optimized DockerFile

Dockerfile

-FROM gitlab.lcsb.uni.lu:4567/eci/shinyscreen/dep/ssuser:latest
-MAINTAINER todor.kondic@uni.lu
-EXPOSE 5432
-ENV SS_MF_DB="PubChemLite_exposomics.csv"
+# Use a base image with R pre-installed
+FROM ubuntu:jammy-20230126
+
+# Set non-interactive frontend and timezone
+ENV DEBIAN_FRONTEND=noninteractive
+ENV TZ=Etc/UTC
 ENV SS_CPU 2
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    apt-utils \
+    r-base \
+    r-recommended \
+    g++ \
+    gfortran \
+    curl \
+    wget \
+    libxml2-dev \
+    libssl-dev \
+    libssh2-1-dev \
+    zlib1g-dev \
+    xdg-utils \
+    automake \
+    autoconf \
+    gcc \
+    make \
+    pkg-config \
+    net-tools \
+    git-all \
+    default-jre-headless \
+    default-jdk \
+    libpng16-16 \
+    libpng-tools \
+    libpng-dev \
+    libpng++-dev \
+    libnetcdf* \
+    openbabel \
+    libhdf5-1* \
+    libhdf5-hl-1* \
+    r-cran-rcolorbrewer \
+    r-cran-data.table \
+    r-cran-biocmanager \
+    r-cran-tidyverse \
+    r-cran-cowplot \
+    r-cran-curl \
+    r-cran-promises \
+    r-cran-yaml \
+    r-cran-dt \
+    r-cran-future \
+    r-cran-rjava \
+    r-cran-rsvg \
+    r-cran-png \
+    r-cran-rmarkdown \
+    r-cran-shiny \
+    r-cran-htmltools \
+    r-cran-rcdklibs \
+    r-cran-rcdk \
+    r-cran-fingerprint \
+    r-bioc-affy \
+    r-bioc-affyio \
+    r-cran-devtools
+
+# Clean up
+RUN rm -rf /var/lib/apt/lists/* /tmp/*
+
+# Install R packages
+RUN R -e 'install.packages("enviPat", dependencies=TRUE)'
+RUN R -e 'BiocManager::install(c("Rhdf5lib","mzR","MSnbase","RMassBank"), update=FALSE)'
+RUN R -e 'devtools::install_git("https://github.com/schymane/RChemMass", dependencies=FALSE)'
+
+# Set JAVA_HOME
+ENV JAVA_HOME=/usr/lib/jvm/default-java
+ENV PATH=$JAVA_HOME/bin:$PATH
+
+# Clean up
+RUN apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Create a user and directories
+RUN useradd -ms /bin/bash ssuser
+USER root
+WORKDIR /home/ssuser
+RUN mkdir -p top_data_dir projects users
+RUN chown -R ssuser:ssuser /home/ssuser
+
+# Copy and build the Shiny app
 ADD . shinyscreen/
 RUN R CMD build shinyscreen
-USER root
 RUN R CMD INSTALL shinyscreen
+
+# Switch back to ssuser
 USER ssuser
 RUN cp shinyscreen/runme /home/ssuser/runme
 RUN chmod u+x /home/ssuser/runme
-# RUN chown ssuser /home/ssuser/runme
-# RUN chown -R ssuser /home/ssuser/shinyscreen
-RUN R -e 'library(shinyscreen);setwd("~");init(top_data_dir="~/top_data_dir",projects="~/projects",users_dir="~/users",metfrag_db_dir=Sys.getenv("SS_MF_DB_DIR"),metfrag_jar="/usr/local/bin/MetFragCommandLine.jar",no_structure_plots=T,save=T,merge=F)'
+
+# Initialize the app with absolute paths
+RUN R -e 'library(shinyscreen); setwd("~"); init(top_data_dir="/home/ssuser/top_data_dir", projects="/home/ssuser/projects", users_dir="/home/ssuser/users", no_structure_plots=TRUE, save=TRUE, merge=FALSE)'
+
+# Expose the port and set the entrypoint
+EXPOSE 3838
 ENTRYPOINT ["/home/ssuser/runme"]
 CMD ["app"]
+