labkeyDocker/config/web/Dockerfile19

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

ARG USER_ID
ARG GROUP_ID
ARG TOMCAT_DIR

RUN apt-get update && apt-get install -y sudo;
RUN update-ca-certificates && \
   wget --no-parent https://download.java.net/java/GA/jdk13.0.1/cec27d702aa74d5a8630c65ae61e4305/9/GPL/openjdk-13.0.1_linux-x64_bin.tar.gz && \
   tar xvzf openjdk-13.0.1_linux-x64_bin.tar.gz -C /opt/java && \
   mv /opt/java/openjdk /opt/java/openjdk-11 && \
   ln -s /opt/java/jdk-13.0.1 /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"))'


COPY SSL/CA* /usr/local/tomcat/temp/
#OK for docker compose 
#RUN --mount=type=bind,src=${TOMCAT_DIR}/conf/SSL,dst=/mnt/SSL\
#  	for f in /mnt/SSL/CA* ; do sudo cp $f /usr/local/share/ca-certificates/ ; done \
#	&& sudo update-ca-certificates
#


RUN for f in /usr/local/tomcat/temp/CA* ; do sudo cp $f /usr/local/share/ca-certificates/ ; done \
	&& sudo update-ca-certificates

LABEL "name"="labkey19"