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ARG MAKE_JOBS="1"
ARG DEBIAN_FRONTEND="noninteractive"
FROM python:3.8-slim AS base
FROM buildpack-deps:bookworm AS base-builder
FROM base-builder AS mrtrix3-builder
# Git commitish from which to build MRtrix3.
ARG MRTRIX3_GIT_COMMITISH="3.0.8"
# Command-line arguments for `./configure`
ARG MRTRIX3_CONFIGURE_FLAGS=""
# Command-line arguments for `./build`
ARG MRTRIX3_BUILD_FLAGS="-persistent -nopaginate"
RUN apt-get -qq update \
&& apt-get install -yq --no-install-recommends \
libeigen3-dev \
libfftw3-dev \
libgl1-mesa-dev \
libpng-dev \
libqt5opengl5-dev \
libqt5svg5-dev \
libtiff5-dev \
python3 \
qtbase5-dev \
zlib1g-dev \
&& rm -rf /var/lib/apt/lists/*
# Clone, build, and install MRtrix3.
ARG MAKE_JOBS
WORKDIR /opt/mrtrix3
RUN git clone -b $MRTRIX3_GIT_COMMITISH --depth 1 https://github.com/MRtrix3/mrtrix3.git . \
&& python3 ./configure $MRTRIX3_CONFIGURE_FLAGS \
&& NUMBER_OF_PROCESSORS=$MAKE_JOBS python3 ./build $MRTRIX3_BUILD_FLAGS \
&& rm -rf tmp
# Download minified ART ACPCdetect (V2.0).
FROM base-builder AS acpcdetect-installer
WORKDIR /opt/art
RUN curl -fsSL https://osf.io/73h5s/download \
| tar xz --strip-components 1
# Download minified ANTs (2.3.4-2).
FROM base-builder AS ants-installer
WORKDIR /opt/ants
RUN curl -fsSL https://osf.io/yswa4/download \
| tar xz --strip-components 1
# Download FreeSurfer files.
FROM base-builder AS freesurfer-installer
WORKDIR /opt/freesurfer
RUN curl -fsSLO https://raw.githubusercontent.com/freesurfer/freesurfer/v7.1.1/distribution/FreeSurferColorLUT.txt
# Download minified FSL (6.0.7.7)
FROM base-builder AS fsl-installer
WORKDIR /opt/fsl
RUN curl -fsSL https://osf.io/ph9ex/download \
| tar xz --strip-components 1
# Build final image.
FROM base AS final
# Install runtime system dependencies.
RUN apt-get -qq update \
&& apt-get install -yq --no-install-recommends \
binutils \
dc \
less \
libfftw3-single3 \
libfftw3-double3 \
libgl1-mesa-glx \
libgomp1 \
liblapack3 \
libpng16-16 \
libqt5core5a \
libqt5gui5 \
libqt5network5 \
libqt5svg5 \
libqt5widgets5 \
libquadmath0 \
libtiff5-dev \
python3 \
python3-distutils \
procps \
&& rm -rf /var/lib/apt/lists/*
COPY --from=acpcdetect-installer /opt/art /opt/art
COPY --from=ants-installer /opt/ants /opt/ants
COPY --from=freesurfer-installer /opt/freesurfer /opt/freesurfer
COPY --from=fsl-installer /opt/fsl /opt/fsl
COPY --from=mrtrix3-builder /opt/mrtrix3 /opt/mrtrix3
ENV ANTSPATH="/opt/ants/bin" \
ARTHOME="/opt/art" \
FREESURFER_HOME="/opt/freesurfer" \
FSLDIR="/opt/fsl" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLTCLSH="/opt/fsl/bin/fsltclsh" \
FSLWISH="/opt/fsl/bin/fslwish" \
PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/share/fsl/bin:$PATH"
# Fix "Singularity container cannot load libQt5Core.so.5" on CentOS 7
RUN strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5 \
&& ldconfig \
&& apt-get purge -yq binutils
RUN ln -s /usr/bin/python3 /usr/bin/python
CMD ["/bin/bash"]
|
