freesurfer/Dockerfile_fs7 at master · bids-apps/freesurfer · GitHub

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# Generated by Neurodocker and Reproenv.

FROM ubuntu:jammy
ENV LANG="en_US.UTF-8" \
    LC_ALL="en_US.UTF-8" \
    ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
    && apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           apt-utils \
           bzip2 \
           ca-certificates \
           curl \
           locales \
           unzip \
    && rm -rf /var/lib/apt/lists/* \
    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
    && dpkg-reconfigure --frontend=noninteractive locales \
    && update-locale LANG="en_US.UTF-8" \
    && chmod 777 /opt && chmod a+s /opt \
    && mkdir -p /neurodocker \
    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
         echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
    &&   echo 'set -e' >> "$ND_ENTRYPOINT" \
    &&   echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
    &&   echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
    fi \
    && chmod -R 777 /neurodocker && chmod a+s /neurodocker
RUN apt-get update -qq \
           && apt-get install -y -q --no-install-recommends \
                  bc \
                  curl \
                  libglu1-mesa \
                  libgomp1 \
                  libsm-dev \
                  libx11-dev \
                  libxext-dev \
                  libxt-dev \
                  perl-modules \
                  tar \
                  tcsh \
                  wget \
           && rm -rf /var/lib/apt/lists/*
ENV OS="Linux" \
    PATH="/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:$PATH" \
    FREESURFER_HOME="/opt/freesurfer" \
    FREESURFER="/opt/freesurfer" \
    SUBJECTS_DIR="/opt/freesurfer/subjects" \
    LOCAL_DIR="/opt/freesurfer/local" \
    FSFAST_HOME="/opt/freesurfer/fsfast" \
    FMRI_ANALYSIS_DIR="/opt/freesurfer/fsfast" \
    FUNCTIONALS_DIR="/opt/freesurfer/sessions" \
    FS_OVERRIDE="0" \
    FIX_VERTEX_AREA="" \
    FSF_OUTPUT_FORMAT="nii.gz" \
    MINC_BIN_DIR="/opt/freesurfer/mni/bin" \
    MINC_LIB_DIR="/opt/freesurfer/mni/lib" \
    MNI_DIR="/opt/freesurfer/mni" \
    MNI_DATAPATH="/opt/freesurfer/mni/data" \
    MNI_PERL5LIB="/opt/freesurfer/mni/share/perl5" \
    PERL5LIB="/opt/freesurfer/mni/share/perl5"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           ca-certificates \
           curl \
           libgomp1 \
           libxmu6 \
           libxt6 \
           perl \
           tcsh \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FreeSurfer ..." \
    && mkdir -p /opt/freesurfer \
    && curl -fL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-centos7_x86_64-7.4.1.tar.gz \
    | tar -xz -C /opt/freesurfer --owner root --group root --no-same-owner --transform='s,freesurfer/,,' \
         --exclude='average/mult-comp-cor' \
         --exclude='lib/cuda' \
         --exclude='lib/qt' \
         --exclude='subjects/V1_average' \
         --exclude='subjects/bert' \
         --exclude='subjects/cvs_avg35' \
         --exclude='subjects/cvs_avg35_inMNI152' \
         --exclude='subjects/fsaverage3' \
         --exclude='subjects/fsaverage4' \
