118 lines
4.3 KiB
Docker
118 lines
4.3 KiB
Docker
FROM public.ecr.aws/j1r0q0g6/notebooks/notebook-servers/base:master-1831e436
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USER root
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# use bash instead of sh
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SHELL ["/bin/bash", "-c"]
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# args - software versions
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ARG CONDA_VERSION="4.9.2"
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ARG MINIFORGE_ARCH="x86_64"
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ARG MINIFORGE_SHA256="91d5aa5f732b5e02002a371196a2607f839bab166970ea06e6ecc602cb446848"
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ARG MINIFORGE_VERSION="${CONDA_VERSION}-7"
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ARG PIP_VERSION="21.0.1"
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ARG PYTHON_VERSION="3.8.8"
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ARG RSTUDIO_ARCH="amd64"
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ARG RSTUDIO_SHA256="a46bbfbcb468e7af6aa12280adb830056f4a10e3457fd2f5969bb31d4d476939"
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ARG RSTUDIO_VERSION="1.4.1106"
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ARG R_BASE_VERSION="4.0.3"
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ARG R_RETICULATE_VERSION="1.18"
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ARG R_PNG_VERSION="0.1_7"
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# install - binary rstudio dependencies
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RUN apt-get -yq update \
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&& apt-get -yq install --no-install-recommends \
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libapparmor1 \
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libc6 \
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libclang-dev \
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libedit2 \
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libpq5 \
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psmisc \
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rrdtool \
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sudo \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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# setup environment for conda
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ENV CONDA_DIR /opt/conda
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ENV PATH "${CONDA_DIR}/bin:${PATH}"
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RUN mkdir -p ${CONDA_DIR} \
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&& echo ". /opt/conda/etc/profile.d/conda.sh" >> ${HOME}/.bashrc \
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&& echo ". /opt/conda/etc/profile.d/conda.sh" >> /etc/profile \
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&& echo "conda activate base" >> ${HOME}/.bashrc \
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&& echo "conda activate base" >> /etc/profile \
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&& chown -R ${NB_USER}:users ${CONDA_DIR} \
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&& chown -R ${NB_USER}:users ${HOME}
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# setup environment for R
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ENV R_HOME ${CONDA_DIR}/lib/R
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USER ${NB_UID}
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# install - conda, pip, python, r-base
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RUN curl -sL "https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/Miniforge3-${MINIFORGE_VERSION}-Linux-${MINIFORGE_ARCH}.sh" -o /tmp/Miniforge3.sh \
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&& echo "${MINIFORGE_SHA256} /tmp/Miniforge3.sh" | sha256sum --check \
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&& /bin/bash /tmp/Miniforge3.sh -b -f -p ${CONDA_DIR} \
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&& rm /tmp/Miniforge3.sh \
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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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&& echo "conda ${CONDA_VERSION}" >> ${CONDA_DIR}/conda-meta/pinned \
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&& echo "python ${PYTHON_VERSION}" >> ${CONDA_DIR}/conda-meta/pinned \
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&& echo "r-base ${R_BASE_VERSION}" >> ${CONDA_DIR}/conda-meta/pinned \
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&& conda install -y -q \
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python=${PYTHON_VERSION} \
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conda=${CONDA_VERSION} \
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pip=${PIP_VERSION} \
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r-base=${R_BASE_VERSION} \
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r-reticulate=${R_RETICULATE_VERSION} \
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r-png=${R_PNG_VERSION} \
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&& conda update -y -q --all \
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&& conda clean -a -f -y \
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&& chown -R ${NB_USER}:users ${CONDA_DIR} \
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&& chown -R ${NB_USER}:users ${HOME}
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# set default CRAN repo to RSPM (it has pre-compiled R packages, increasing user install speed)
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RUN echo 'options(repos=c(CRAN="https://packagemanager.rstudio.com/all/__linux__/focal/latest"))' >> ${R_HOME}/etc/Rprofile.site \
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&& echo 'options(HTTPUserAgent=sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))' >> ${R_HOME}/etc/Rprofile.site
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# R needs TZ set
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ENV TZ Etc/UTC
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RUN echo "TZ=${TZ}" >> ${R_HOME}/etc/Renviron.site
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USER root
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# install - rstudio-server
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# Affero General Public License may apply to RStudio: https://www.gnu.org/licenses/agpl-3.0.en.html
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RUN curl -sL "https://download2.rstudio.org/server/bionic/${RSTUDIO_ARCH}/rstudio-server-${RSTUDIO_VERSION}-${RSTUDIO_ARCH}.deb" -o /tmp/rstudio-server.deb \
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&& echo "${RSTUDIO_SHA256} /tmp/rstudio-server.deb" | sha256sum --check \
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&& dpkg -i /tmp/rstudio-server.deb \
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&& rm -f /tmp/rstudio-server.deb \
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# our Kaniko build excludes `/var/run/*` but RStudio needs those files,
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# so we move them to `/run`, wich is actually the same place due to symbolic links
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&& mv -n /var/run/rstudio-server* /run \
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# use advisory file-locks to improve PVC support
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&& echo "lock-type=advisory" > /etc/rstudio/file-locks \
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# allows the non-root NB_USER to run rstudio
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&& chown -R ${NB_USER}:users /etc/rstudio \
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&& chown -R ${NB_USER}:users /run/rstudio-server* \
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&& chown -R ${NB_USER}:users /usr/lib/rstudio-server \
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&& chown -R ${NB_USER}:users /var/lib/rstudio-server
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# tell rstudio to use conda python by setting `RETICULATE_PYTHON` with `--rsession-path=/opt/rsession.sh`
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COPY --chown=jovyan:users rsession.sh /opt
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RUN chmod +x /opt/rsession.sh
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# s6 - copy scripts
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COPY --chown=jovyan:users s6/ /etc
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# s6 - 01-copy-tmp-home
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RUN mkdir -p /tmp_home \
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&& cp -r ${HOME} /tmp_home \
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&& chown -R ${NB_USER}:users /tmp_home
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USER ${NB_UID}
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EXPOSE 8888
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ENTRYPOINT ["/init"]
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