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yarikopticyarikoptic
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Fixup miniconda spec for neurodocker so it produces dockerfile now
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‎Dockerfile

Lines changed: 124 additions & 129 deletions
Original file line numberDiff line numberDiff line change
@@ -1,164 +1,159 @@
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# Generated by Neurodocker version 0.4.2-3-gf7055a1
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# Timestamp: 2022-04-06 17:10:29 UTC
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#
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# Thank you for using Neurodocker. If you discover any issues
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# or ways to improve this software, please submit an issue or
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# pull request on our GitHub repository:
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#
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# https://github.com/kaczmarj/neurodocker
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# Generated by Neurodocker and Reproenv.
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FROM neurodebian:bullseye
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ARG DEBIAN_FRONTEND="noninteractive"
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ENV LANG="en_US.UTF-8" \
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LC_ALL="en_US.UTF-8" \
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ND_ENTRYPOINT="/neurodocker/startup.sh"
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RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
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&& apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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apt-utils \
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bzip2 \
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ca-certificates \
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curl \
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locales \
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unzip \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
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&& dpkg-reconfigure --frontend=noninteractive locales \
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&& update-locale LANG="en_US.UTF-8" \
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&& chmod 777 /opt && chmod a+s /opt \
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&& mkdir -p /neurodocker \
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&& if [ ! -f "$ND_ENTRYPOINT" ]; then \
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echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
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&& echo 'set -e' >> "$ND_ENTRYPOINT" \
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&& echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
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fi \
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&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
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ENTRYPOINT ["/neurodocker/startup.sh"]
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ENV PATH="/opt/dcm2niix-v1.0.20211006/bin:$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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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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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 v1.0.20211006 \
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&& mkdir /tmp/dcm2niix/build \
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&& cd /tmp/dcm2niix/build \
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&& cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20211006 .. \
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&& make \
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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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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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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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COPY [".", "/src/heudiconv"]
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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-latest" \
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PATH="/opt/miniconda-latest/bin:$PATH"
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RUN export PATH="/opt/miniconda-latest/bin:$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-latest/bin:$PATH" \
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&& echo "Downloading Miniconda installer ..." \
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&& conda_installer="/tmp/miniconda.sh" \
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&& curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
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&& curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
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&& bash "$conda_installer" -b -p /opt/miniconda-latest \
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&& rm -f "$conda_installer" \
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&& conda update -yq -nbase conda \
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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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&& sync && conda clean -y --all && sync \
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&& conda install -y -q --name base \
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'python=3.7' \
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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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&& sync && conda clean -y --all && sync \
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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=3.7" \
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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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&& bash -c "source activate base \
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&& pip install --no-cache-dir --editable \
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'/src/heudiconv[all]'" \
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&& rm -rf ~/.cache/pip/* \
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&& sync
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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 echo '{ \
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\n "pkg_manager": "apt", \
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\n "instructions": [ \
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\n [ \
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\n "base", \
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\n "neurodebian:bullseye" \
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\n ], \
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\n [ \
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\n "dcm2niix", \
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\n { \
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\n "version": "v1.0.20211006", \
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\n "method": "source" \
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\n } \
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\n ], \
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\n [ \
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\n "install", \
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\n [ \
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\n "git", \
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\n "gcc", \
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\n "pigz", \
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\n "liblzma-dev", \
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\n "libc-dev", \
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\n "git-annex-standalone", \
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\n "netbase" \
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\n ] \
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\n ], \
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\n [ \
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\n "copy", \
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\n [ \
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\n ".", \
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\n "/src/heudiconv" \
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\n ] \
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\n ], \
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\n [ \
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\n "miniconda", \
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\n { \
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\n "use_env": "base", \
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\n "conda_install": [ \
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\n "python=3.7", \
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\n "traits>=4.6.0", \
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\n "scipy", \
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\n "numpy", \
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\n "nomkl", \
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\n "pandas" \
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\n ], \
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\n "pip_install": [ \
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\n "/src/heudiconv[all]" \
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\n ], \
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\n "pip_opts": "--editable" \
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\n } \
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\n ], \
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\n [ \
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\n "entrypoint", \
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\n "heudiconv" \
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\n ] \
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\n ] \
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\n}' > /neurodocker/neurodocker_specs.json
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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-v1.0.20211006/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 v1.0.20211006\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20211006 ..\\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-latest", \
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"PATH": "/opt/miniconda-latest/bin:$PATH" \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-latest/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-latest\\nrm -f \\"$conda_installer\\"\\nconda update -yq -nbase conda\\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=3.7\\" \\\\\\n \\"traits>=4.6.0\\" \\\\\\n \\"scipy\\" \\\\\\n \\"numpy\\" \\\\\\n \\"nomkl\\" \\\\\\n \\"pandas\\"\\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.

‎utils/gen-docker-image.sh

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Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ docker run --rm $image generate docker -b neurodebian:bullseye -p apt \
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--dcm2niix version=v1.0.20211006 method=source \
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--install git gcc pigz liblzma-dev libc-dev git-annex-standalone netbase \
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--copy . /src/heudiconv \
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--miniconda use_env=base conda_install="python=3.7 traits>=4.6.0 scipy numpy nomkl pandas" \
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--miniconda version=latest conda_install="python=3.7 traits>=4.6.0 scipy numpy nomkl pandas" \
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pip_install="/src/heudiconv[all]" \
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pip_opts="--editable" \
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--entrypoint "heudiconv" \

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