Merge branch 'cleanup-dockerfile' into 'main'

cleanup Dockerfile

See merge request hub/rshiny-k8s!3

.gitlab-ci.yml

@@ -21,7 +21,7 @@ build:
       --cache-from "$CI_REGISTRY_IMAGE/master:latest"
       --tag "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG:$CI_COMMIT_SHA"
       --tag "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG:latest"
-      -f Dockerfile2
+      -f Dockerfile
       ./
     # push image as latest for the current branch
     - docker push "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG:latest"

Dockerfile

-FROM rocker/shiny:4.2.3
-
-RUN cp -r $R_HOME /usr/myR
-
-ENV R_HOME=/usr/myR
-
-RUN R -e 'print("hello world")'
-
-WORKDIR /srv/shiny-server/
-
-USER root
-
-# RUN sed -i "s/test -x/test -d/g" /usr/local/bin/R
-# RUN sed -i '/test -x/,+4d' /usr/local/bin/R
-
-# RUN grep " \${gui}"  /usr/local/bin/R  -A 10
-
-# change permission for user shiny
-# RUN sudo chown -R shiny:shiny /usr/local/lib/R/etc/
-
-## Install R packages from CRAN or bioconductor
-# COPY ./script_r_to_docker/script_install_r_packages.R .
-# COPY ./script_r_to_docker/packages_to_install.csv .
-
-#RUN ls -lah /usr/local/lib/R
-#RUN printenv
-
-# RUN /usr/local/lib/R/bin/Rscript script_install_r_packages.R
-# RUN Rscript script_install_r_packages.R
-
-RUN R -e 'print("hello world")'
+FROM ubuntu:focal
+
+# define geographic location during R installation
+ENV TZ=Etc/UTC
+ENV DEBIAN_FRONTEND noninteractive
+ARG SHINY_SERVER_VERSION
+
+EXPOSE 3838
+CMD ["shiny-server"]
+
+# install R
+RUN apt-get update \
+ && apt-get install -y \
+        nano \
+        wget \
+        curl \
+        r-base \
+        r-base-dev \
+        r-recommended \
+        lsb-release \
+ && rm -rf /var/lib/apt/lists/* \
+ && R --version
+
+COPY ./scripts /opt/scripts
+
+# Install R packages included Shiny, then install shiny server
+RUN Rscript /opt/scripts/install_r_packages.R
+RUN /opt/scripts/install_shiny_server.sh
+ 
+# allows trafic from all ips
+RUN sed -i "s/3838/3838 0.0.0.0/g" /etc/shiny-server/shiny-server.conf
+
+# copy my shiny app.
+COPY ./example_proj /srv/shiny-server
 
-ENV OPENBLAS_NUM_THREADS=1
+#RUN chown shiny:shiny /var/lib/shiny-server
+RUN mkdir -p /var/log/shiny-server \
+ && chown shiny:shiny /var/log/shiny-server
 
-RUN install2.r \
-      shinythemes
+# USER shiny
 
-# copy the app directory into the image
-COPY ./example_proj /srv/shiny-server
 
-RUN ls /srv/shiny-server
 
-USER shiny
 
-# CMD ["/usr/bin/shiny-server"]

Dockerfile2

-#FROM rocker/shiny
-FROM ubuntu:focal
-# define geographic location during R installation
-ENV TZ=Etc/UTC
-ENV DEBIAN_FRONTEND noninteractive
-
-# install R
-RUN apt-get update \
- && apt-get install -y \
-        nano \
-        wget \
-        curl \
-        r-base \
-        r-base-dev \
-        r-recommended \
- && rm -rf /var/lib/apt/lists/*
-
-RUN R --version
-
-# install R packages included Shiny
-#COPY ./scripts/install_r_packages.R .
-#COPY ./scripts/packages_to_install.csv .
-COPY ./scripts /opt/scripts
-
-RUN cd /opt/scripts/ \
- && Rscript /opt/scripts/install_r_packages.R
-
-#Install shiny server
-#RUN apt-get update \
-# && apt-get install -y \
-#        gdebi-core \
-# && rm -rf /var/lib/apt/lists/*
-
-RUN apt-get update \
- && apt-get install -y \
-        lsb-release \
- && rm -rf /var/lib/apt/lists/*
-
-
-RUN wget https://download3.rstudio.org/ubuntu-18.04/x86_64/shiny-server-1.5.20.1002-amd64.deb \
- && apt-get install ./shiny-server-1.5.20.1002-amd64.deb
-
-# copy my shiny app.
-COPY ./example_proj /srv/shiny-server
-
-RUN cat /etc/passwd
-
-#RUN addgroup --gid 999 shiny \
-# && adduser --disabled-password --gecos '' --uid 999 --gid 999 shiny
-
-RUN chown shiny:shiny /var/lib/shiny-server
-RUN mkdir -p /var/log/shiny-server
-RUN chown shiny:shiny /var/log/shiny-server
-
-RUN sed -i "s/3838/3838 0.0.0.0/g" /etc/shiny-server/shiny-server.conf
-
-CMD ["shiny-server"]
-
-EXPOSE 3838
-
-USER shiny
-
-
-# stolen from https://github.com/qutebrowser/qutebrowser/commit/478e4de7bd1f26bebdcdc166d5369b2b5142c3e2
-# WORKAROUND for glibc 2.33 and old Docker
-# See https://github.com/actions/virtual-environments/issues/2658
-# (GitLab ticket: https://gitlab.com/gitlab-org/gitlab-runner/-/issues/27557)
-# Thanks to https://github.com/lxqt/lxqt-panel/pull/1562
-#RUN patched_glibc=glibc-linux4-2.33-4-x86_64.pkg.tar.zst && \
-#    curl -LO "https://repo.archlinuxcn.org/x86_64/$patched_glibc" && \
-#    bsdtar -C / -xvf "$patched_glibc"

scripts/install_r_packages.R

@@ -5,7 +5,7 @@
 
 
 #### Load file with the list of packages and the name of the deposit
-packages_list <- read.csv(file = "packages_to_install.csv", header = TRUE, sep = ";", stringsAsFactors = FALSE )
+packages_list <- read.csv(file = "/opt/scripts/packages_to_install.csv", header = TRUE, sep = ";", stringsAsFactors = FALSE )
 
 ### CRAN Packages
 cran_pkgs <- packages_list[which(packages_list$Deposit_name == "cran"),"Package_name"]
@@ -20,4 +20,4 @@ if (length(cran_pkgs) >= 1) {
 if (length(bioconductor_pkgs) >= 1) {
   requireNamespace("BiocManager")
   BiocManager::install(bioconductor_pkgs, ask = FALSE)
-}
\ No newline at end of file
+}

scripts/install_shiny_server.sh

+#!/bin/bash
+set -e
+
+SHINY_SERVER_VERSION=${1:-${SHINY_SERVER_VERSION:-latest}}
+
+
+if [ "$SHINY_SERVER_VERSION" = "latest" ]; then
+    SHINY_SERVER_VERSION=$(wget -qO- https://download3.rstudio.org/ubuntu-18.04/x86_64/VERSION)
+fi
+
+wget --no-verbose "https://download3.rstudio.org/ubuntu-18.04/x86_64/shiny-server-${SHINY_SERVER_VERSION}-amd64.deb" -O /tmp/shiny.deb
+apt install /tmp/shiny.deb
+rm /tmp/shiny.deb

scripts/packages_to_install.csv

 Package_name;Deposit_name
 shiny;cran
 shinythemes;cran
-BiocManager;cran
-biomaRt;bioconductor
-ggplot2;cran
\ No newline at end of file