Dockerfile

FROM bioconductor/bioconductor_docker:RELEASE_3_19

# Update apt-get and install necessary libraries
RUN apt-get update \
    && apt-get install -y \
        libcurl4-openssl-dev \
        libxml2-dev \
        openjdk-11-jdk \
        libcairo2-dev \
        libxt-dev \
        nginx \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

# Install R packages
RUN R -e "install.packages(c('shinyjqui','BiocManager','bslib','rstatix','ggpubr','remotes', 'devtools', 'shiny','shinyscreenshot', 'readr', 'shinyAce', 'ggplot2', 'dplyr', 'shinythemes', 'openintro', 'plotly', 'DT', 'ggprism', 'ggbeeswarm', 'shinyFiles', 'stringr', 'shinyBS', 'shinydashboard', 'shinyWidgets', 'tidyr', 'pheatmap', 'grid', 'gridExtra', 'ggeasy', 'ggtext', 'colorspace', 'shinyjqui', 'tidyverse', 'gprofiler2', 'colourpicker', 'shinydashboardPlus', 'jsonlite', 'reshape2','shinyalert'))"

RUN R -e 'BiocManager::install("graph")'
RUN R -e "source('https://install-github.me/dreamRs/esquisse')"

# Install plumber and cyjshiny
RUN R -e "install.packages(c('plumber','cyjShiny','svglite'))"

RUN mkdir -p /srv/app/modules \
    && mkdir -p /srv/app/pathwaymap \
    && mkdir -p /srv/app/svg \
    && mkdir -p /srv/app/www \
    && mkdir -p /srv/app/data

RUN rm /etc/nginx/sites-enabled/default \
    && mkdir -p /var/cache/nginx \
    && mkdir -p /var/log/nginx \
    && mkdir -p /var/lib/nginx \
    && mkdir -p /var/lib/nginx/body \
    #&& chown -R www-data:www-data /var/log/nginx \
    #&& chown -R www-data:www-data /var/lib/nginx \
    #&& chown -R www-data:www-data /var/cache/nginx \
    && chmod -R 777 /var/log/nginx \
    && chmod -R 777 /var/lib/nginx \
    && chmod -R 777 /var/cache/nginx \
    && touch /var/run/nginx.pid \
    && chmod 777 /var/run/nginx.pid 
    #&& chown -R www-data:www-data /var/run/nginx.pid

COPY nginx.conf /etc/nginx/nginx.conf
RUN chmod 666 /etc/nginx/nginx.conf

COPY ./app/ui.R /srv/app/
COPY ./app/server.R /srv/app/
COPY ./app/plumber.R /srv/app/
COPY ./app/R /srv/app/modules/
COPY ./app/data /srv/app/pathwaymap/
COPY ./app/svg /srv/app/svg/
COPY ./app/www /srv/app/www/
COPY ./scripts/start.sh /usr/local/bin/start.sh


RUN chmod +x /usr/local/bin/start.sh

RUN chmod -R 777 /srv/app \
    && chmod -R 777 /srv/app/data

EXPOSE 7860
EXPOSE 8000
EXPOSE 9000

CMD ["sh", "/usr/local/bin/start.sh"]