         --exclude='subjects/fsaverage5' \
         --exclude='subjects/fsaverage6' \
         --exclude='subjects/fsaverage_sym' \
         --exclude='trctrain'
RUN if [ ! -z `which node` ] ; then \
         echo "node is installed, skipping its install." ; \
       else \
         apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           apt-utils \
           ca-certificates \
           curl \
           gnupg \
    && rm -rf /var/lib/apt/lists/* \
    &&     curl -SLO https://deb.nodesource.com/nsolid_setup_deb.sh \
    &&     chmod 500 nsolid_setup_deb.sh \
    &&     ./nsolid_setup_deb.sh 20 \
    &&     apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           nodejs \
    && rm -rf /var/lib/apt/lists/* ; \
         fi \
    && node --version \
    && npm --version \
    && npm install -g bids-validator@1.12.0
ENV FSLDIR="/usr/share/fsl/5.0" \
    FSLOUTPUTTYPE="NIFTI_GZ" \
    FSLMULTIFILEQUIT="TRUE" \
    POSSUMDIR="/usr/share/fsl/5.0" \
    LD_LIBRARY_PATH="/usr/lib/fsl/5.0:" \
    FSLTCLSH="/usr/bin/tclsh" \
    FSLWISH="/usr/bin/wish"
ENV OS="Linux" \
    FS_OVERRIDE="0" \
    FIX_VERTEX_AREA="" \
    SUBJECTS_DIR="/opt/freesurfer/subjects" \
    FSF_OUTPUT_FORMAT="nii.gz" \
    MNI_DIR="/opt/freesurfer/mni" \
    LOCAL_DIR="/opt/freesurfer/local" \
    FREESURFER_HOME="/opt/freesurfer" \
    FSFAST_HOME="/opt/freesurfer/fsfast" \
    MINC_BIN_DIR="/opt/freesurfer/mni/bin" \
    MINC_LIB_DIR="/opt/freesurfer/mni/lib" \
    MNI_DATAPATH="/opt/freesurfer/mni/data" \
    FMRI_ANALYSIS_DIR="/opt/freesurfer/fsfast" \
    PERL5LIB="/opt/freesurfer/mni/share/perl5" \
    MNI_PERL5LIB="/opt/freesurfer/mni/share/perl5/" \
    PATH="/opt/miniconda-latest/bin:/opt/freesurfer/python/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin" \
    PYTHONPATH=""
RUN mkdir root/matlab && touch root/matlab/startup.m
RUN mkdir /scratch
RUN mkdir /local-scratch
COPY ["run.py", \
      "/run.py"]
RUN chmod +x /run.py
COPY ["version", \
      "/version"]
ENTRYPOINT ["python3", "/run.py"]

# Save specification to JSON.
RUN printf '{ \
  "pkg_manager": "apt", \
  "existing_users": [ \
    "root" \
  ], \
  "instructions": [ \
    { \
      "name": "from_", \
      "kwds": { \
        "base_image": "ubuntu:jammy" \
      } \
    }, \
    { \
      "name": "env", \
      "kwds": { \
        "LANG": "en_US.UTF-8", \
        "LC_ALL": "en_US.UTF-8", \
        "ND_ENTRYPOINT": "/neurodocker/startup.sh" \
      } \
    }, \
    { \
      "name": "run", \
      "kwds": { \
        "command": "export ND_ENTRYPOINT=\\"/neurodocker/startup.sh\\"\\napt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    apt-utils \\\\\\n    bzip2 \\\\\\n    ca-certificates \\\\\\n    curl \\\\\\n    locales \\\\\\n    unzip\\nrm -rf /var/lib/apt/lists/*\\nsed -i -e '"'"'s/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/'"'"' /etc/locale.gen\\ndpkg-reconfigure --frontend=noninteractive locales\\nupdate-locale LANG=\\"en_US.UTF-8\\"\\nchmod 777 /opt && chmod a+s /opt\\nmkdir -p /neurodocker\\nif [ ! -f \\"$ND_ENTRYPOINT\\" ]; then\\n  echo '"'"'#!/usr/bin/env bash'"'"' >> \\"$ND_ENTRYPOINT\\"\\n  echo '"'"'set -e'"'"' >> \\"$ND_ENTRYPOINT\\"\\n  echo '"'"'export USER=\\"${USER:=`whoami`}\\"'"'"' >> \\"$ND_ENTRYPOINT\\"\\n  echo '"'"'if [ -n \\"$1\\" ]; then \\"$@\\"; else /usr/bin/env bash; fi'"'"' >> \\"$ND_ENTRYPOINT\\";\\nfi\\nchmod -R 777 /neurodocker && chmod a+s /neurodocker" \
