install_apptainer.sh

#!/usr/bin/env bash
# Made by Kasper Skytte Andersen (https://github.com/KasperSkytte)
# Only for ubuntu/debian 64-bit linux machines
# License: GNU General Public License v3.0
set -eu

VERSION="1.3"

# GO version
GOVERSION=1.19.3

# singularity/apptainer version
APPTAINER_VERSION="v1.1.8"

# required system packages for apptainer
pkgs="build-essential libseccomp-dev pkg-config uidmap squashfs-tools squashfuse fuse2fs fuse-overlayfs fakeroot cryptsetup curl wget git"

scriptMessage() {
  #check user arguments
  if [ ! $# -eq 1 ]
  then
    echo "Error: function must be passed exactly 1 argument" >&2
    exit 1
  fi
  echo " *** [$(date '+%Y-%m-%d %H:%M:%S')] script message: $1"
}

#default error message if bad usage
usageError() {
  echo "Invalid usage: $1" 1>&2
  echo ""
  eval "bash $0 -h"
}

#help text
description() {
  echo "This script installs apptainer/singularity ${APPTAINER_VERSION}. By default for all users in /usr/local/apptainer. To install for the current user only provide a (writable) path with the -p option. This also assumes that all system dependencies are already installed."
  echo "Please provide sudo password when asked."
}

OS=$(cat /etc/os-release | grep '^ID' | grep -oE 'debian|ubuntu')

if [ -n "$OS" ]
then
  installDir=""
  #fetch and check options provided by user
  while getopts ":hp:" opt; do
  case ${opt} in
    h )
      description
      echo "Version: $VERSION"
      echo "Options:"
      echo "  -h    Display this help text and exit."
      echo "  -p    Path to folder where apptainer will be installed (/apptainer subfolder will be created). If not provided, will be installed system-wide for all users in /usr/local/apptainer."
      exit 1
      ;;
    p )
      installDir=$(realpath -m "$OPTARG")
      mkdir -p "$installDir"
      if [ ! -w "$installDir" ]
      then
        usageError "Destination folder ${installDir} is not writable, exiting..."
        exit 1
      fi
      ;;
    \? )
      usageError "Invalid Option: -$OPTARG"
      exit 1
      ;;
    : )
      usageError "Option -$OPTARG requires an argument"
      exit 1
      ;;
  esac
  done
  shift $((OPTIND -1)) #reset option pointer
  description
  
  #sleep if interactive to be able to read message
  if [ -t 0 ]
  then
    echo "sleeping for 10 seconds"
    sleep 10
  fi

  scriptMessage "installing system requirements via APT..."
  #first check if installed before running a sudo command
  #ubuntu versions before 2018 need libgpgme11-dev instead of libgpgme-dev
  ubuntuMajor=$(cat /etc/lsb-release |\
   grep '^DISTRIB_RELEASE.*' |\
   grep -o '=[0-9]*\.' |\
   grep -o '[0-9]*')
  if [ $ubuntuMajor -lt 18 ]
  then
    pkgs="${pkgs} libgpgme11-dev"
  else
    pkgs="${pkgs} libgpgme-dev"
  fi
  
  if ! dpkg -s $pkgs >/dev/null 2>&1
  then
    echo "One or more system dependencies are not installed, will try to install..."
    sudo apt-get update -qqy
    sudo apt-get install -y $pkgs
  else
    echo "all requirements are already installed..."
  fi
  
  scriptMessage "creating temporary folder for downloads and build files..."
  tmp_dir=$(mktemp -d -t apptainer_installer_XXXXX)
  pushd "$tmp_dir"
  
  scriptMessage "downloading GO lang..."
  wget -O go.tar.gz https://dl.google.com/go/go${GOVERSION}.linux-amd64.tar.gz

  scriptMessage "unpacking go..."
  tar -zxf go.tar.gz
  rm -f go.tar.gz

  #go is only needed for compiling apptainer
  export GOPATH=${PWD}/go
  export OLDPATH=${PATH} #save for later to avoid also adding Go path to $PATH
  export PATH=${PWD}/go/bin:${PATH}

  scriptMessage "downloading apptainer..."
  git clone https://github.com/apptainer/apptainer.git apptainer
  pushd apptainer
  git checkout ${APPTAINER_VERSION}
  
  if [ -n "$installDir" ]
  then
    scriptMessage "installing apptainer into ${installDir}/apptainer..."
    ./mconfig --without-suid --prefix=${installDir}/apptainer
    make -j -C ./builddir
    make -j -C ./builddir install

    scriptMessage "Adding apptainer path to \$PATH and enabling apptainer bash auto-completion for current user by adjusting ${HOME}/.bashrc..."
    #detect and remove lines in ~/.bashrc previously added by this 
    #script to avoid inflating $PATH if script is run more than once
    sed -i '/# >>> apptainer installer >>>/,/# <<< apptainer installer <<</d' ${HOME}/.bashrc
    
    #then add lines
    echo "# >>> apptainer installer >>>" >> ${HOME}/.bashrc
    echo "#these lines have been added by the install_apptainer.sh script" >> ${HOME}/.bashrc
    echo "export PATH=${installDir}/apptainer/bin:$OLDPATH" >> ${HOME}/.bashrc
    echo ". ${installDir}/apptainer/etc/bash_completion.d/apptainer" >> ${HOME}/.bashrc
    echo "# <<< apptainer installer <<<" >> ${HOME}/.bashrc

    scriptMessage "Removing temporary folder and its contents..."
    chmod -R 777 "$tmp_dir"
    rm -rf "$tmp_dir"
  else
    scriptMessage "installing apptainer system-wide into /usr/local/bin..."
    ./mconfig
    sudo make -j -C ./builddir
    sudo make -j -C ./builddir install
    
    scriptMessage "enabling system-wide apptainer bash auto-completion by adjusting /etc/profile..."
    #detect and remove lines in /etc/profile previously added by this script to avoid inflation
    sudo sed -i '/# >>> apptainer installer >>>/,/# <<< apptainer installer <<</d' /etc/profile

    #then add lines
    echo "# >>> apptainer installer >>>" | sudo tee -a /etc/profile
    echo "#these lines have been added by the install_apptainer.sh script" | sudo tee -a /etc/profile
    echo ". /usr/local/etc/bash_completion.d/apptainer" | sudo tee -a /etc/profile
    echo "# <<< apptainer installer <<<" | sudo tee -a /etc/profile
    
    scriptMessage "Removing temporary folder and its contents..."
    sudo rm -rf "$tmp_dir"
  fi
  scriptMessage "Done installing. Reload the current shell to enable apptainer command auto-completion right away."
else
  echo "Unsupported OS type: ${OS}"
  echo "This script is designed only for Ubuntu or Debian Linux, exiting..."
  exit 1
fi