build-cnvnator.sh

apt-get update
apt-get -qy install libcurl4-openssl-dev curl cmake make build-essential libbz2-dev lzma-dev liblzma-dev git \
    python-dev
mkdir -p /home/ubuntu
cd /home/ubuntu
git clone --depth 1 http://root.cern.ch/git/root.git
mkdir root/ibuild
cd root/ibuild
cmake -D x11=OFF ../
make -j4 install

cd /home/ubuntu
git clone --depth 1 https://github.com/abyzovlab/CNVnator
cd CNVnator
git clone --depth 1 --branch 1.4 https://github.com/samtools/samtools
git clone --depth 1 --branch 1.4 https://github.com/samtools/htslib
cd htslib
make libhts.a
cd ..
cd samtools
make lib
cd ..
make HTSDIR=htslib/ LIBS="-llzma -lbz2"
ldconfig
cp ./cnvnator /usr/local/bin
rm -rf /home/ubuntu/root