Dockerfile_anomanor

FROM rocker/r-ver:latest

LABEL maintainer="dieter.menne@menne-biomed.de"

RUN apt-get update -qq && apt-get -y --no-install-recommends install \
    libxml2-dev \
    libcairo2-dev \
    libsqlite3-dev \
    libpq-dev \
    libssh2-1-dev \
    libcurl4-openssl-dev \
    libssl-dev \
    libmagick++-dev \
    pandoc \
    net-tools \
    gsfonts \
    iputils-ping \
    libharfbuzz-dev \
    libfribidi-dev \
    curl

RUN install2.r --error --ncpus 4 --skipinstalled \
    DBI \
    DT \
    R6 \
    RSQLite \
    Rcpp \
    checkmate \
    colorspace \
    config \
    corrplot \
    digest \
    dplyr \
    flextable \
    ggplot2 \
    golem \
    httr \
    icr \
    keys \
    later \
    lubridate \
    magick \
    markdown \
    pingr \
    png \
    pool \
    purrr \
    ragg \
    readr \
    readxl \
    remotes \
    rprojroot \
    scales \
    shiny \
    shinyWidgets \
    shinyjs \
    shinyvalidate \
    stinepack \
    stringr \
    tidyr \
    visNetwork \
    withr \
    xtable

RUN R -e 'remotes::install_github("JohnCoene/tippy")'

ARG R_CONFIG_ACTIVE
ARG ANOMANOR_DATA
ARG ANOMANOR_ADMIN_USERNAME
ARG ANOMANOR_ADMIN_PASSWORD
ARG ANOMANOR_SECRET
ARG DOCKER_ANOMANOR_STANDALONE

ENV ANOMANOR_DOCKER=${DOCKER_ANOMANOR_STANDALONE:-FALSE}
ENV DOCKER_ANOMANOR_STANDALONE=${DOCKER_ANOMANOR_STANDALONE}
ENV ANOMANOR_DATA=${ANOMANOR_DATA}
ENV R_CONFIG_ACTIVE=${R_CONFIG_ACTIVE}
ENV ANOMANOR_ADMIN_USERNAME=${ANOMANOR_ADMIN_USERNAME:-anomanor_admin}
ENV ANOMANOR_ADMIN_PASSWORD=${ANOMANOR_ADMIN_PASSWORD:-anomanor_admin}
ENV ANOMANOR_SECRET=${ANOMANOR_SECRET}

ENV TZ="Europe/Berlin"

RUN mkdir -p /root/anomanor
RUN mkdir -p ${ANOMANOR_DATA}/data
RUN mkdir -p ${ANOMANOR_DATA}/cache
RUN mkdir -p ${ANOMANOR_DATA}/db

RUN mkdir /build_zone
# The following line fails when RStudio IDE is active
ADD . /build_zone
WORKDIR /build_zone
RUN R CMD INSTALL --preclean --no-multiarch --with-keep.source .
RUN rm -rf /build_zone


COPY  ./inst/config.yml /usr/local/lib/R/site-library/anomanor/
COPY  ./inst/Renviron_production /usr/local/lib/R/site-library/anomanor/
COPY  ./inst/Renviron_devel /usr/local/lib/R/site-library/anomanor/


HEALTHCHECK --start-period=20s --interval=1m --timeout=5s \
  CMD curl -I --fail http://localhost:3838 || exit 1

EXPOSE 3838
CMD R -e "anomanor::run_app()"
# Debug
# https://stackoverflow.com/questions/43308319/how-can-i-run-bash-in-a-docker-container
# docker run -v /home/hrmconsensus/anomanor_data/anomanor:${ANOMANOR_DATA} --rm -it --entrypoint bash anomanor