Dockerfile

# Generated by Neurodocker and Reproenv.

FROM neurodebian:bookworm
ENV PATH="/opt/dcm2niix-v1.0.20240202/bin:$PATH"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           ca-certificates \
           cmake \
           g++ \
           gcc \
           git \
           make \
           pigz \
           zlib1g-dev \
    && rm -rf /var/lib/apt/lists/* \
    && git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
    && cd /tmp/dcm2niix \
    && git fetch --tags \
    && git checkout v1.0.20240202 \
    && mkdir /tmp/dcm2niix/build \
    && cd /tmp/dcm2niix/build \
    && cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20240202 .. \
    && make -j1 \
    && make install \
    && rm -rf /tmp/dcm2niix
RUN apt-get update -qq \
           && apt-get install -y -q --no-install-recommends \
                  gcc \
                  git \
                  git-annex-standalone \
                  libc-dev \
                  liblzma-dev \
                  netbase \
                  pigz \
           && rm -rf /var/lib/apt/lists/*
COPY [".", \
      "/src/heudiconv"]
ENV CONDA_DIR="/opt/miniconda-py39_4.12.0" \
    PATH="/opt/miniconda-py39_4.12.0/bin:$PATH"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bzip2 \
           ca-certificates \
           curl \
    && rm -rf /var/lib/apt/lists/* \
    # Install dependencies.
    && export PATH="/opt/miniconda-py39_4.12.0/bin:$PATH" \
    && echo "Downloading Miniconda installer ..." \
    && conda_installer="/tmp/miniconda.sh" \
    && curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh \
    && bash "$conda_installer" -b -p /opt/miniconda-py39_4.12.0 \
    && rm -f "$conda_installer" \
    # Prefer packages in conda-forge
    && conda config --system --prepend channels conda-forge \
    # Packages in lower-priority channels not considered if a package with the same
    # name exists in a higher priority channel. Can dramatically speed up installations.
    # Conda recommends this as a default
    # https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html
    && conda config --set channel_priority strict \
    && conda config --system --set auto_update_conda false \
    && conda config --system --set show_channel_urls true \
    # Enable `conda activate`
    && conda init bash \
    && conda install -y  --name base \
           "python=3.9" \
           "traits>=4.6.0" \
           "scipy" \
           "numpy" \
           "nomkl" \
           "pandas" \
           "gdcm" \
    && bash -c "source activate base \
    &&   python -m pip install --no-cache-dir --editable \
             "/src/heudiconv[all]"" \
    # Clean up
    && sync && conda clean --all --yes && sync \
    && rm -rf ~/.cache/pip/*
ENTRYPOINT ["heudiconv"]

# Save specification to JSON.
RUN printf '{ \
  "pkg_manager": "apt", \
  "existing_users": [ \
    "root" \
  ], \
  "instructions": [ \
    { \
      "name": "from_", \
      "kwds": { \
        "base_image": "neurodebian:bookworm" \
      } \
    }, \
    { \
      "name": "env", \
      "kwds": { \
        "PATH": "/opt/dcm2niix-v1.0.20240202/bin:$PATH" \
      } \
    }, \
    { \
      "name": "run", \
      "kwds": { \
        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    ca-certificates \\\\\\n    cmake \\\\\\n    g++ \\\\\\n    gcc \\\\\\n    git \\\\\\n    make \\\\\\n    pigz \\\\\\n    zlib1g-dev\\nrm -rf /var/lib/apt/lists/*\\ngit clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix\\ncd /tmp/dcm2niix\\ngit fetch --tags\\ngit checkout v1.0.20240202\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20240202 ..\\nmake -j1\\nmake install\\nrm -rf /tmp/dcm2niix" \
      } \
    }, \
    { \
      "name": "install", \
      "kwds": { \
        "pkgs": [ \
          "git", \
          "gcc", \
          "pigz", \
          "liblzma-dev", \
          "libc-dev", \
          "git-annex-standalone", \
          "netbase" \
        ], \
        "opts": null \
      } \
    }, \
    { \
      "name": "run", \
      "kwds": { \
        "command": "apt-get update -qq \\\\\\n    && apt-get install -y -q --no-install-recommends \\\\\\n           gcc \\\\\\n           git \\\\\\n           git-annex-standalone \\\\\\n           libc-dev \\\\\\n           liblzma-dev \\\\\\n           netbase \\\\\\n           pigz \\\\\\n    && rm -rf /var/lib/apt/lists/*" \
      } \
    }, \
    { \
      "name": "copy", \
      "kwds": { \
        "source": [ \
          ".", \
          "/src/heudiconv" \
        ], \
        "destination": "/src/heudiconv" \
      } \
    }, \
    { \
      "name": "env", \
      "kwds": { \
        "CONDA_DIR": "/opt/miniconda-py39_4.12.0", \
        "PATH": "/opt/miniconda-py39_4.12.0/bin:$PATH" \
      } \
    }, \
    { \
      "name": "run", \
      "kwds": { \
        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    bzip2 \\\\\\n    ca-certificates \\\\\\n    curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-py39_4.12.0/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-py39_4.12.0\\nrm -f \\"$conda_installer\\"\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y  --name base \\\\\\n    \\"python=3.9\\" \\\\\\n    \\"traits>=4.6.0\\" \\\\\\n    \\"scipy\\" \\\\\\n    \\"numpy\\" \\\\\\n    \\"nomkl\\" \\\\\\n    \\"pandas\\" \\\\\\n    \\"gdcm\\"\\nbash -c \\"source activate base\\n  python -m pip install --no-cache-dir --editable \\\\\\n      \\"/src/heudiconv[all]\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
      } \
    }, \
    { \
      "name": "entrypoint", \
      "kwds": { \
        "args": [ \
          "heudiconv" \
        ] \
      } \
    } \
  ] \
}' > /.reproenv.json
# End saving to specification to JSON.