Singularity

BootStrap: docker
From: ubuntu:18.04

%labels
  Maintainer: Suxing Liu
  Version v1.01

%setup
  #----------------------------------------------------------------------
  # commands to be executed on host outside container during bootstrap
  #----------------------------------------------------------------------
  mkdir ${SINGULARITY_ROOTFS}/opt/code/

%files
  ./* /opt/code/

%post
  #----------------------------------------------------------
  # Install common dependencies and create default entrypoint,
  # commands to be executed inside container during bootstrap
  #----------------------------------------------------------
  # Install dependencies
  apt update
  apt install -y \
    build-essential \
    python3-setuptools \
    python3-pip \
    python3-numexpr \
    libgl1-mesa-glx \
    libsm6 \
    libxext6 \
    libfontconfig1 \
    libxrender1 \
    libzbar-dev \
    libzbar0 \
    python3-pandas \
    libdmtx0b
    
  pip3 install numpy \
                Pillow \
                scipy \
                scikit-image \
                matplotlib \
                opencv-python \
                openpyxl \
                python-magic \
                imutils \
                tabulate \
                skan \
                networkx \
                pandas \
                numba \
                psutil \
                pylibdmtx


  pip3 install -U scikit-learn
  

  mkdir /lscratch /db /work /scratch
  
  chmod -R a+rwx /opt/code/
  
%environment
  #----------------------------------------------------------
  # Setup environment variables
  #----------------------------------------------------------
  PYTHONPATH=$PYTHONPATH:/opt/code/
  export PATH
  LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/code/
  export LD_LIBRARY_PATH

%runscript
  #----------------------------------------------------------
  # Run scripts inside container
  #----------------------------------------------------------
   # commands to be executed when the container runs
   echo "Arguments received: $*"
   exec /usr/bin/python "$@"
  
%test
  #----------------------------------------------------------
  # commands to be executed within container at close of bootstrap process
  #----------------------------------------------------------
   python3 --version
   #python3 requirement.py