bison.def

BootStrap: docker
From: centos:latest

%post
    BUILD_DIR=/tmp

    umask 0002
    yum clean all
    yum -y update
    yum -y install wget git libz.so.1 tbb-devel zlib-devel bzip2-devel
    yum -y groupinstall "Development Tools" # gcc 4.8.5-11
    cd $BUILD_DIR

    # build openmpi
    VER=1.10.3
    wget https://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-$VER.tar.gz
    tar xvf openmpi-$VER.tar.gz
    cd openmpi-$VER
    ./configure
    make install 
    echo /usr/local/lib >> /etc/ld.so.conf
    ldconfig
    cd $BUILD_DIR
    rm openmpi-$VER.tar.gz

    # build bowtie
    VER=2.3.2
    wget https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/$VER/bowtie2-$VER-source.zip
    unzip bowtie2-$VER-source.zip
    cd bowtie2-$VER
    make install 
    cd $BUILD_DIR
    rm bowtie2-$VER-source.zip

    # build bison
    DIR=/usr/local/apps
    APP=bison
    VER=0.4.0 
    wget https://github.com/dpryan79/bison/archive/$VER.tar.gz
    tar xvf $VER.tar.gz
    cd bison-$VER
    git clone https://github.com/samtools/htslib.git
    cd htslib
    git checkout 9b1cb94
    cd ..
    mkdir -p $DIR/$APP/$VER
    make CC=mpicc
    make herd CC=mpicc
    make auxiliary CC=mpicc 
    make install PREFIX=$DIR/$APP/$VER
    
    # add to PATH
    echo "" >> /environment
    echo "export PATH=$DIR/$APP/$VER:"'$PATH' >> /environment

    # create bind points for NIH HPC environment
    mkdir /gpfs /spin1 /gs2 /gs3 /gs4 /gs5 /gs6 /data /scratch /fdb /lscratch