Dockerfile

# dMRIPrep Docker Container Image distribution
#
# MIT License
#
# Copyright (c) 2021 The NiPreps Developers
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.

# Use Ubuntu 16.04 LTS
FROM ubuntu:xenial-20201030

# Prepare environment
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
                    autoconf \
                    build-essential \
                    bzip2 \
                    ca-certificates \
                    curl \
                    cython3 \
                    git \
                    libtool \
                    lsb-release \
                    pkg-config \
                    xvfb && \
    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"

# Pre-cache neurodebian key
COPY .docker/neurodebian.gpg /usr/local/etc/neurodebian.gpg
# 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 && \
    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"

COPY .docker/fsl-6.0/bin/topup /usr/share/fsl/5.0/bin/topup
COPY .docker/fsl-6.0/bin/imglob /usr/share/fsl/5.0/bin/imglob
COPY .docker/fsl-6.0/bin/eddy_openmp  /usr/lib/fsl/5.0/eddy_openmp
COPY .docker/fsl-6.0/lib/* /usr/lib/fsl/5.0/

# 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

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

# 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=3.7.1 \
                     graphviz=2.40 \
                     git-annex \
                     libxml2=2.9.8 \
                     libxslt=1.1.32 \
                     matplotlib=2.2 \
                     mkl \
                     mkl-service \
                     nodejs \
                     numpy=1.20 \
                     pandoc=2.11 \
                     pip=20.3 \
                     scikit-learn=0.19 \
                     scipy=1.5 \
                     setuptools=51.1 \
                     traits=4.6.0 \
                     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

# 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())" )

# Installing SVGO
RUN npm install -g svgo

# Installing bids-validator
RUN npm install -g bids-validator@1.4.0

# Refresh linked libraries
RUN ldconfig

WORKDIR /src

# Installing dMRIPrep
COPY . /src/dmriprep
ARG VERSION
# Force static versioning within container
RUN echo "${VERSION}" > /src/dmriprep/dmriprep/VERSION && \
    echo "include dmriprep/VERSION" >> /src/dmriprep/MANIFEST.in && \
    cd /src/dmriprep && \
    pip install --no-cache-dir .[all]

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

WORKDIR /tmp/
ENTRYPOINT ["/usr/local/miniconda/bin/dmriprep"]

ARG BUILD_DATE
ARG VCS_REF
ARG VERSION
LABEL org.label-schema.build-date=$BUILD_DATE \
      org.label-schema.name="dMRIPrep" \
      org.label-schema.description="dMRIPrep - robust dMRI preprocessing tool" \
      org.label-schema.url="http://dmriprep.org" \
      org.label-schema.vcs-ref=$VCS_REF \
      org.label-schema.vcs-url="https://github.com/nipreps/dmriprep" \
      org.label-schema.version=$VERSION \
      org.label-schema.schema-version="1.0"