Sequencing

Download BEADS

The latest version of BEADS is available freely on the SourceForge download page.

Install BEADS

The BEADS package consists of Java and Python files.

You can do this to install BEADS in a standard way on a Unix system:

1. unpack the distribution tarball, go to the extracted distribution directory and run:

python install

2. move the BEADSjava.jar to a directory of your choice (e.g. /home/msc51/javaLib/)

3. configure enviroment variables. For example, for bash shell users, add to ~/.bashrc :

export $PATH=/usr/local/bin:$PATH

export PYTHONPATH=/usr/local/lib/python2.5/site-packages:$PYTHONPATH

export CLASSPATH=/home/msc51/javaLib/BEADSjava.jar:$CLASSPATH

The convention of setting environment variables vary between operating systems and between command line interpreter, but the basic idea is the same.

After editing the .bashrc file, you will need to restart the terminal to put into effect the modifications you have made. Alternatively, you can run this command:

source ~/.bashrc


Python version 2.4 or above is recommended.

Last updated 29 Mar 2011 by Nicole Cheung.

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Copyright © 2010 Nicole Cheung (The Gurdon Institute, University of Cambridge)