      } \
    }, \
    { \
      "name": "install", \
      "kwds": { \
        "pkgs": [ \
          "tcsh", \
          "bc", \
          "tar", \
          "libgomp1", \
          "perl-modules", \
          "wget", \
          "curl", \
          "libsm-dev", \
          "libx11-dev", \
          "libxt-dev", \
          "libxext-dev", \
          "libglu1-mesa" \
        ], \
        "opts": null \
      } \
    }, \
    { \
      "name": "run", \
      "kwds": { \
        "command": "apt-get update -qq \\\\\\n    && apt-get install -y -q --no-install-recommends \\\\\\n           bc \\\\\\n           curl \\\\\\n           libglu1-mesa \\\\\\n           libgomp1 \\\\\\n           libsm-dev \\\\\\n           libx11-dev \\\\\\n           libxext-dev \\\\\\n           libxt-dev \\\\\\n           perl-modules \\\\\\n           tar \\\\\\n           tcsh \\\\\\n           wget \\\\\\n    && rm -rf /var/lib/apt/lists/*" \
      } \
    }, \
    { \
      "name": "env", \
      "kwds": { \
        "OS": "Linux", \
        "PATH": "/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:$PATH", \
        "FREESURFER_HOME": "/opt/freesurfer", \
        "FREESURFER": "/opt/freesurfer", \
        "SUBJECTS_DIR": "/opt/freesurfer/subjects", \
        "LOCAL_DIR": "/opt/freesurfer/local", \
        "FSFAST_HOME": "/opt/freesurfer/fsfast", \
        "FMRI_ANALYSIS_DIR": "/opt/freesurfer/fsfast", \
        "FUNCTIONALS_DIR": "/opt/freesurfer/sessions", \
        "FS_OVERRIDE": "0", \
        "FIX_VERTEX_AREA": "", \
        "FSF_OUTPUT_FORMAT": "nii.gz", \
        "MINC_BIN_DIR": "/opt/freesurfer/mni/bin", \
        "MINC_LIB_DIR": "/opt/freesurfer/mni/lib", \
        "MNI_DIR": "/opt/freesurfer/mni", \
        "MNI_DATAPATH": "/opt/freesurfer/mni/data", \
        "MNI_PERL5LIB": "/opt/freesurfer/mni/share/perl5", \
        "PERL5LIB": "/opt/freesurfer/mni/share/perl5" \
      } \
    }, \
    { \
      "name": "run", \
      "kwds": { \
        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    bc \\\\\\n    ca-certificates \\\\\\n    curl \\\\\\n    libgomp1 \\\\\\n    libxmu6 \\\\\\n    libxt6 \\\\\\n    perl \\\\\\n    tcsh\\nrm -rf /var/lib/apt/lists/*\\necho \\"Downloading FreeSurfer ...\\"\\nmkdir -p /opt/freesurfer\\ncurl -fL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-centos7_x86_64-7.4.1.tar.gz \\\\\\n| tar -xz -C /opt/freesurfer --owner root --group root --no-same-owner --transform='"'"'s,freesurfer/,,'"'"' \\\\\\n  --exclude='"'"'average/mult-comp-cor'"'"' \\\\\\n  --exclude='"'"'lib/cuda'"'"' \\\\\\n  --exclude='"'"'lib/qt'"'"' \\\\\\n  --exclude='"'"'subjects/V1_average'"'"' \\\\\\n  --exclude='"'"'subjects/bert'"'"' \\\\\\n  --exclude='"'"'subjects/cvs_avg35'"'"' \\\\\\n  --exclude='"'"'subjects/cvs_avg35_inMNI152'"'"' \\\\\\n  --exclude='"'"'subjects/fsaverage3'"'"' \\\\\\n  --exclude='"'"'subjects/fsaverage4'"'"' \\\\\\n  --exclude='"'"'subjects/fsaverage5'"'"' \\\\\\n  --exclude='"'"'subjects/fsaverage6'"'"' \\\\\\n  --exclude='"'"'subjects/fsaverage_sym'"'"' \\\\\\n  --exclude='"'"'trctrain'"'"'" \
