Dockerfile

FROM satijalab/seurat:4.3.0

WORKDIR /code

RUN apt-get update && apt-get install -y --no-install-recommends \
    pandoc \
    pandoc-citeproc \
    curl \
    gdebi-core \
    && rm -rf /var/lib/apt/lists/*

# Install stable packages from CRAN
RUN install2.r --error \
    ggExtra \
    shiny \
    jsonlite \
    ggplot2 \
    htmltools \
    remotes \
    renv \
    knitr \
    rmarkdown \
    quarto \
    rgl \
    rjson \
    ggdark \
    viridis \
    dplyr \
    waiter
    

# Install development packages from GitHub
RUN installGithub.r \
    rstudio/bslib \
    rstudio/httpuv \
    thomasp85/patchwork

RUN curl -LO https://quarto.org/download/latest/quarto-linux-amd64.deb
RUN gdebi --non-interactive quarto-linux-amd64.deb

RUN useradd -m -u 1000 user
USER user
ENV HOME=/home/user \
	PATH=/home/user/.local/bin:$PATH
WORKDIR $HOME/app

COPY --chown=user . $HOME/app

CMD ["quarto", "serve", "PFCapp.qmd", "--port", "7860", "--host", "0.0.0.0"]
#CMD ["R", "--quiet", "-e", "shiny::runApp(host='0.0.0.0', port=7860)"]