Dockerfile

# Ubuntu 20.04 LTS
FROM ubuntu:focal-20210827
ENV DEBIAN_FRONTEND="noninteractive" \
    LANG="en_US.UTF-8" \
    LC_ALL="en_US.UTF-8"

# Pre-cache neurodebian key
COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg

# Prepare environment
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
                    apt-utils \
                    autoconf \
                    build-essential \
                    bzip2 \
                    ca-certificates \
                    curl \
                    git \
                    graphviz \
                    libtool \
                    locales \
                    lsb-release \
                    pandoc \
                    pandoc-citeproc \
                    pkg-config \
                    xvfb && \
    curl -sSL https://deb.nodesource.com/setup_14.x | bash - && \
    apt-get install -y --no-install-recommends \
                    nodejs && \
    locale-gen en_US.UTF-8 && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Installing Neurodebian packages (workbench, git-annex)
RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
    apt-key add /usr/local/etc/neurodebian.gpg && \
    (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
                    connectome-workbench=1.5.0-1~nd20.04+1 \
                    git-annex-standalone=8.20210903-1~ndall+1 && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Installing ANTs 2.3.4 (NeuroDocker build)
ENV ANTSPATH="/usr/lib/ants" \
    PATH="/usr/lib/ants:$PATH"
WORKDIR $ANTSPATH
RUN curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
    | tar -xzC $ANTSPATH --strip-components 1

# AFNI latest (neurodocker build)
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           ed \
           gsl-bin \
           libglib2.0-0 \
           libglu1-mesa-dev \
           libglw1-mesa \
           libgomp1 \
           libjpeg62 \
           libxm4 \
           netpbm \
           tcsh \
           xfonts-base \
           xvfb \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && curl -sSL --retry 5 -o /tmp/multiarch.deb http://archive.ubuntu.com/ubuntu/pool/main/g/glibc/multiarch-support_2.27-3ubuntu1.2_amd64.deb \
    && dpkg -i /tmp/multiarch.deb \
    && rm /tmp/multiarch.deb \
    && curl -sSL --retry 5 -o /tmp/libxp6.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
    && dpkg -i /tmp/libxp6.deb \
    && rm /tmp/libxp6.deb \
    && curl -sSL --retry 5 -o /tmp/libpng.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
    && dpkg -i /tmp/libpng.deb \
    && rm /tmp/libpng.deb \
    && apt-get install -f \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
    && if [ -n "$gsl2_path" ]; then \
         ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
    fi \
    && ldconfig \
    && echo "Downloading AFNI ..." \
    && mkdir -p /opt/afni-latest \
    && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
    | tar -xz -C /opt/afni-latest --strip-components 1 \
    --exclude "linux_openmp_64/*.gz" \
    --exclude "linux_openmp_64/funstuff" \
    --exclude "linux_openmp_64/shiny" \
    --exclude "linux_openmp_64/afnipy" \
    --exclude "linux_openmp_64/lib/RetroTS" \
    --exclude "linux_openmp_64/meica.libs" \
    # Keep only what we use
    && find /opt/afni-latest -type f -not \( \
        -name "3dTshift" -or \
        -name "3dUnifize" -or \
        -name "3dAutomask" -or \
        -name "3dvolreg" \) -delete
ENV PATH="/opt/afni-latest:$PATH" \
    AFNI_IMSAVE_WARNINGS="NO" \
    AFNI_PLUGINPATH="/opt/afni-latest"

# Convert3D (neurodocker build)
RUN echo "Downloading Convert3D ..." \
    && mkdir -p /opt/convert3d-1.0.0 \
    && curl -fsSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download \
    | tar -xz -C /opt/convert3d-1.0.0 --strip-components 1 \
    --exclude "c3d-1.0.0-Linux-x86_64/lib" \
    --exclude "c3d-1.0.0-Linux-x86_64/share" \
    --exclude "c3d-1.0.0-Linux-x86_64/bin/c3d_gui"
ENV C3DPATH="/opt/convert3d-1.0.0" \
    PATH="/opt/convert3d-1.0.0/bin:$PATH"