      } \
    }, \
    { \
      "name": "run", \
      "kwds": { \
        "command": "if [ ! -z `which node` ] ; then \\\\\\n  echo \\"node is installed, skipping its install.\\" ; \\\\\\nelse \\\\\\n  apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    apt-utils \\\\\\n    ca-certificates \\\\\\n    curl \\\\\\n    gnupg\\nrm -rf /var/lib/apt/lists/*\\n    curl -SLO https://deb.nodesource.com/nsolid_setup_deb.sh\\n    chmod 500 nsolid_setup_deb.sh\\n    ./nsolid_setup_deb.sh 20\\n    apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    nodejs\\nrm -rf /var/lib/apt/lists/* ; \\\\\\n  fi\\nnode --version\\nnpm --version\\nnpm install -g bids-validator@1.12.0" \
      } \
    }, \
    { \
      "name": "env", \
      "kwds": { \
        "FSLDIR": "/usr/share/fsl/5.0", \
        "FSLOUTPUTTYPE": "NIFTI_GZ", \
        "FSLMULTIFILEQUIT": "TRUE", \
        "POSSUMDIR": "/usr/share/fsl/5.0", \
        "LD_LIBRARY_PATH": "/usr/lib/fsl/5.0:", \
        "FSLTCLSH": "/usr/bin/tclsh", \
        "FSLWISH": "/usr/bin/wish" \
      } \
    }, \
    { \
      "name": "env", \
      "kwds": { \
        "OS": "Linux", \
        "FS_OVERRIDE": "0", \
        "FIX_VERTEX_AREA": "", \
        "SUBJECTS_DIR": "/opt/freesurfer/subjects", \
        "FSF_OUTPUT_FORMAT": "nii.gz", \
        "MNI_DIR": "/opt/freesurfer/mni", \
        "LOCAL_DIR": "/opt/freesurfer/local", \
        "FREESURFER_HOME": "/opt/freesurfer", \
        "FSFAST_HOME": "/opt/freesurfer/fsfast", \
        "MINC_BIN_DIR": "/opt/freesurfer/mni/bin", \
        "MINC_LIB_DIR": "/opt/freesurfer/mni/lib", \
        "MNI_DATAPATH": "/opt/freesurfer/mni/data", \
        "FMRI_ANALYSIS_DIR": "/opt/freesurfer/fsfast", \
        "PERL5LIB": "/opt/freesurfer/mni/share/perl5", \
        "MNI_PERL5LIB": "/opt/freesurfer/mni/share/perl5/", \
        "PATH": "/opt/miniconda-latest/bin:/opt/freesurfer/python/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin", \
        "PYTHONPATH": "" \
      } \
    }, \
    { \
      "name": "run", \
      "kwds": { \
        "command": "mkdir root/matlab && touch root/matlab/startup.m" \
      } \
    }, \
    { \
      "name": "run", \
      "kwds": { \
        "command": "mkdir /scratch" \
      } \
    }, \
    { \
      "name": "run", \
      "kwds": { \
        "command": "mkdir /local-scratch" \
      } \
    }, \
    { \
      "name": "copy", \
      "kwds": { \
        "source": [ \
          "run.py", \
          "/run.py" \
        ], \
        "destination": "/run.py" \
      } \
    }, \
    { \
      "name": "run", \
      "kwds": { \
        "command": "chmod +x /run.py" \
      } \
    }, \
    { \
      "name": "copy", \
      "kwds": { \
        "source": [ \
          "version", \
          "/version" \
        ], \
        "destination": "/version" \
      } \
    }, \
    { \
      "name": "entrypoint", \
      "kwds": { \
        "args": [ \
          "python3", \
          "/run.py" \
        ] \
      } \
    } \
  ] \
}' > /.reproenv.json
# End saving to specification to JSON.