Dockerfile

FROM ubuntu:xenial-20200114

# 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 \
                    curl \
                    bzip2 \
                    ca-certificates \
                    xvfb \
                    build-essential \
                    autoconf \
                    libtool \
                    pkg-config \
                    git && \
    curl -sL https://deb.nodesource.com/setup_10.x | bash - && \
    apt-get install -y --no-install-recommends \
                    nodejs && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Installing freesurfer
RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
    --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/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 FSL_DIR="/usr/share/fsl/5.0" \
    OS="Linux" \
    FS_OVERRIDE=0 \
    FIX_VERTEX_AREA="" \
    FSF_OUTPUT_FORMAT="nii.gz" \
    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="$FREESURFER_HOME/mni/data"
ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
    MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
    PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"

# Installing Neurodebian packages (FSL, AFNI, git)
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 \
                    fsl-core=5.0.9-5~nd16.04+1 \
                    fsl-mni152-templates=5.0.7-2 \
                    afni=16.2.07~dfsg.1-5~nd16.04+1 \
                    convert3d \
                    connectome-workbench=1.3.2-2~nd16.04+1 \
                    git-annex-standalone && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

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:$LD_LIBRARY_PATH" \
    FSLTCLSH="/usr/bin/tclsh" \
    FSLWISH="/usr/bin/wish" \
    AFNI_MODELPATH="/usr/lib/afni/models" \
    AFNI_IMSAVE_WARNINGS="NO" \
    AFNI_TTATLAS_DATASET="/usr/share/afni/atlases" \
    AFNI_PLUGINPATH="/usr/lib/afni/plugins"
ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH"

# Installing ANTs 2.3.3 (NeuroDocker build)
# Note: the URL says 2.3.4 but it is actually 2.3.3
ENV ANTSPATH=/usr/lib/ants
RUN mkdir -p $ANTSPATH && \
    curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
    | tar -xzC $ANTSPATH --strip-components 1
ENV PATH=$ANTSPATH:$PATH

# Installing and setting up miniconda
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh && \
    bash Miniconda3-4.5.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
    rm Miniconda3-4.5.11-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" \
    LANG="C.UTF-8" \
    LC_ALL="C.UTF-8" \
    PYTHONNOUSERSITE=1

# Installing precomputed python packages
RUN conda install -y -c anaconda -c conda-forge \
                     python=3.7 \
                     libxml2=2.9 \
                     libxslt=1.1 \
                     lxml \
                     mkl \
                     mkl-service \
                     numpy=1.20 \
                     pip=21 \
                     scipy=1.6 \
                     setuptools \
                     setuptools_scm \
                     toml \
                     zlib; sync && \
    chmod -R a+rX /usr/local/miniconda; sync && \
    chmod +x /usr/local/miniconda/bin/*; sync && \
    conda build purge-all; sync && \
    conda clean -tipsy && sync

# Unless otherwise specified each process should only use one thread - nipype
# will handle parallelization
ENV MKL_NUM_THREADS=1 \
    OMP_NUM_THREADS=1

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

# Install package
# CRITICAL: Make sure python setup.py --version has been run at least once
#           outside the container, with access to the git history.
COPY . /src/nitransforms
RUN pip install --no-cache-dir "/src/nitransforms[all]"

RUN find $HOME -type d -exec chmod go=u {} + && \
    find $HOME -type f -exec chmod go=u {} +


RUN ldconfig
WORKDIR /tmp/

ARG BUILD_DATE
ARG VCS_REF
ARG VERSION
LABEL org.label-schema.build-date=$BUILD_DATE \
      org.label-schema.name="nitransforms" \
      org.label-schema.vcs-url="https://github.com/nipy/nitransforms" \
      org.label-schema.version=$VERSION \
      org.label-schema.schema-version="1.0"