# FSL 5.0.11 (neurodocker build)
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           dc \
           file \
           libfontconfig1 \
           libfreetype6 \
           libgl1-mesa-dev \
           libgl1-mesa-dri \
           libglu1-mesa-dev \
           libgomp1 \
           libice6 \
           libxcursor1 \
           libxft2 \
           libxinerama1 \
           libxrandr2 \
           libxrender1 \
           libxt6 \
           sudo \
           wget \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FSL ..." \
    && mkdir -p /opt/fsl-5.0.11 \
    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-centos6_64.tar.gz \
    | tar -xz -C /opt/fsl-5.0.11 --strip-components 1 \
    --exclude "fsl/config" \
    --exclude "fsl/data/atlases" \
    --exclude "fsl/data/first" \
    --exclude "fsl/data/mist" \
    --exclude "fsl/data/possum" \
    --exclude "fsl/data/standard/bianca" \
    --exclude "fsl/data/standard/tissuepriors" \
    --exclude "fsl/doc" \
    --exclude "fsl/etc/default_flobs.flobs" \
    --exclude "fsl/etc/fslconf" \
    --exclude "fsl/etc/js" \
    --exclude "fsl/etc/luts" \
    --exclude "fsl/etc/matlab" \
    --exclude "fsl/extras" \
    --exclude "fsl/include" \
    --exclude "fsl/python" \
    --exclude "fsl/refdoc" \
    --exclude "fsl/src" \
    --exclude "fsl/tcl" \
    --exclude "fsl/bin/FSLeyes" \
    && find /opt/fsl-5.0.11/bin -type f -not \( \
        -name "applywarp" -or \
        -name "bet" -or \
        -name "bet2" -or \
        -name "convert_xfm" -or \
        -name "fast" -or \
        -name "flirt" -or \
        -name "fsl_regfilt" -or \
        -name "fslhd" -or \
        -name "fslinfo" -or \
        -name "fslmaths" -or \
        -name "fslmerge" -or \
        -name "fslroi" -or \
        -name "fslsplit" -or \
        -name "fslstats" -or \
        -name "imtest" -or \
        -name "mcflirt" -or \
        -name "melodic" -or \
        -name "prelude" -or \
        -name "remove_ext" -or \
        -name "susan" -or \
        -name "topup" -or \
        -name "zeropad" \) -delete \
    && find /opt/fsl-5.0.11/data/standard -type f -not -name "MNI152_T1_2mm_brain.nii.gz" -delete
ENV FSLDIR="/opt/fsl-5.0.11" \
    PATH="/opt/fsl-5.0.11/bin:$PATH" \
    FSLOUTPUTTYPE="NIFTI_GZ" \
    FSLMULTIFILEQUIT="TRUE" \
    FSLTCLSH="/opt/fsl-5.0.11/bin/fsltclsh" \
    FSLWISH="/opt/fsl-5.0.11/bin/fslwish" \
    FSLLOCKDIR="" \
    FSLMACHINELIST="" \
    FSLREMOTECALL="" \
    FSLGECUDAQ="cuda.q" \
    POSSUMDIR="/opt/fsl-5.0.11" \
    LD_LIBRARY_PATH="/opt/fsl-5.0.11:$LD_LIBRARY_PATH"

# Install FreeSurfer
RUN apt update && \
    apt-get install -y --no-install-recommends \
            bc \
            libgomp1 \
            perl \
            tar \
            tcsh \
            wget \
            vim-common \
            libgl1-mesa-dev \
            libsm-dev \
            libxrender-dev \
            libxmu-dev \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
    && echo "Downloading FreeSurfer + InfantFS" \
    && mkdir -p /opt/freesurfer \
    && curl -fSL --retry 5 https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/infant/freesurfer-linux-centos7_x86_64-infant-dev-4a14499.tar.gz \
    | tar -xz -C /opt/freesurfer --no-same-owner --strip-components 1 \
    --exclude='freesurfer/average/mult-comp-cor' \
    --exclude='freesurfer/diffusion' \
    --exclude='freesurfer/docs' \
    --exclude='freesurfer/fsfast' \
    --exclude='freesurfer/lib/cuda' \
    --exclude='freesurfer/lib/qt' \
    --exclude='freesurfer/matlab' \
    --exclude='freesurfer/mni/share/man' \
    --exclude='freesurfer/subjects/fsaverage_sym' \
    --exclude='freesurfer/subjects/fsaverage3' \
    --exclude='freesurfer/subjects/fsaverage4' \
    --exclude='freesurfer/subjects/fsaverage5' \
    --exclude='freesurfer/subjects/fsaverage6' \
    --exclude='freesurfer/subjects/cvs_avg35' \
    --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
    --exclude='freesurfer/subjects/bert' \
    --exclude='freesurfer/subjects/lh.EC_average' \
    --exclude='freesurfer/subjects/rh.EC_average' \
    --exclude='freesurfer/subjects/sample-*.mgz' \
    --exclude='freesurfer/subjects/V1_average' \
    --exclude='freesurfer/trctrain'
ENV FREESURFER_HOME="/opt/freesurfer"
ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
    FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
    MNI_DIR="$FREESURFER_HOME/mni" \
    LOCAL_DIR="$FREESURFER_HOME/local" \
    MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
    MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
    MNI_DATAPATH="$FREESURFER_HOME/mni/data" \
    FSL_DIR=${FSLDIR}
ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
    MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
    PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
# remove build-stamp to play nice with nipype

