Dockerfile

# Use an official R runtime as a parent image
FROM rocker/shiny:latest
#  "shiny"

ENV USER=shiny

# Install system dependencies including those for tidyverse
RUN apt-get update && \
    apt-get upgrade -y && \
    apt-get install --no-install-recommends -y \
    git libxml2-dev libmagick++-dev \
    wget libgomp1 \  
    libssl-dev \     
    make \
    pandoc && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

#    libcurl4-gnutls-dev \
#    libcurl4-openssl-dev \
# Install Blast
# FROM ncbi/blast:2.13.0

RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.13.0/ncbi-blast-2.13.0+-x64-linux.tar.gz -O /tmp/blast.tar.gz && \
	tar zxvf /tmp/blast.tar.gz -C /opt/ && rm /tmp/blast.tar.gz

ENV PATH="/opt/ncbi-blast-2.13.0+/bin:${PATH}"

# Install Basic Utility R Packages

RUN R -e "install.packages('remotes')" \
    && R -e "install.packages('BiocManager')" \
    && R -e "BiocManager::install('KEGGREST')" \
    && R -e "remotes::install_version('tidyverse', version = '2.0.0', dependencies= T)" \
    && R -e "remotes::install_version('arrow', version = '14.0.0', dependencies= T)" \
    && R -e "remotes::install_version('data.table', version = '1.14.8', dependencies= T)" \
    && R -e "remotes::install_version('rBLAST', repos = 'https://mhahsler.r-universe.dev', dependencies= T, version='0.99.0')" \
    #&& R -e "remotes::install_github('mhahsler/rBLAST', dependencies= T)" \
    && R -e "remotes::install_version('leaflet', version = '2.1.2', dependencies= T)" \
    && R -e "remotes::install_version('sp', version = '1.6-1', dependencies= T)" \
    && R -e "remotes::install_version('magrittr', version = '2.0.3', dependencies= T)" \
    && R -e "remotes::install_version('shinythemes', version = '1.2.0', dependencies= T)" \
    && R -e "remotes::install_version('DT', version = '0.28', dependencies= T)" \
    && R -e "remotes::install_version('shinyjs', version = '2.1.0', dependencies= T)" \
    && R -e "remotes::install_version('vembedr', version = '0.1.5', dependencies= T)" \
    && R -e "remotes::install_version('multidplyr', version = '0.1.3', dependencies= T)" \
    && R -e "remotes::install_version('shinybusy', version = '0.3.1', dependencies= T)"


# Additional packages for logging and diagnosis
RUN R -e "install.packages('log4r')" \
    && R -e "install.packages('readr')" \
    && R -e "install.packages('RcppTOML')"


RUN mkdir /data \
    && mkdir /rlogs \
    && chown -R shiny:shiny /data \
    && chown -R shiny:shiny /rlogs


RUN rm -rf /srv/shiny-server/*
COPY /app/ /srv/shiny-server/app
COPY .Renviron.template /srv/shiny-server/app/.Renviron
COPY shiny-customized.config /etc/shiny-server/shiny-server.conf

WORKDIR /srv/shiny-server/app

RUN chown -R shiny:shiny . && \
    chmod ug+x start-script.sh


USER $USER
EXPOSE 3838

CMD ["/usr/bin/shiny-server"]