singularity_py3.def

Bootstrap: docker
From: ubuntu:18.04

%help
   Singularity definition file that builds a container with Python3 and PyBDSF. Note that must use my forked PyBDSF repo (i have submitted a pull reques) with additional lines in the setup.py file that look for libboost_python3 files (from Alex Clarke).

%environment
    
%post
    # Install common dependencies
    export DEBIAN_FRONTEND=noninteractive
    apt-get update \
      && apt-get --yes install --no-install-recommends \
      bison \
      build-essential \
      cmake \
      eog \
      flex \
      g++ \
      gcc \
      gettext-base \
      gfortran \
      git \
      libarmadillo-dev \
      libblas-dev \
      libcfitsio-dev \
      libfftw3-dev \
      libgsl-dev \
      libgtkmm-3.0-dev \
      libhdf5-serial-dev \
      liblapacke-dev \
      liblog4cplus-1.1-9 \
      liblog4cplus-dev \
      libncurses5-dev \
      libpng-dev \
      libpython3-dev \
      libreadline-dev \
      libxml2-dev \
      openssh-server \
      python3.6 \
      python3-pip \
      python3-tk \
      python3-setuptools \
      subversion \
      vim \
      wcslib-dev \
      wget \
      screen \

    # Install python3 packages
    python3.6 -m pip install setuptools Cython
    python3.6 -m pip install --upgrade \
      wheel \
      aplpy \
      astropy \
      numpy \
      matplotlib \
      scipy \
      wcsaxes \
      scikit-learn \
      umap-learn \
      datashader \
      memory_profiler \

    
    # Install boost python 1.63 with python 3
    cd / \
    && wget https://dl.bintray.com/boostorg/release/1.63.0/source/boost_1_63_0.tar.bz2 \
    && tar xvf boost_1_63_0.tar.bz2 \
    && cd boost_1_63_0 \
    && ./bootstrap.sh \
           --with-python=/usr/bin/python3.6 \
           --with-libraries=python,date_time,filesystem,system,program_options,test \
    && ./b2 install \
    && cd / && rm -r boost_1_63_0*
    
    # Install pyBDSF
    git clone https://github.com/informationcake/PyBDSF.git \
    && cd PyBDSF \
    && python3.6 -m pip install . \
    && cd .. \
    && rm -rf PyBDSF \
    && echo 'export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}/usr/local/lib' >>$SINGULARITY_ENVIRONMENT