This package was used to create the simulations and figures for the CN-AVG theory publication (In preparation).

• DNAcopy package from BioConductor/R. Inside R:

source("http://bioconductor.org/biocLite.R")
biocLite("DNAcopy")

• Python libraries

pip install pyvcf 

• Scipy: I suffered many times to install Scipy till I discovered Anaconda: http://docs.continuum.io/anaconda/index.html

• Cactus library

git clone git://github.com/benedictpaten/sonLib.git
git clone git://github.com/benedictpaten/cactus.git

• For the automated pipeline:

git clone git://github.com/benedictpaten/jobTree.git

bedGraphToBigWig

make
make install

Point PYTHONPATH to this directory.