# this is documentation on how to build HAL library to support halSnake's in
# the genome browser

mkdir  /hive/groups/browser/hal
cd  /hive/groups/browser/hal
git clone git://github.com/glennhickey/hal.git

wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.11.tar.gz
tar xzf hdf5-1.8.11.tar.gz
cd hdf5-1.8.11
./configure --enable-cxx --prefix `pwd`/hdf5
make -j 40  && make -j 40  install

export PATH=`pwd`/hdf5/bin:${PATH}
export h5prefix=-prefix=`pwd`/hdf5

cd  /hive/groups/browser/hal
git clone git://github.com/benedictpaten/sonLib.git
pushd sonLib && make && popd

export  ENABLE_UDC=1
export  KENTSRC=$HOME/kent

cd  /hive/groups/browser/hal/hal
make