Untested Dockerfile19

config/web/Dockerfile19

@@ -1,10 +1,5 @@
-#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 && \
@@ -12,51 +7,24 @@ RUN update-ca-certificates && \
    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 \
+RUN apt-get update && 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"))'
-
+	&& add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/"\
+	&& apt-get update --fix-missing\
+	&& apt-get install -y r-base \
+	&& apt-get install -y git \
+	&& apt-get install -y libcurl4-openssl-dev libxml2-dev libssl-dev libfontconfig1-dev  libharfbuzz-dev libfribidi-dev libtiff5-dev git \
+	&& rm -rf /var/lib/apt/lists/* 
 
-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 R -e 'install.packages(c("devtools","ggplot2","Rlabkey","ggsurvfit","ggalluvial","gridExtra","comprehenr","ggsci","paletteer","tidyverse","swimplot","gtsummary"))'
 
-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"