CancerDeepLearning/tf_openslide_cv2 at master · xiao233333/CancerDeepLearning · GitHub

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Bootstrap: docker
From: tensorflow/tensorflow:2.0.0a0-gpu-py3

%environment
  # use bash as default shell
  SHELL=/bin/bash
  export SHELL

%setup
  # runs on host - the path to the image is $SINGULARITY_ROOTFS

%post
  # post-setup script

  # load environment variables
  . /environment

  # use bash as default shell
  echo 'SHELL=/bin/bash' >> /environment

  # make environment file executable
  chmod +x /environment

  # default mount paths
  mkdir /scratch /data

  # additional packages
  apt-get update
  DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends apt-utils
  apt-get install -y build-essential checkinstall wget swig monodevelop r-base r-base-dev ruby ruby-dev python3 python3-dev tcl tcl-dev tk tk-dev
  apt-get install -y libreadline-gplv2-dev libncursesw5-dev libssl-dev libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev libffi-dev zlib1g-dev
  apt-get install -y git vim
  apt-get install -y openslide-tools
  apt-get install -y libsm6 libxext6
  apt-get install -y python3-tk python3-pip
  python3 -m pip install --upgrade pip
  python3 -m pip install opencv-python
  python3 -m pip install openslide-python
  python3 -m pip install numpy scipy matplotlib ipython jupyter pandas sympy nose pydicom dicom
  python3 -m pip install tensorflow==2.0.0-alpha0
  python3 -m pip install keras pydot graphviz
  python3 -m pip install scikit-learn scikit-image
  python3 -m pip install xgboost minecart quilt
  quilt install ResidentMario/missingno_data

  apt-get clean
%runscript
  # executes with the singularity run command
  # delete this section to use existing docker ENTRYPOINT command

%test
  # test that script is a success