Creating a Singularity Container

Singularity is a container engine alternative to Docker. Singularity containers are well suited for the requirements of High Performance Computing (HPC) workloads.

A container contains all code as well as all its dependencies so that the an application runs reliably on different computers (or different computing environments). It can be used to run on servers or as a way to ensure computational reproducibility (that the code run on other systems, and in the future). For an introduction to the concept of containers see Computational Reproducibility via Containers in Psychology. Below is code to build a Singularity container for running the text-package.

Code to build a singularity container

Bootstrap: docker
From: ubuntu:20.04

%environment
  export LANG=C.UTF-8 LC_ALL=C.UTF-8
  export XDG_RUNTIME_DIR=/tmp/.run_$(uuidgen)

%post
    # Install
    apt-get -y update

    export R_VERSION=4.1.3
    echo "export R_VERSION=${R_VERSION}" >> $SINGULARITY_ENVIRONMENT

     # Install R
     apt-get update
     apt-get install -y --no-install-recommends software-properties-common dirmngr  wget uuid-runtime
     wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | \
       tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
     add-apt-repository \
       "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
     apt-get install -y --no-install-recommends \
     r-base=${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 \
     libopenblas-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

    # Fix R package libpaths (helps RStudio Server find the right directories)
    mkdir -p /usr/lib64/R/etc
    echo "R_LIBS_USER='/usr/lib64/R/library'" >> /usr/lib64/R/etc/Renviron
    echo "R_LIBS_SITE='${R_PACKAGE_DIR}'" >> /usr/lib64/R/etc/Renviron
    # Clean up
    rm -rf /var/lib/apt/lists/*

    # Install python3
    apt-get -y install python3 wget
    apt-get -y clean

    # Install Miniconda
    cd /
    wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
    bash Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda

/bin/bash <<EOF
    rm Miniconda3-latest-Linux-x86_64.sh
    source /miniconda/etc/profile.d/conda.sh
    conda update -y conda
    # Install reticulate and text
    Rscript -e 'install.packages("reticulate")'
    Rscript -e 'install.packages("devtools")'
    Rscript -e 'install.packages("glmnet")'
    Rscript -e 'devtools::install_github("oscarkjell/text")'
    # Create the Conda environment at a system folder
    Rscript -e 'text::textrpp_install(prompt = FALSE)'
    Rscript -e 'text::textrpp_initialize(save_profile = TRUE, prompt = FALSE, textEmbed_test = TRUE)'
EOF