Update Dockerfile

Author: fcomte

Dockerfile

@@ -1,20 +1,22 @@
-FROM rocker/ml-gpu
-RUN userdel nobody
-RUN groupadd --gid 99 nobody
-RUN useradd nobody --uid 99 --home /home/nobody/ --create-home --groups nobody --gid nobody --shell /bin/bash
-RUN echo "nobody ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
+FROM rocker/ml
 
-ENV \
+USER root
 
-    # Change the locale
-    LANG=fr_FR.UTF-8 
+# Install common softwares
+RUN apt-get -y update && \ 
+    curl -s https://raw.githubusercontent.com/InseeFrLab/onyxia/main/resources/common-software-docker-images.sh | bash -s && \
+    apt-get -y install tini && \
+    rm -rf /var/lib/apt/lists/*
 
+ENV \
+    # Change the locale
+    LANG=fr_FR.UTF-8 \
+    # option for include s3 support in arrow package
+    LIBARROW_MINIMAL=false
 
 RUN \
     # Add Shiny support
-    export ADD=shiny \
-    && bash /etc/cont-init.d/add \
-    
+    bash /rocker_scripts/install_shiny_server.sh \
     # Install system librairies
     && apt-get update \
     && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends apt-utils software-properties-common \
@@ -24,32 +26,35 @@ RUN \
         libudunits2-dev \
         libgdal-dev \
         curl \
+        jq \
+        bash-completion \
         gnupg2 \
         unixodbc \
         unixodbc-dev \
-	odbc-postgresql \
-	libsqliteodbc \
-	alien \
+        odbc-postgresql \
+        libsqliteodbc \
+        alien \
         libsodium-dev \
         libsecret-1-dev \
         libarchive-dev \
-        libglpk-dev \        
+        libglpk-dev \
+#        chromium \
+        ghostscript \
+        fontconfig \
+        fonts-symbola \
+        fonts-noto \
+        fonts-freefont-ttf \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* \
-    && wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | apt-key add - \
-    && add-apt-repository --yes https://adoptopenjdk.jfrog.io/adoptopenjdk/deb/ \
-    && sudo apt update -y \
-    && apt install -y adoptopenjdk-8-hotspot \
-
     # Handle localization
     && cp /usr/share/zoneinfo/Europe/Paris /etc/localtime \
     && sed -i -e 's/# fr_FR.UTF-8 UTF-8/fr_FR.UTF-8 UTF-8/' /etc/locale.gen \
     && dpkg-reconfigure --frontend=noninteractive locales \
     && update-locale LANG=fr_FR.UTF-8
 
+RUN kubectl completion bash >/etc/bash_completion.d/kubectl
 
 RUN \
-    
     R -e "update.packages(ask = 'no')" \
     && install2.r --error \
         RPostgreSQL \
@@ -58,8 +63,18 @@ RUN \
         keyring \
         aws.s3 \
         Rglpk \
-	paws \
-        SparkR
-    
-    
+        paws \
+        vaultr \
+	    arrow \
+    && installGithub.r \
+        inseeFrLab/doremifasol \
+        `# pkgs for PROPRE reproducible publications:` \
+        rstudio/pagedown \
+        spyrales/gouvdown \
+        spyrales/gouvdown.fonts \
+    && R -e "devtools::install_github('apache/spark@v$SPARK_VERSION', subdir='R/pkg')" \
+    && find /usr/local/lib/R/site-library/gouvdown.fonts -name "*.ttf" -exec cp '{}' /usr/local/share/fonts \; \
+    && fc-cache \
+    && Rscript -e "gouvdown::check_fonts_in_r()"
+
 VOLUME ["/home"]