Dockerfile

FROM rocker/shiny:4.5
LABEL maintainer="Veit Schwaemmle <veits@bmb.sdu.dk>"
LABEL description="Docker image of PolySTest implementation on top of shiny-server. The number of to-be-installed R packages requires patience when building this image."

#RUN  sudo mount -o ro,remount /sys && sudo  mount -o rw,remount /sys
#RUN echo N | tee /sys/module/overlay/parameters/metacopy
#RUN rm -rf /var/cache/apt/* /var/lib/apt/lists/* /tmp/* /var/tmp/*
#RUN apt-get clean && apt-get update && apt-get install -y apt-utils

RUN apt-get -o Acquire::AllowInsecureRepositories=true -o Acquire::AllowDowngradeToInsecureRepositories=true update && apt-get install -y libssl-dev liblzma-dev libbz2-dev libicu-dev && apt-get clean 


RUN R -e "install.packages('BiocManager', repos='https://cloud.r-project.org', version = '3.21'); update.packages(ask=F); \
  BiocManager::install(c('dplyr','plotly'),ask=F)"
RUN R -e "library(BiocManager); BiocManager::install(c('matrixStats','fdrtool','parallel','qvalue','circlize', \
                                                       'DT','UpSetR','heatmaply','gplots','shinyBS','shinydashboard','limma', \
                                                       'shinyWidgets','shinycssloaders','shinythemes','shinyjs','data.table', \
                                                       'openxlsx','readxl','stringdist','MsCoreUtils','jsonlite','BEclear',\
                                                       'dplyr', 'sva','viridis','UniProt.ws','ggrepel','ggiraph',\
                                                       'UniProt.ws'),ask=F)"


RUN rm -rf /srv/shiny-server
RUN mkdir /srv/shiny-server
RUN mkdir /srv/shiny-server/www
RUN mkdir /srv/shiny-server/data
COPY www/* /srv/shiny-server/www/
COPY www/tutorial/ /srv/shiny-server/www/tutorial
COPY *R  /srv/shiny-server/
COPY data/*csv  /srv/shiny-server/data/
COPY VERSION /srv/shiny-server/
#COPY *pdf  /srv/shiny-server/