Configuration for version 20 of labkey

config/labkey-compose20.yaml

@@ -28,12 +28,14 @@ services:
 
     build: 
             context: ./web
-            dockerfile: Dockerfile19
+            dockerfile: Dockerfile20
             args:
                     USER_ID: ${USER_ID}
                     GROUP_ID: ${GROUP_ID}
     volumes:
       - ${LABKEY_DIR}:/usr/local/labkey
+      - ${LABKEY_FILES}:/data/labkey/files
+      - ${EXTERNAL_MODULES}:/usr/local/labkey/externalModules
       #- ${LABKEY_DIR}/labkeywebapp:/usr/local/labkey/labkeywebapp
       #- ${LABKEY_DIR}/modules:/usr/local/labkey/modules
       #- ${LABKEY_DIR}/pipeline-lib:/usr/local/labkey/pipeline-lib
@@ -41,7 +43,7 @@ services:
       #- ${LABKEY_DIR}/files:/usr/local/labkey/files
       #- ${TOMCAT_DIR}:/usr/local/tomcat
       #- ${TOMCAT_DIR}/conf/server.xml:/usr/local/tomcat/conf/server.xml
-      #- ${TOMCAT_DIR}/bin/setenv.sh:/usr/local/tomcat/bin/setenv.sh
+      - ${TOMCAT_DIR}/bin/setenv.sh:/usr/local/tomcat/bin/setenv.sh
       #- ${TOMCAT_DIR}/bin/setenv.sh:/usr/local/tomcat/bin/setenv.sh
       #- ${TOMCAT_DIR}/conf/key.pem:/usr/local/tomcat/conf/key.pem
       #- ${TOMCAT_DIR}/conf/cert.pem:/usr/local/tomcat/conf/cert.pem
@@ -49,9 +51,10 @@ services:
       - ${TOMCAT_DIR}/lib/labkeyBootstrap.jar:/usr/local/tomcat/lib/labkeyBootstrap.jar
       - ${TOMCAT_DIR}/lib/javax.activation.jar:/usr/local/tomcat/lib/javax.activation.jar
       - ${TOMCAT_DIR}/lib/mail.jar:/usr/local/tomcat/lib/mail.jar
+      #- ${TOMCAT_DIR}/lib/postgresql.jar:/usr/local/tomcat/lib/postgresql.jar
       - ${TOMCAT_DIR}/conf/Catalina/localhost/labkey.xml:/usr/local/tomcat/conf/Catalina/localhost/labkey.xml  
     ports:
-      - 8081:8080
+      - 8080:8080
       - 8444:8443
     
 

config/web/Dockerfile20

@@ -0,0 +1,50 @@
+#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"