container.def

Bootstrap: docker
From: ubuntu:22.04

%files
  requirements.txt
  
%post
  apt -y update
  apt -y install wget zlib1g-dev libbz2-dev
  apt -y install libssl-dev openssl make gcc
  
  ### install java
  # installing dbus runs into issues running the post script, this is the workaround
  apt -y download dbus
  dpkg --unpack dbus*.deb
  rm /var/lib/dpkg/info/dbus.postinst -f
  apt --fix-broken -y install
  apt install -yf dbus
  
  # same thing for systemd
  apt -y download systemd
  dpkg --unpack systemd*.deb
  rm /var/lib/dpkg/info/systemd.postinst -f
  apt --fix-broken -y install
  
  # finally install java 8
  apt install -y openjdk-8-jdk
  
  # download ImageJ
  apt -y install wget unzip
  wget https://downloads.imagej.net/fiji/latest/fiji-linux64.zip
  unzip fiji-linux64.zip
  
  # add BoneJ plugin
  ./Fiji.app/ImageJ-linux64 --update add-update-sites "BoneJ" "https://sites.imagej.net/BoneJ/"
  ./Fiji.app/ImageJ-linux64 --update update
  
  # install tkinter (this is to be able to use plt.show()
  DEBIAN_FRONTEND=noninteractive apt -y install python3-tk tk-dev 
  
  # install python 3.9.7
  wget https://www.python.org/ftp/python/3.9.7/Python-3.9.7.tgz
  tar xzvf Python-3.9.7.tgz
  cd Python-3.9.7
  ./configure
  make
  make install
  cd ..
  
  # adjust alias (so that we can call python instead of python3.9) -> only works for w/in the post section
  alias python="/usr/local/bin/python3.9"
  
  # install pip and adjust alias
  apt -y install python-pip
  python -m pip install --upgrade wheel setuptools pip
    
  # set up python environment 
  pip3 install -r requirements.txt 
  
  

####################
# Example apps
####################

%apprun example
  echo "Running example..."
  python3.9 Examples/BoneJ_Module_Example.py -f /Fiji.app/ImageJ-linux64
  
%apphelp example
  The app "example" runs an example of the BoneJ Headless Module by running the python script: Examples/BoneJ_Module_Example.py.