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Adding binder
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‎.github/workflows/build-binder.yaml‎

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name: Build Binder
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on:
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release:
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types:
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- published
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workflow_dispatch: {}
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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permissions:
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actions: write
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packages: write
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jobs:
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build-docker:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Free disk space
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run: |
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sudo docker rmi $(docker image ls -aq) >/dev/null 2>&1 || true
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sudo rm -rf \
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/usr/share/dotnet /usr/local/lib/android /opt/ghc \
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/usr/local/share/powershell /usr/share/swift /usr/local/.ghcup \
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/usr/lib/jvm || true
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sudo apt install aptitude -y >/dev/null 2>&1
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sudo aptitude purge aria2 ansible azure-cli shellcheck rpm xorriso zsync \
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esl-erlang firefox gfortran-8 gfortran-9 google-chrome-stable \
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google-cloud-sdk imagemagick \
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libmagickcore-dev libmagickwand-dev libmagic-dev ant ant-optional kubectl \
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mercurial apt-transport-https mono-complete libmysqlclient \
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unixodbc-dev yarn chrpath libssl-dev libxft-dev \
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libfreetype6 libfreetype6-dev libfontconfig1 libfontconfig1-dev \
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snmp pollinate libpq-dev postgresql-client powershell ruby-full \
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sphinxsearch subversion mongodb-org azure-cli microsoft-edge-stable \
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-y -f >/dev/null 2>&1
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sudo aptitude purge google-cloud-sdk -f -y >/dev/null 2>&1
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sudo aptitude purge microsoft-edge-stable -f -y >/dev/null 2>&1 || true
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sudo apt purge microsoft-edge-stable -f -y >/dev/null 2>&1 || true
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sudo aptitude purge '~n ^mysql' -f -y >/dev/null 2>&1
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sudo aptitude purge '~n ^php' -f -y >/dev/null 2>&1
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sudo aptitude purge '~n ^dotnet' -f -y >/dev/null 2>&1
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sudo swapoff -a
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sudo rm -f /swapfile
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sudo apt-get remove -y azure-cli mono-devel
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sudo apt-get autoremove -y
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sudo apt-get clean
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sudo apt-get autoremove -y >/dev/null 2>&1
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sudo apt-get autoclean -y >/dev/null 2>&1
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sudo rm -rf /usr/share/dotnet
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sudo rm -rf "$AGENT_TOOLSDIRECTORY"
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df -h
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- name: Set up QEMU
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uses: docker/setup-qemu-action@v3
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Login to GitHub Package Registry
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uses: docker/login-action@v2
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with:
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registry: ghcr.io
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username: ${{ github.repository_owner }}
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password: ${{ secrets.GHCR_TOKEN }}
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- name: Docker push binder
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run: |
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docker compose build binder
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docker compose push binder

‎binder/Dockerfile‎

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FROM ghcr.io/plant-food-research-open/binder-rpipelines:0.1.0

‎docker-compose.yaml‎

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version: "3.9"
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services:
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postgres:
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image: postgres:15.3-bullseye
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restart: always
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- 8088:8088
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volumes:
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- superset-data:/app/superset_home
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shiny:
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image: ghcr.io/plant-food-research-open/shiny-rpipelines:${APP_VERSION:-latest}
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build:
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stop_grace_period: 10s
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ports:
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- 8787:8787
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environment:
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USER: user
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PASSWORD: password
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ROOT: "TRUE"
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DISABLE_AUTH: "TRUE"
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command: >
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rserver --server-user rstudio --www-port 8787 --server-daemonize=0
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binder:
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image: ghcr.io/plant-food-research-open/binder-rpipelines:${APP_VERSION:-latest}
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build:
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context: .
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dockerfile: ./dockerfiles/binder/Dockerfile.${APP_VERSION}
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args:
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BUILD_DATE: date -u +'%Y-%m-%dT%H:%M:%SZ'
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APP_VERSION: ${APP_VERSION:-latest}
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tags:
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- ghcr.io/plant-food-research-open/binder-rpipelines:latest
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mlflow:
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image: ghcr.io/plant-food-research-open/mlflow-rpipelines:${APP_VERSION:-latest}

