labkeyDocker/config/web/Dockerfile

FROM tomcat:9-jdk17-temurin-jammy

ARG USER_ID
ARG GROUP_ID
ARG DEBR="deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/"
ARG RKEY=https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc 
ARG GPGKEY=/etc/apt/trusted.gpg.d/cran_ubuntu_key.asc 


RUN apt-get update && apt-get install -y sudo;

RUN addgroup --gid ${GROUP_ID} labkey
RUN adduser --gecos 'LabKey' --uid ${USER_ID} --gid ${GROUP_ID} --disabled-password labkey 
RUN echo 'labkey ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
RUN usermod -G root,sudo labkey

USER labkey

RUN sudo apt-get update \
   && sudo apt-get install -y dirmngr gnupg apt-transport-https\
      ca-certificates software-properties-common wget\
	&& wget -qO- $RKEY | sudo tee -a $GPGKEY\
	&& sudo add-apt-repository "${DEBR}"\
	&& sudo apt-get update --fix-missing\
	&& sudo apt-get install -y r-base \
   && sudo apt-get install -y git libcurl4-openssl-dev libxml2-dev libssl-dev \
      libfontconfig1-dev  libharfbuzz-dev libfribidi-dev libtiff5-dev\ 
	&& sudo rm -rf /var/lib/apt/lists/*

#prepare directory where files will be mapped 
RUN sudo mkdir -p /data/labkey && \
	sudo chown -R labkey:labkey /data/labkey && \
	sudo chown -R labkey:labkey /usr/local/tomcat 

#install (labkey local) R packages and dependencies
RUN mkdir -p /home/labkey/R/site-library \
   && export R_LIBS=/home/labkey/R/site-library \
   && echo ${R_LIBS} \
   && R -e 'install.packages("devtools")' \
   && R -e 'install.packages("ggplot2")' \
   && R -e 'install.packages("Rlabkey")' \
   && R -e 'install.packages("ggsurvfit")' \
   && R -e 'install.packages("ggalluvial")' \
   && R -e 'install.packages("gridExtra")' \
   && R -e 'install.packages("comprehenr")' \
   && R -e 'install.packages("ggsci")' \
   && R -e 'install.packages("paletteer")' \
   && R -e 'install.packages("tidyverse")'\
   && R -e 'install.packages("swimplot")'\
   && R -e 'install.packages("gtsummary")'


LABEL "name"="labkey22"