BAM_V1.2.1.def

Bootstrap: docker
From: ubuntu:18.04

%files
    /mnt/beegfs/carlos.bastarz/pacotes/BAM_V1.2.1.tar.gz /root/

%post
    apt-get -y update
    apt-get -y upgrade

    export DEBIAN_FRONTEND=noninteractive

    apt install -y build-essential
    apt install -y automake autoconf autoconf-archive libtool pkg-config
    apt install -y libssl-dev uuid-dev libgpgme11-dev squashfs-tools
    apt install -y wget
    apt install -y gcc-4.8 g++-4.8 gfortran-4.8
    apt install -y libstdc++-6-dev manpages-dev
    apt install -y libhugetlbfs0 libhugetlbfs-dev libblas3 liblapack3
    apt install -y grads
    apt install -y glueviz libjpeg8 imagemagick

    cd $SINGULARITY_ROOTFS/usr/bin
    ln -s make gmake

    update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 100
    update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 100
    update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-4.8 100
    update-alternatives --auto gcc
    update-alternatives --auto g++
    update-alternatives --auto gfortran

    apt-get -y autoremove
    apt-get -y autoclean
    apt-get -y clean

    echo
    echo ">>> BUILDING THE MPICH 3.3..."
    echo

    cd $SINGULARITY_ROOTFS/opt
    wget https://www.mpich.org/static/downloads/3.3/mpich-3.3.tar.gz

    mkdir -p $SINGULARITY_ROOTFS/opt/mpich
    cd $SINGULARITY_ROOTFS/opt
    tar -zxvf mpich-3.3.tar.gz
    cd $SINGULARITY_ROOTFS/opt/mpich-3.3
     
    ./configure --prefix=$SINGULARITY_ROOTFS/usr/local
    make 
    make install

    ldconfig

    echo
    echo ">>> BUILDING THE BAM_V1.2.1 MODEL..."
    echo

    tar -zxvf /root/BAM_V1.2.1.tar.gz -C $SINGULARITY_ROOTFS/opt

    echo
    echo ">>> PRE"
    echo

    cd $SINGULARITY_ROOTFS/opt/BAM_V1.2.1/pre/sources/bacio/v2.0.2/src_32bits
    ./makebacio_linux_gnu.sh 

    cd $SINGULARITY_ROOTFS/opt/BAM_V1.2.1/pre/sources/bacio/v2.0.2/src_64bits 
    ln -s ../gnu/libbacio_8.a

    cd $SINGULARITY_ROOTFS/opt/BAM_V1.2.1/pre/sources/
    make clean linux_gnu

    echo
    echo ">>> MODEL"
    echo

    cd $SINGULARITY_ROOTFS/opt/BAM_V1.2.1/model/source/
    make clean linux_gnu

    echo 
    echo ">>> POS"
    echo 

    cd $SINGULARITY_ROOTFS/opt/BAM_V1.2.1/pos/source/
    make clean linux2

    echo 
    echo ">>> BAM_V1.2.1 EXECUTABLES"
    echo

    ls $SINGULARITY_ROOTFS/usr/local/bin

    echo
    echo ">>> ALL DONE!"
    echo