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@tsalo
tsalo committed May 8, 2024
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294 changes: 165 additions & 129 deletions Dockerfile
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#
# MIT License
#
# Copyright (c) 2023 The NiPreps Developers
# Copyright (c) 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
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# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.

# Ubuntu 22.04 LTS - Jammy
ARG BASE_IMAGE=ubuntu:jammy-20240125

#
# Build wheel
#
FROM python:slim AS src
RUN pip install build
RUN apt-get update && \
apt-get install -y --no-install-recommends git
COPY . /src/fmripost_aroma
RUN python -m build /src/fmripost_aroma
COPY . /src
RUN python -m build /src

# Use Ubuntu 22.04 LTS
FROM ubuntu:jammy-20221130
#
# Download stages
#

# Prepare environment
# Utilities for downloading packages
FROM ${BASE_IMAGE} as downloader
# Bump the date to current to refresh curl/certificates/etc
RUN echo "2023.07.20"
RUN apt-get update && \
apt-get install -y --no-install-recommends \
apt-utils \
autoconf \
build-essential \
binutils \
bzip2 \
ca-certificates \
curl \
unzip && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# AFNI
FROM downloader as afni
# Bump the date to current to update AFNI
RUN echo "2023.07.20"
RUN 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/lib_RetroTS" \
--exclude "linux_openmp_64/meica.libs" \
# Keep only what we use
&& find /opt/afni-latest -type f -not -name "3dTshift" -delete

# Connectome Workbench 1.5.0
FROM downloader as workbench
RUN mkdir /opt/workbench && \
curl -sSLO https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && \
unzip workbench-linux64-v1.5.0.zip -d /opt && \
rm workbench-linux64-v1.5.0.zip && \
rm -rf /opt/workbench/libs_linux64_software_opengl /opt/workbench/plugins_linux64 && \
strip --remove-section=.note.ABI-tag /opt/workbench/libs_linux64/libQt5Core.so.5

# Convert3d 1.4.0
FROM downloader as c3d
RUN mkdir /opt/convert3d && \
curl -fsSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/Experimental/c3d-1.4.0-Linux-gcc64.tar.gz/download \
| tar -xz -C /opt/convert3d --strip-components 1

# Micromamba
FROM downloader as micromamba

# Install a C compiler to build extensions when needed.
# traits<6.4 wheels are not available for Python 3.11+, but build easily.
RUN apt-get update && \
apt-get install -y --no-install-recommends build-essential && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

WORKDIR /
# Bump the date to current to force update micromamba
RUN echo "2024.02.06"
RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba

ENV MAMBA_ROOT_PREFIX="/opt/conda"
COPY env.yml /tmp/env.yml
WORKDIR /tmp
RUN micromamba create -y -f /tmp/env.yml && \
micromamba clean -y -a

# UV_USE_IO_URING for apparent race-condition (https://github.com/nodejs/node/issues/48444)
# Check if this is still necessary when updating the base image.
ENV PATH="/opt/conda/envs/fmripost_aroma/bin:$PATH" \
UV_USE_IO_URING=0
RUN npm install -g svgo@^3.2.0 bids-validator@^1.14.0 && \
rm -r ~/.npm

#
# Main stage
#
FROM ${BASE_IMAGE} as fmripost_aroma

# Configure apt
ENV DEBIAN_FRONTEND="noninteractive" \
LANG="en_US.UTF-8" \
LC_ALL="en_US.UTF-8"

# Some baseline tools; bc is needed for FreeSurfer, so don't drop it
RUN apt-get update && \
apt-get install -y --no-install-recommends \
bc \
ca-certificates \
curl \
git \
gnupg \
libtool \
lsb-release \
netbase \
pkg-config \
unzip \
xvfb && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

ENV DEBIAN_FRONTEND="noninteractive" \
LANG="en_US.UTF-8" \
LC_ALL="en_US.UTF-8"
# Configure PPAs for libpng12 and libxp6
RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \
&& GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/zeehio.gpg --recv 0xA1301338A3A48C4A \
&& echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list \
&& echo "deb [signed-by=/usr/share/keyrings/zeehio.gpg] https://ppa.launchpadcontent.net/zeehio/libxp/ubuntu jammy main" > /etc/apt/sources.list.d/zeehio.list

# FSL 6.0.5.1
# Dependencies for AFNI; requires a discontinued multiarch-support package from bionic (18.04)
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bc \
dc \
file \
libfontconfig1 \
libfreetype6 \
libgl1-mesa-dev \
libgl1-mesa-dri \
ed \
gsl-bin \
libglib2.0-0 \
libglu1-mesa-dev \
libglw1-mesa \
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-6.0.5.1 \
&& curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz \
| tar -xz -C /opt/fsl-6.0.5.1 --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-6.0.5.1/bin -type f -not \( \
-name "melodic" -or \
-name "susan" -or \) -delete \
&& find /opt/fsl-6.0.5.1/data/standard -type f -not -name "MNI152_T1_2mm_brain.nii.gz" -delete
ENV FSLDIR="/opt/fsl-6.0.5.1" \
PATH="/opt/fsl-6.0.5.1/bin:$PATH" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLLOCKDIR="" \
FSLMACHINELIST="" \
FSLREMOTECALL="" \
FSLGECUDAQ="cuda.q" \
LD_LIBRARY_PATH="/opt/fsl-6.0.5.1/lib:$LD_LIBRARY_PATH"
libjpeg62 \
libpng12-0 \
libxm4 \
libxp6 \
netpbm \
tcsh \
xfonts-base \
xvfb \
&& curl -sSL --retry 5 -o /tmp/multiarch.deb http://archive.ubuntu.com/ubuntu/pool/main/g/glibc/multiarch-support_2.27-3ubuntu1.5_amd64.deb \
&& dpkg -i /tmp/multiarch.deb \
&& rm /tmp/multiarch.deb \
&& apt-get install -f \
&& apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& 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

