bin/env.sh.sample

@@ -3,10 +3,12 @@ export LBDOCKER=$HOME/labkeyDocker
 export POSTGRES_DIR=$LBDOCKER/postgresql/data;
 export LABKEY_DIR=$LBDOCKER/labkeyBase
 export TOMCAT_DIR=$LBDOCKER/tomcat
-export COMPOSE=$HOME/config/labkey-compose22.3.yaml
+export COMPOSE=$LBDOCKER/config/labkey-compose22.3.yaml
 #export COMPOSE=$HOME/config/labkey-compose19.yaml
 export DOCKERCOMPOSE=$HOME/.docker/cli-plugins/docker-compose
 export PGPASS=somethingSecret
+export LABKEY_FILES=$HOME/files
+export EXTERNAL_MODULES=$HOME/externalModules
 #other variables
 export USER_ID=$(id -u labkey)
 export GROUP_ID=$(id -g labkey)

bin/installLabkey.sh

@@ -36,7 +36,7 @@ fi;
 echo "Using $LABKEY";
 
 #full path to source
-SFW_SRC=$LBDOCKER/packages/$LABKEY.tar.gz
+SFW_SRC=$HOME/packages/$LABKEY.tar.gz
 
 #this is temp only
 TMP_DIR=$HOME/tmp

bin/startLabkey.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
 . $(dirname $0)/env.sh
-docker network create -d bridge $NETWORK
+docker network create -d bridge --subnet=172.18.1.0/24 --ip-range=172.18.1.0/24 $NETWORK 
 $DOCKERCOMPOSE -f $COMPOSE up -d;
 

config/labkey-compose19.yaml

@@ -34,6 +34,8 @@ services:
                     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
@@ -52,7 +54,7 @@ services:
       - ${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/Dockerfile19

@@ -5,7 +5,8 @@ ARG USER_ID
 ARG GROUP_ID
 
 RUN apt-get update && apt-get install -y sudo;
-RUN wget --no-parent https://download.java.net/java/GA/jdk13.0.1/cec27d702aa74d5a8630c65ae61e4305/9/GPL/openjdk-13.0.1_linux-x64_bin.tar.gz && \
+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
@@ -29,9 +30,32 @@ RUN sudo apt-get update && sudo apt-get install -y \
 	&& 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 rm -rf /var/lib/apt/lists/*
+	&& 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"))'
+
+RUN mkdir -p /home/labkey/software/src && \
+   cd /home/labkey/software/src && \
+   git clone https://git0.fmf.uni-lj.si/studen/websocket && \
+   sed -i.bu 's/origin=\".*\"/origin="labkey-vm"/' websocket/send.py 
+
+RUN sudo apt-get update &&\
+   sudo apt-get install -y python3-pip &&\
+   pip install websockets
+
 
-RUN sudo chown -R labkey:labkey /usr/local/tomcat 
 #RUN sudo mkdir /usr/local/labkey \
 #   && sudo chown -R labkey:labkey /usr/local/tomcat \
 #   && sudo chown -R labkey:labkey /usr/local/labkey

tomcat/bin/setenv.sh

@@ -2,3 +2,5 @@
 export CATALINA_OPTS="-Dlog4j2.formatMsgNoLookups=true"
 export CATALINA_OPTS="${CATALINA_OPTS} -Duser.language.en -Duser.region=US -Ddevmode=true"
 export JAVA_OPTS="$JAVA_OPTS -Xms2g -Xmx2g -XX:-HeapDumpOnOutOfMemoryError"
+export JDK_JAVA_OPTIONS="$JDK_JAVA_OPTIONS --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.io=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.desktop/java.awt.font=ALL-UNNAMED --add-opens java.base/java.text=ALL-UNNAMED"
+export JDK_JAVA_OPTIONS="$JDK_JAVA_OPTIONS --add-exports java.net.http/jdk.internal.net.http.websocket=ALL-UNNAMED"

tomcat/conf/server.xml

@@ -1 +1 @@
-serverHTTPS.xml
+serverHTTP.xml