kinc-recipe

BootStrap: debootstrap
OSVersion: trusty
MirrorURL: http://us.archive.ubuntu.com/ubuntu/

%environment

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/bin:/usr/local/bin/include:/usr/local/bin/lib
export PATH=$PATH:/usr/local/bin:/usr/local/bin/include:/usr/local/bin/lib

%runscript
echo "Please run "singularity exec kinc.simg kinc" to view options"

%post

# set bind points for directories on host filesystems

mkdir /cvmfs /oasis /projects /scratch /scratch2 /scratch3 /zfs  

# install libraries 

echo "Installing software dependencies"
apt-get -y --force-yes install build-essential wget git cmake libblas-dev liblapack-dev libgsl0-dev


# download and extract mixmod source
wget http://www.mixmod.org/IMG/tgz/libmixmod_3.2.2_src.tgz
tar -xvf libmixmod_3.2.2_src.tgz
rm libmixmod_3.2.2_src.tgz

# build and install libmixmod
cd libmixmod_3.2.2/BUILD
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/bin
make
make install
cd

export INSTALL_PREFIX=/usr/local/bin
export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:$INSTALL_PREFIX/include
export LIBRARY_PATH=$LIBRARY_PATH:$INSTALL_PREFIX/lib
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$INSTALL_PREFIX/lib


echo "cloning the version1 branch of KINC and compiling"

git clone https://github.com/SystemsGenetics/KINC.git
cd KINC
make
chmod +x kinc
cp kinc /usr/local/bin