content: FROM ghcr.io/fcp-indi/c-pac/ubuntu:bionic-non-free as AFNI
  USER root
  
  # install AFNI
  COPY dev/docker_data/required_afni_pkgs.txt /opt/required_afni_pkgs.txt
  RUN if [ -f /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0]; then \
          ln -svf /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0 /usr/lib/x86_64-linux-gnu/libGL.so.1; \
      fi && \
      libs_path=/usr/lib/x86_64-linux-gnu && \
      if [ -f $libs_path/libgsl.so.23 ]; then \
          ln -svf $libs_path/libgsl.so.23 $libs_path/libgsl.so.19 && \
          ln -svf $libs_path/libgsl.so.23 $libs_path/libgsl.so.0; \
      elif [ -f $libs_path/libgsl.so.23.0.0 ]; then \
          ln -svf $libs_path/libgsl.so.23.0.0 $libs_path/libgsl.so.19 && \
          ln -svf $libs_path/libgsl.so.23.0.0 $libs_path/libgsl.so.0; \
      elif [ -f $libs_path/libgsl.so ]; then \
          ln -svf $libs_path/libgsl.so $libs_path/libgsl.so.0; \
      fi && \
      LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH && \
      export LD_LIBRARY_PATH && \
      apt-get update && apt-get install -y libglw1-mesa-dev && \
      AFNI_VERSION="21.1.00" && \
      curl -LOJ https://github.com/afni/afni/archive/AFNI_${AFNI_VERSION}.tar.gz && \
      mkdir /opt/afni && \
      tar -xvf afni-AFNI_${AFNI_VERSION}.tar.gz -C /opt/afni --strip-components 1 && \
      rm -rf afni-AFNI_${AFNI_VERSION}.tar.gz && \
      cd /opt/afni/src && \
      sed '/^INSTALLDIR =/c INSTALLDIR = /opt/afni' Makefile.linux_ubuntu_16_64 > Makefile && \
      make vastness && make cleanest && \
      cd /opt/afni && \
      # filter down to required packages
      ls > full_ls && \
      sed 's/linux_openmp_64\///g' /opt/required_afni_pkgs.txt | sort > required_ls && \
      comm -2 -3 full_ls required_ls | xargs rm -rf full_ls required_ls && \
      apt-get remove -y libglw1-mesa-dev && \
      ldconfig
  
  # set up AFNI
  ENV PATH=/opt/afni:$PATH
  
  ENTRYPOINT ["/bin/bash"]
  
  # Link libraries for Singularity images
  RUN ldconfig
  
  RUN apt-get clean && \
      apt-get autoremove -y && \
      rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
  
  FROM scratch
  LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
  AFNI 21.1.00 (Domitian) stage"
  LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
  COPY --from=AFNI /lib/x86_64-linux-gnu/ld* /lib/x86_64-linux-gnu/
  COPY --from=AFNI /lib/x86_64-linux-gnu/lib*so* /lib/x86_64-linux-gnu/
  COPY --from=AFNI /lib64/ld* /lib64/
  COPY --from=AFNI /opt/afni/ /opt/afni/
  COPY --from=AFNI /usr/lib/x86_64-linux-gnu/lib*so* /usr/lib/x86_64-linux-gnu/
  