‎dockerfiles/binder/Dockerfile.0.1.0‎

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FROM rocker/binder:4.4.1 AS base
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ARG BUILD_DATE
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ARG APP_VERSION
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LABEL [email protected]
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LABEL org.label-schema.build-date=$BUILD_DATE
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LABEL version=$APP_VERSION
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WORKDIR /app
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USER root
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COPY README.md README.md
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ENV DEBIAN_FRONTEND=noninteractive \
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RENV_PATHS_ROOT=/app/renv \
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RENV_PATHS_LIBRARY=/app/renv/library \
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RENV_PATHS_CACHE=/app/renv/.cache \
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RENV_CONFIG_REPOS_OVERRIDE=https://cloud.r-project.org \
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JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64/bin/java
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RUN apt-get update \
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&& apt-get install -y --no-install-recommends openjdk-17-jdk pandoc libsodium-dev graphviz \
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libglpk-dev cmake libnng-dev libmbedtls-dev openssh-client liblzma-dev libpq-dev libcurl4-openssl-dev \
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libbz2-dev software-properties-common build-essential libmagic-dev libmagick++-dev curl g++ make \
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libharfbuzz-dev libfribidi-dev \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* \
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&& rm -rf /tmp/downloaded_packages \
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&& install2.r -e -n -1 --skipinstalled remotes \
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&& R -e 'remotes::install_version("renv","1.0.7", repos = "https://cran.rstudio.com/")' \
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&& R -e 'remotes::install_version("pak","0.7.2", repos = "https://cran.rstudio.com/")' \
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&& R CMD javareconf -e
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FROM base AS r_builder
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COPY renv.lock .renvignore .Rprofile ./
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COPY renv /app/renv
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RUN mkdir -p $RENV_PATHS_LIBRARY \
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&& mkdir -p $RENV_PATHS_CACHE \
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&& R -e \
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"options(renv.config.pak.enabled=TRUE, renv.consent=TRUE); renv::restore()"
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FROM base AS python_builder
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ENV POETRY_NO_INTERACTION=1 \
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POETRY_VIRTUALENVS_IN_PROJECT=1 \
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POETRY_VIRTUALENVS_CREATE=1 \
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POETRY_CACHE_DIR=/tmp/poetry_cache \
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PATH="/root/.local/bin:$PATH"
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COPY pyproject.toml poetry.lock ./
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RUN curl -sSL https://install.python-poetry.org | python3 -\
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&& poetry install --no-root --with dev \
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&& rm -rf $POETRY_CACHE_DIR \
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&& curl -sSL https://install.python-poetry.org | python3 - --uninstall
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FROM base AS runtime
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ENV R_LIBS=/app/renv/library/R-4.4/x86_64-pc-linux-gnu \
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R_LIBS_SITE=/app/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu \
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VIRTUAL_ENV=/app/.venv \
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PATH="/app/.venv/bin:$PATH"
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COPY --chown=${NB_USER}:${NB_USER} ./app .
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COPY --from=r_builder --chown=${NB_USER}:${NB_USER} /app .
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COPY --from=python_builder --chown=${NB_USER}:${NB_USER} ${VIRTUAL_ENV} ${VIRTUAL_ENV}
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RUN chown -R ${NB_USER}:${NB_USER} /app \
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&& chmod -R 755 /app \
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&& R -e "cmdstanr::install_cmdstan()" \
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&& echo '.libPaths(c("/app/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu", .libPaths()))' \
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>> /usr/local/lib/R/etc/Rprofile.site
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USER ${NB_USER}
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EXPOSE 8787 8787

‎dockerfiles/rstudio/Dockerfile.0.1.0‎

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&& install2.r -e -n -1 --skipinstalled remotes \
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&& R -e 'remotes::install_version("renv","1.0.7", repos = "https://cran.rstudio.com/")' \
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&& R -e 'remotes::install_version("pak","0.7.2", repos = "https://cran.rstudio.com/")' \
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&& R CMD javareconf -e \
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&& adduser shiny
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&& R CMD javareconf -e
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FROM base AS r_builder
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FROM base AS runtime
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ENV R_LIBS=/app/renv/library/R-4.4/x86_64-pc-linux-gnu \
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R_LIBS_SITE=/app/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu \
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VIRTUAL_ENV=/app/.venv \
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PATH="/app/.venv/bin:$PATH"
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COPY --chown=shiny:shiny ./app .
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COPY --chown=rstudio:rstudio ./app .
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COPY --from=r_builder --chown=shiny:shiny /app .
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COPY --from=r_builder --chown=rstudio:rstudio /app .
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COPY --from=python_builder --chown=shiny:shiny ${VIRTUAL_ENV} ${VIRTUAL_ENV}
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COPY --from=python_builder --chown=rstudio:rstudio ${VIRTUAL_ENV} ${VIRTUAL_ENV}
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RUN chown -R shiny:shiny /app \
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RUN chown -R rstudio:rstudio /app \
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&& chmod -R 755 /app \
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&& R -e "cmdstanr::install_cmdstan()"
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&& R -e "cmdstanr::install_cmdstan()" \
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&& echo '.libPaths(c("/app/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu", .libPaths()))' \
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>> /usr/local/lib/R/etc/Rprofile.site
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EXPOSE 3838
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EXPOSE 8088
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CMD ["R", "-e", "shiny::runApp('/app', launch.browser = FALSE, host = '0.0.0.0', port = 3838)"]
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EXPOSE 8787 8787

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