bonito.recipe

Bootstrap: docker

#first choose a docker base image that includes CUDA.  Various python packages may only
FROM: nvidia/cuda:12.4.1-runtime-ubuntu20.04

#instructions executed while the container is being built, after the base container OS has been installed
%post
  . /environment
  SHELL=/bin/bash
  CPATH="/usr/local/cuda/include:$CPATH"
  PATH="/usr/local/cuda/bin:$PATH"
  LD_LIBRARY_PATH="/usr/local/cuda/lib64:$LD_LIBRARY_PATH"
  CUDA_HOME="/usr/local/cuda"

  #update the linux distribution within the container
  apt-get update
  DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata
  apt-get install -y wget git vim build-essential cmake libgtk2.0-0 python3.8 python3.8-dev python3.8-venv python3-distutils python3-apt libgtk-3-dev xauth curl
  wget https://bootstrap.pypa.io/pip/get-pip.py
  python3.8 get-pip.py
  ln -s /usr/bin/python3.8 /usr/local/bin/python3

  #download packages and install them, or use pip
  pip install --upgrade pip
  pip install ont-bonito

#this section sets up the runtime environment within the container to be created
%environment

  # use bash as default shell
  SHELL=/bin/bash

  # add CUDA paths
  CPATH="/usr/local/cuda/include:$CPATH"
  PATH="/usr/local/cuda/bin:$PATH"
  LD_LIBRARY_PATH="/usr/local/cuda/lib64:$LD_LIBRARY_PATH"
  CUDA_HOME="/usr/local/cuda"

  export PATH LD_LIBRARY_PATH CPATH CUDA_HOME