Adding /data/labkey to container for file mapping, and allowing the image to install some commonly used R libraries (particularly devtools)

config/web/Dockerfile

@@ -14,22 +14,31 @@ 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 \
+RUN sudo apt-get update \
+   & sudo apt-get install -y dirmngr gnupg apt-transport-https ca-certificates software-properties-common wget\
 	&& wget -qO- $RKEY | sudo tee -a $GPGKEY\
 	&& sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/"\
 	&& sudo apt-get update --fix-missing\
 	&& sudo apt-get install -y r-base \
 	&& sudo rm -rf /var/lib/apt/lists/*
 
-RUN sudo chown -R labkey:labkey /usr/local/tomcat 
+#prepare directory where files will be mapped 
+RUN sudo mkdir -p /data/labkey && \
+	sudo chown -R labkey:labkey /data/labkey && \
+	sudo chown -R labkey:labkey /usr/local/tomcat 
+
+#install (labkey local) R packages and dependencies
+RUN mkdir -p /home/labkey/R/site-library \
+	&& sudo apt-get update\
+   && sudo apt-get install -y libcurl4-openssl-dev libxml2-dev libssl-dev libfontconfig1-dev  libharfbuzz-dev libfribidi-dev libtiff5-dev \
+   && export R_LIBS=/home/labkey/R/site-library \
+   && echo ${R_LIBS} \
+   && R -e 'install.packages(c("devtools","ggplot2","Rlabkey"))'
+
+
 #RUN sudo mkdir /usr/local/labkey \
 #   && sudo chown -R labkey:labkey /usr/local/tomcat \
 #   && sudo chown -R labkey:labkey /usr/local/labkey
 #USER root
 
-LABEL "name"="tomcatR"
+LABEL "name"="tomcatLabkeyR"