# Installing SVGO and bids-validator
RUN npm install -g svgo@^2.3 bids-validator@^1.8.4 \
  && rm -rf ~/.npm ~/.empty /root/.npm

# ICA AROMA
WORKDIR /opt/ICA-AROMA
RUN curl -sSL "https://github.com/oesteban/ICA-AROMA/archive/v0.4.5.tar.gz" \
  | tar -xzC /opt/ICA-AROMA --strip-components 1 && \
  chmod +x /opt/ICA-AROMA/ICA_AROMA.py
ENV PATH="/opt/ICA-AROMA:$PATH" \
    AROMA_VERSION="0.4.5"

# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users nibabies
WORKDIR /home/nibabies
ENV HOME="/home/nibabies"

# Installing and setting up miniconda
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-py38_4.9.2-Linux-x86_64.sh && \
    bash Miniconda3-py38_4.9.2-Linux-x86_64.sh -b -p /usr/local/miniconda && \
    rm Miniconda3-py38_4.9.2-Linux-x86_64.sh

# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
ENV PATH="/usr/local/miniconda/bin:$PATH" \
    CPATH="/usr/local/miniconda/include:$CPATH" \
    PYTHONNOUSERSITE=1 \
    MKL_NUM_THREADS=1 \
    OMP_NUM_THREADS=1 \
    IS_DOCKER_8395080871=1

# Installing precomputed python packages
RUN conda install -y python=3.8 \
                     pip=21.0 \
                     mkl=2021.2 \
                     mkl-service=2.3 \
                     numpy=1.20 \
                     scipy=1.6 \
                     scikit-image=0.18 \
                     scikit-learn=0.24 \
                     matplotlib=3.3 \
                     pandas=1.2 \
                     libxslt=1.1 \
                     traits=6.2 \
                     zstd=1.4; sync && \
    chmod -R a+rX /usr/local/miniconda; sync && \
    chmod +x /usr/local/miniconda/bin/*; sync && \
    conda clean -y --all && sync && \
    rm -rf ~/.conda ~/.cache/pip/*; sync

# Precaching fonts, set 'Agg' as default backend for matplotlib
RUN python -c "from matplotlib import font_manager" && \
    sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )

# Precaching atlases
COPY setup.cfg nibabies-setup.cfg
COPY scripts/fetch_templates.py fetch_templates.py
RUN pip install --no-cache-dir "$( grep templateflow nibabies-setup.cfg | xargs )" && \
    python fetch_templates.py && \
    rm nibabies-setup.cfg fetch_templates.py && \
    find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && \
    find $HOME/.cache/templateflow -type f -exec chmod go=u {} +

COPY . /src/nibabies
# Force static versioning within container
RUN echo "${VERSION}" > /src/nibabies/nibabies/VERSION && \
    echo "include nibabies/VERSION" >> /src/nibabies/MANIFEST.in && \
    pip install --no-cache-dir -e "/src/nibabies[all]" && \
    rm ${FREESURFER_HOME}/build-stamp.txt

# ABI tags can interfere when running on Singularity
RUN strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5

# Final settings
RUN ldconfig
WORKDIR /tmp
ARG BUILD_DATE
ARG VCS_REF
ARG VERSION
LABEL org.label-schema.build-date=$BUILD_DATE \
      org.label-schema.name="nibabies" \
      org.label-schema.description="nibabies - NeuroImaging tools for babies" \
      org.label-schema.url="https://github.com/nipreps/nibabies" \
      org.label-schema.vcs-ref=$VCS_REF \
      org.label-schema.vcs-url="https://github.com/nipreps/nibabies" \
      org.label-schema.version=$VERSION \
      org.label-schema.schema-version="1.0"

ENTRYPOINT ["/usr/local/miniconda/bin/nibabies"]