From 596adef606b057df3365e0f582a548adc9c84fdb Mon Sep 17 00:00:00 2001
From: eldrid01 <matthew.d.eldridge@gmail.com>
Date: Tue, 15 Jun 2021 17:40:09 +0100
Subject: [PATCH] Install R using CRAN Debian package, no longer need to
 specify repo for R packages (defaults to cloud.r-project.org), added optparse
 R package

---
 docker/Dockerfile | 60 +++++++++++++++++++++++++++++------------------
 1 file changed, 37 insertions(+), 23 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 7c9a3bf..13205d6 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -2,38 +2,61 @@ FROM debian:buster-20210511-slim
 
 MAINTAINER Matt Eldridge "matthew.eldridge@cruk.cam.ac.uk"
 
+ARG DEBIAN_FRONTEND=noninteractive
+
 RUN apt-get update
+RUN apt-get install -y apt-utils
+
+# update locale
+RUN apt-get install -y locales
+RUN sed -i 's/^# en_GB/en_GB/' /etc/locale.gen
+RUN locale-gen
+
+# install packages and libraries needed to build/install Shiny server, R and
+# R packages/dependencies
 RUN apt-get install -y build-essential
 RUN apt-get install -y libxml2-dev
 RUN apt-get install -y libssl-dev
 RUN apt-get install -y libreadline7
+RUN apt-get install -y libcurl4-openssl-dev
 RUN apt-get install -y curl
 RUN apt-get install -y gdebi-core
 RUN apt-get clean
 
-# install R
-ARG R_VERSION=4.1.0
-RUN curl -O https://cdn.rstudio.com/r/debian-10/pkgs/r-${R_VERSION}_1_amd64.deb
-RUN gdebi -n r-${R_VERSION}_1_amd64.deb
-RUN rm r-${R_VERSION}_1_amd64.deb
-RUN ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R
-RUN ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript
-
 # install Shiny server
 ARG SHINY_SERVER_VERSION=1.5.16.958-amd64
 RUN curl -O https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-${SHINY_SERVER_VERSION}.deb
 RUN gdebi -n shiny-server-${SHINY_SERVER_VERSION}.deb
 RUN rm shiny-server-${SHINY_SERVER_VERSION}.deb
 
+# expose port that Shiny server listens on (can be mapped to another port on the host)
+EXPOSE 3838
+
+# ensure the user account that is running the shiny server process has write privilege for /var/lib/shiny-server
+RUN chmod ugo+rwx /var/lib/shiny-server
+
+# command to run when starting the container using 'docker run'
+CMD exec shiny-server >> /var/log/shiny-server/shiny-server.log 2>&1
+
+# install R
+RUN apt-key adv --keyserver keys.gnupg.net --recv-key E19F5F87128899B192B1A2C2AD5F960A256A04AF
+RUN echo 'deb http://cloud.r-project.org/bin/linux/debian buster-cran40/' >> /etc/apt/sources.list
+RUN apt-get update
+RUN apt-get install -y -t buster-cran40 r-base
+
+# update pre-installed R packages
+RUN R -e 'update.packages(ask = FALSE)'
+
 # install R packages
-RUN R -e 'install.packages("shiny", repos = "https://cloud.r-project.org")'
-RUN R -e 'install.packages("tidyverse", repos = "https://cloud.r-project.org")'
-RUN R -e 'install.packages("DT", repos = "https://cloud.r-project.org")'
-RUN R -e 'install.packages("shinyjs", repos = "https://cloud.r-project.org")'
-RUN R -e 'install.packages("colourpicker", repos = "https://cloud.r-project.org")'
+RUN R -e 'install.packages("tidyverse")'
+RUN R -e 'install.packages("optparse")'
+RUN R -e 'install.packages("shiny")'
+RUN R -e 'install.packages("shinyjs")'
+RUN R -e 'install.packages("colourpicker")'
+RUN R -e 'install.packages("DT")'
 
 # install Bioconductor packages
-RUN R -e 'install.packages("BiocManager", repos = "https://cloud.r-project.org")'
+RUN R -e 'install.packages("BiocManager")'
 RUN R -e 'BiocManager::install("Biobase")'
 RUN R -e 'BiocManager::install("QDNAseq")'
 
@@ -46,12 +69,3 @@ RUN R CMD INSTALL /opt/rascal_${RASCAL_VERSION}.tgz
 RUN tar zxf /opt/rascal_${RASCAL_VERSION}.tgz -C /opt
 RUN ln -s /opt/rascal/shiny /srv/shiny-server/rascal
 
-# ensure the user account that is running the shiny server process has write privilege for /var/lib/shiny-server
-RUN chmod ugo+rwx /var/lib/shiny-server
-
-# expose port that Shiny server listens on (can be mapped to another port on the host)
-EXPOSE 3838
-
-# command to run when starting the container using 'docker run'
-CMD exec shiny-server >> /var/log/shiny-server/shiny-server.log 2>&1
-