# Configure PPA for libpng12
RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \
&& echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list

# Installing and setting up 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"

WORKDIR /opt
RUN curl -sSLO https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && \
unzip workbench-linux64-v1.5.0.zip && \
rm workbench-linux64-v1.5.0.zip && \
rm -rf /opt/workbench/libs_linux64_software_opengl /opt/workbench/plugins_linux64 && \
strip --remove-section=.note.ABI-tag /opt/workbench/libs_linux64/libQt5Core.so.5
# ABI tags can interfere when running on Singularity
# Install files from stages
COPY --from=afni /opt/afni-latest /opt/afni-latest
COPY --from=workbench /opt/workbench /opt/workbench
COPY --from=c3d /opt/convert3d/bin/c3d_affine_tool /usr/bin/c3d_affine_tool

# AFNI config
ENV PATH="/opt/afni-latest:$PATH" \
AFNI_IMSAVE_WARNINGS="NO" \
AFNI_PLUGINPATH="/opt/afni-latest"

# Workbench config
ENV PATH="/opt/workbench/bin_linux64:$PATH" \
LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"

# nipreps/miniconda:py39_4.12.0rc0
COPY --from=nipreps/miniconda@sha256:5aa4d2bb46e7e56fccf6e93ab3ff765add74e79f96ffa00449504b4869790cb9 /opt/conda /opt/conda

RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate base" >> ~/.bashrc

# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
ENV PATH="/opt/conda/bin:$PATH" \
CPATH="/opt/conda/include:$CPATH" \
LD_LIBRARY_PATH="/opt/conda/lib:$LD_LIBRARY_PATH" \
LANG="C.UTF-8" \
LC_ALL="C.UTF-8" \
PYTHONNOUSERSITE=1

RUN conda install -y -n base \
-c anaconda \
-c conda-forge \
convert3d=1.3.0 \
&& sync \
&& conda clean -afy; sync \
&& rm -rf ~/.conda ~/.cache/pip/*; sync \
&& ldconfig

# 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 $HOME directory
RUN useradd -m -s /bin/bash -G users fmripost_aroma
WORKDIR /home/fmripost_aroma
ENV HOME="/home/fmripost_aroma" \
LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"

RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> $HOME/.bashrc && \
echo "conda activate base" >> $HOME/.bashrc
COPY --from=micromamba /bin/micromamba /bin/micromamba
COPY --from=micromamba /opt/conda/envs/fmripost_aroma /opt/conda/envs/fmripost_aroma

RUN /opt/conda/bin/python -m pip install --no-cache-dir --upgrade templateflow
ENV MAMBA_ROOT_PREFIX="/opt/conda"
RUN micromamba shell init -s bash && \
echo "micromamba activate fmripost_aroma" >> $HOME/.bashrc
ENV PATH="/opt/conda/envs/fmripost_aroma/bin:$PATH" \
CPATH="/opt/conda/envs/fmripost_aroma/include:$CPATH" \
LD_LIBRARY_PATH="/opt/conda/envs/fmripost_aroma/lib:$LD_LIBRARY_PATH"

# Precaching atlases
COPY scripts/fetch_templates.py fetch_templates.py

RUN /opt/conda/bin/python fetch_templates.py && \
RUN python fetch_templates.py && \
rm fetch_templates.py && \
find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && \
find $HOME/.cache/templateflow -type f -exec chmod go=u {} +

# FSL environment
ENV LANG="C.UTF-8" \
LC_ALL="C.UTF-8" \
PYTHONNOUSERSITE=1 \
FSLDIR="/opt/conda/envs/fmripost_aroma" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLLOCKDIR="" \
FSLMACHINELIST="" \
FSLREMOTECALL="" \
FSLGECUDAQ="cuda.q"

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

# Installing fMRIPost-AROMA
COPY --from=src /src/fmripost_aroma/dist/*.whl .
RUN /opt/conda/bin/python -m pip install --no-cache-dir $( ls *.whl )[all]
COPY --from=src /src/dist/*.whl .
RUN pip install --no-cache-dir $( ls *.whl )[test]

RUN find $HOME -type d -exec chmod go=u {} + && \
find $HOME -type f -exec chmod go=u {} + && \
rm -rf $HOME/.npm $HOME/.conda $HOME/.empty

# For detecting the container
ENV IS_DOCKER_8395080871=1

RUN ldconfig
WORKDIR /tmp
ENTRYPOINT ["/opt/conda/bin/fmripost_aroma"]
ENTRYPOINT ["/opt/conda/envs/fmripost_aroma/bin/fmripost_aroma"]

ARG BUILD_DATE
ARG VCS_REF
ARG VERSION
LABEL org.label-schema.build-date=$BUILD_DATE \
org.label-schema.name="fMRIPost-AROMA" \
org.label-schema.description="fMRIPost-AROMA - robust fMRI preprocessing tool" \
org.label-schema.url="http://fmripost_aroma.org" \
org.label-schema.description="fMRIPost-AROMA - fMRI post-processing with AROMA" \
org.label-schema.url="https://fmripost_aroma.org" \
org.label-schema.vcs-ref=$VCS_REF \
org.label-schema.vcs-url="https://github.com/nipreps/fmripost_aroma" \
org.label-schema.version=$VERSION \
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