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bpinsardbpinsard
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make lighter alpine multi-stage build docker image, ~60% smaller
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‎Dockerfile

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# Generated by Neurodocker and Reproenv.
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FROM python:3.10-alpine AS builder
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FROM neurodebian:bullseye
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ENV PATH="/opt/dcm2niix-v1.0.20220720/bin:$PATH"
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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ca-certificates \
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cmake \
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g++ \
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gcc \
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git \
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make \
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pigz \
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zlib1g-dev \
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&& rm -rf /var/lib/apt/lists/* \
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&& git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
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&& cd /tmp/dcm2niix \
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&& git fetch --tags \
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&& git checkout v1.0.20220720 \
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&& mkdir /tmp/dcm2niix/build \
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&& cd /tmp/dcm2niix/build \
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&& cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 .. \
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&& make -j1 \
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&& make install \
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&& rm -rf /tmp/dcm2niix
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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gcc \
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git \
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git-annex-standalone \
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libc-dev \
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liblzma-dev \
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netbase \
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pigz \
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&& rm -rf /var/lib/apt/lists/*
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COPY [".", \
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"/src/heudiconv"]
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ENV CONDA_DIR="/opt/miniconda-py39_4.12.0" \
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PATH="/opt/miniconda-py39_4.12.0/bin:$PATH"
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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bzip2 \
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ca-certificates \
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curl \
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&& rm -rf /var/lib/apt/lists/* \
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# Install dependencies.
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&& export PATH="/opt/miniconda-py39_4.12.0/bin:$PATH" \
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&& echo "Downloading Miniconda installer ..." \
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&& conda_installer="/tmp/miniconda.sh" \
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&& curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh \
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&& bash "$conda_installer" -b -p /opt/miniconda-py39_4.12.0 \
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&& rm -f "$conda_installer" \
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# Prefer packages in conda-forge
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&& conda config --system --prepend channels conda-forge \
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# Packages in lower-priority channels not considered if a package with the same
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# name exists in a higher priority channel. Can dramatically speed up installations.
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# Conda recommends this as a default
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# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html
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&& conda config --set channel_priority strict \
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&& conda config --system --set auto_update_conda false \
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&& conda config --system --set show_channel_urls true \
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# Enable `conda activate`
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&& conda init bash \
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&& conda install -y --name base \
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"python=3.9" \
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"traits>=4.6.0" \
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"scipy" \
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"numpy" \
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"nomkl" \
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"pandas" \
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"gdcm" \
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&& bash -c "source activate base \
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&& python -m pip install --no-cache-dir --editable \
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"/src/heudiconv[all]"" \
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# Clean up
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&& sync && conda clean --all --yes && sync \
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&& rm -rf ~/.cache/pip/*
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ENTRYPOINT ["heudiconv"]
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RUN apk add bash \
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gcc \
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g++ \
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libc-dev \
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make \
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cmake \
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util-linux-dev \
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curl \
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git
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RUN pip install --no-cache-dir pylibjpeg-libjpeg traits==6.3.2
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ARG DCM2NIIX_VERSION=v1.0.20240202
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RUN git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
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&& cd /tmp/dcm2niix \
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&& git fetch --tags \
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&& git checkout $DCM2NIIX_VERSION \
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&& mkdir /tmp/dcm2niix/build \
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&& cd /tmp/dcm2niix/build \
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&& cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr/ .. \
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&& make -j1 \
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&& make install \
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&& rm -rf /tmp/dcm2niix
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FROM python:3.10-alpine
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COPY --from=builder /usr/local/lib/python3.10/site-packages /usr/local/lib/python3.10/site-packages
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COPY --from=builder /usr/bin/dcm2niix /usr/bin/dcm2niix
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# Save specification to JSON.
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RUN printf '{ \
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"pkg_manager": "apt", \
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"existing_users": [ \
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"root" \
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], \
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"instructions": [ \
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{ \
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"name": "from_", \
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"kwds": { \
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"base_image": "neurodebian:bullseye" \
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} \
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}, \
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{ \
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"name": "env", \
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"kwds": { \
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"PATH": "/opt/dcm2niix-v1.0.20220720/bin:$PATH" \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n ca-certificates \\\\\\n cmake \\\\\\n g++ \\\\\\n gcc \\\\\\n git \\\\\\n make \\\\\\n pigz \\\\\\n zlib1g-dev\\nrm -rf /var/lib/apt/lists/*\\ngit clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix\\ncd /tmp/dcm2niix\\ngit fetch --tags\\ngit checkout v1.0.20220720\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 ..\\nmake -j1\\nmake install\\nrm -rf /tmp/dcm2niix" \
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} \
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}, \
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{ \
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"name": "install", \
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"kwds": { \
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"pkgs": [ \
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"git", \
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"gcc", \
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"pigz", \
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"liblzma-dev", \
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"libc-dev", \
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"git-annex-standalone", \
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"netbase" \
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], \
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"opts": null \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "apt-get update -qq \\\\\\n && apt-get install -y -q --no-install-recommends \\\\\\n gcc \\\\\\n git \\\\\\n git-annex-standalone \\\\\\n libc-dev \\\\\\n liblzma-dev \\\\\\n netbase \\\\\\n pigz \\\\\\n && rm -rf /var/lib/apt/lists/*" \
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} \
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}, \
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{ \
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"name": "copy", \
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"kwds": { \
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"source": [ \
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".", \
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"/src/heudiconv" \
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], \
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"destination": "/src/heudiconv" \
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} \
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}, \
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{ \
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"name": "env", \
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"kwds": { \
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"CONDA_DIR": "/opt/miniconda-py39_4.12.0", \
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"PATH": "/opt/miniconda-py39_4.12.0/bin:$PATH" \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-py39_4.12.0/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-py39_4.12.0\\nrm -f \\"$conda_installer\\"\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y --name base \\\\\\n \\"python=3.9\\" \\\\\\n \\"traits>=4.6.0\\" \\\\\\n \\"scipy\\" \\\\\\n \\"numpy\\" \\\\\\n \\"nomkl\\" \\\\\\n \\"pandas\\" \\\\\\n \\"gdcm\\"\\nbash -c \\"source activate base\\n python -m pip install --no-cache-dir --editable \\\\\\n \\"/src/heudiconv[all]\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
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} \
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}, \
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{ \
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"name": "entrypoint", \
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"kwds": { \
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"args": [ \
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"heudiconv" \
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] \
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} \
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} \
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] \
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}' > /.reproenv.json
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# End saving to specification to JSON.
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RUN apk update && apk add --no-cache git git-annex pigz gcompat
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RUN pip install --no-cache-dir heudiconv
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ENTRYPOINT ["heudiconv"]

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