labkeyDocker/config/web/Dockerfile20

#FROM tomcat:9-jdk17-temurin-jammy
FROM tomcat:9-jdk11-temurin-jammy

ARG USER_ID
ARG GROUP_ID

RUN apt-get update && apt-get install -y sudo;
RUN update-ca-certificates && \
   wget --no-parent https://download.java.net/java/GA/jdk14.0.2/205943a0976c4ed48cb16f1043c5c647/12/GPL/openjdk-14.0.2_linux-x64_bin.tar.gz && \
   tar xvzf openjdk-14.0.2_linux-x64_bin.tar.gz -C /opt/java && \
   mv /opt/java/openjdk /opt/java/openjdk-11 && \
   ln -s /opt/java/jdk-14.0.2 /opt/java/openjdk

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

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 sudo apt-get update && sudo apt-get install -y \
		dirmngr \
        	gnupg \
		apt-transport-https \
		ca-certificates \
		software-properties-common \
	&& wget -qO- $RKEY | sudo tee -a $GPGKEY\
	&& sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/"\
	&& sudo apt-get update --fix-missing\
	&& sudo apt-get install -y r-base \
	&& sudo apt-get install -y git \
	&& sudo apt-get install -y libcurl4-openssl-dev libxml2-dev libssl-dev libfontconfig1-dev  libharfbuzz-dev libfribidi-dev libtiff5-dev git \
	&& sudo rm -rf /var/lib/apt/lists/* 


RUN sudo mkdir -p /data/labkey && \
	sudo chown -R labkey:labkey /data/labkey && \
	sudo chown -R labkey:labkey /usr/local/tomcat 



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


LABEL "name"="labkey20"