Singularity.4.0.3

BootStrap: docker
From: ubuntu:20.04

%labels
  Maintainer Josh Granek
  R_Version 4.0.3
  RStudio_Version 1.3.1093
  Image_Name singularity-rstudio-base
  Image_Version singularity-rstudio-base_0004

%help
  This will run RStudio Server with tidyverse and support for knitting

%runscript
  exec port_and_password "${@}"

%apprun R
  exec R "${@}"

%apprun Rscript
  exec Rscript "${@}"

%apprun rserver
  exec rserver "${@}"

%apprun rstudio
  exec rserver "${@}"

%apprun default
  exec "${@}"

%apprun pp
  exec port_and_password "${@}"

%environment
  export PATH=/usr/lib/rstudio-server/bin:${PATH}:/usr/lib/rstudio-server/bin/pandoc
  export SHELL=/bin/bash
  export LC_ALL=en_US.UTF-8
  export LANG=en_US.UTF-8
  export LANGUAGE=en_US.UTF-8

%setup
  install -Dv \
    rstudio_auth_1_3.sh \
    ${SINGULARITY_ROOTFS}/usr/lib/rstudio-server/bin/rstudio_auth
  install -Dv \
    ldap_auth.py \
    ${SINGULARITY_ROOTFS}/usr/lib/rstudio-server/bin/ldap_auth

  install -Dv \
    port_and_password_1_3.sh \
    ${SINGULARITY_ROOTFS}/usr/lib/rstudio-server/bin/port_and_password

%post
  # Software versions
  export R_VERSION=4.0.3
  export RSTUDIO_VERSION=1.3.1093

  export DEBIAN_FRONTEND=noninteractive

  # Get dependencies
  apt-get update
  apt-get install -y --no-install-recommends \
    apt-utils \
    gnupg2 \
    locales

  # Configure default locale
  echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
  locale-gen en_US.utf8
  /usr/sbin/update-locale LANG=en_US.UTF-8
  export LC_ALL=en_US.UTF-8
  export LANG=en_US.UTF-8

  # Install R
  echo "deb http://cran.r-project.org/bin/linux/ubuntu focal-cran40/" > /etc/apt/sources.list.d/r.list
  apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
  # apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
  apt-get update
  apt-get install -y --no-install-recommends \
    r-base=${R_VERSION}* \
    r-base-core=${R_VERSION}* \
    r-base-dev=${R_VERSION}* \
    r-recommended=${R_VERSION}* \
    r-base-html=${R_VERSION}* \
    r-doc-html=${R_VERSION}* \
    libcurl4-openssl-dev \
    libssl-dev \
    libxml2-dev \
    libcairo2-dev \
    libxt-dev

  # Add a default CRAN mirror
  echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/lib/R/etc/Rprofile.site

  # Add a directory for host R libraries
  mkdir -p /library
  echo "R_LIBS_SITE=/library:\${R_LIBS_SITE}" >> /usr/lib/R/etc/Renviron.site

  # Clean up
  # rm -rf /var/lib/apt/lists/*

  # Install RStudio Server
  # apt-get update
  apt-get install -y --no-install-recommends \
    ca-certificates \
    wget \
    gdebi-core \
    libssl1.1 \
    libssl-dev \
    dpkg-sig \
    python3-ldap3

  gpg2 --keyserver keys.gnupg.net --recv-keys 3F32EE77E331692F

  wget --no-verbose \
       -O rstudio-server.deb \
       "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-${RSTUDIO_VERSION}-amd64.deb" && \
       dpkg-sig --verify rstudio-server.deb && \
    gdebi -n rstudio-server.deb && \
    rm rstudio-server.deb

  # Install tidyverse, here, and packages necessary for knitting to HTML 
  Rscript -e "install.packages(pkgs = c('tidyverse','here','caTools','rprojroot','Rcpp', 'base64enc', 'digest', 'evaluate', 'glue', 'highr', 'htmltools', 'jsonlite', 'knitr', 'magrittr', 'markdown', 'mime', 'rmarkdown', 'rprojroot', 'stringi', 'stringr', 'tinytex', 'xfun', 'yaml'), \
     repos='https://mirror.las.iastate.edu/CRAN/', \
     dependencies=TRUE, \
     clean = TRUE)"

  # Install extra stuff
  apt-get install -y --no-install-recommends \
    bsdmainutils \
    iproute2 \
    libxml2-dev \
    curl \
    wget \
    bzip2 \
    ca-certificates \
    sudo \
    locales \
    emacs \
    less \
    make \
    git \
    ssh \
    htop \
    jq

  # Clean up
  apt-get clean && rm -rf /var/lib/apt/lists/*

  # Make Mountpoints
  mkdir -p /data
  mkdir -p /workspace