add vagrantfile and build script to create a VM using docker

docker/Vagrantfile

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+#========================================================================
+# Author: Edoardo Pasca, Ben Thomas
+# Copyright 2018 University College London
+# Copyright 2018-2019 Science Technology Facilities Council
+#
+# This file is part of the CCP PETMR Synergistic Image Reconstruction Framework (SIRF) virtual machine.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#         http://www.apache.org/licenses/LICENSE-2.0.txt
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+#=========================================================================
+
+Vagrant.configure("2") do |config|
+  config.vm.box = "bento/ubuntu-18.04"
+  config.vm.synced_folder '.', '/vagrant', disabled: true
+  config.vm.define "docker"
+
+  # Disable automatic box update checking. If you disable this, then
+  # boxes will only be checked for updates when the user runs
+  # `vagrant box outdated`. This is not recommended.
+  # config.vm.box_check_update = false
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine. In the example below,
+  # accessing "localhost:8080" will access port 80 on the guest machine.
+
+  # Forward port for jupyter notebooks
+  config.vm.network "forwarded_port", guest: 8888, host: 8889
+  config.vm.network "forwarded_port", guest: 9001, host: 9003, protocol: "tcp"
+  config.vm.network "forwarded_port", guest: 9002, host: 9004, protocol: "tcp"
+
+  # Create a private network, which allows host-only access to the machine
+  # using a specific IP.
+  # config.vm.network "private_network", ip: "192.168.33.10"
+
+  # Create a public network, which generally matched to bridged network.
+  # Bridged networks make the machine appear as another physical device on
+  # your network.
+  # config.vm.network "public_network"
+
+  # Share an additional folder to the guest VM. The first argument is
+  # the path on the host to the actual folder. The second argument is
+  # the path on the guest to mount the folder. And the optional third
+  # argument is a set of non-required options.
+  # config.vm.synced_folder "../data", "/vagrant_data"
+
+  # Provider-specific configuration so you can fine-tune various
+  # backing providers for Vagrant. These expose provider-specific options.
+  # Next lines are for VirtualBox:
+  #
+
+  config.vm.provider "virtualbox" do |vb|
+    # Display the VirtualBox GUI when booting the machine
+    vb.gui = true
+
+  # Customize the amount of memory on the VM:
+    vb.cpus = "2"
+    vb.memory = "4096"
+
+	vb.customize "pre-boot", [
+       "storageattach", :id,
+       "--storagectl", "IDE Controller",
+        "--port", "1",
+       "--device", "0",
+       "--type", "dvddrive",
+       "--medium", "emptydrive"
+       ]
+
+	vb.name = "SIRF 3.0.0 Docker"
+    vb.customize ["modifyvm", :id, 
+	              "--clipboard", "bidirectional",
+                  "--vram", "32"]
+
+  end
+
+  #
+  # View the documentation for the provider you are using for more
+  # information on available options.
+
+  # Define a Vagrant Push strategy for pushing to Atlas. Other push strategies
+  # such as FTP and Heroku are also available. See the documentation at
+  # https://docs.vagrantup.com/v2/push/atlas.html for more information.
+  # config.push.define "atlas" do |push|
+  #   push.app = "YOUR_ATLAS_USERNAME/YOUR_APPLICATION_NAME"
+  # end
+
+  # Enable provisioning with a shell script. Additional provisioners such as
+  # Puppet, Chef, Ansible, Salt, and Docker are also available. Please see the
+  # documentation for more information about their specific syntax and use.
+
+  config.vm.provision "shell", path: "../scripts/bootstrap_ubuntu_docker.sh"
+end
+

scripts/bootstrap_ubuntu_docker.sh

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+#!/bin/bash    
+
+set -x
+SIRFUSERNAME=sirfuser
+SIRFPASS=virtual
+
+# check if user exists. if not create it. Useful for vagrant provision
+id -u $SIRFUSERNAME
+if [ $? -eq "1" ] ; then
+  adduser $SIRFUSERNAME
+  adduser $SIRFUSERNAME sudo
+  { echo $SIRFPASS; echo $SIRFPASS; } | passwd $SIRFUSERNAME 
+fi
+
+# fail hard on any step
+set -ex
+# update the apt-get database
+export DEBIAN_FRONTEND=noninteractive
+apt-get update && apt-get upgrade -y -o Dpkg::Options::=--force-confnew
+# upgrade the list of packages
+
+
+#install upgrades
+apt-get update && apt-get install -y --no-install-recommends wget git xorg xterm gdm3 menu policykit-1-gnome synaptic gnome-session gnome-panel metacity
+apt-get update && apt-get install -y at-spi2-core gnome-terminal gnome-control-center nautilus dmz-cursor-theme network-manager network-manager-gnome
+apt=get install -y --no-install-recommends docker-compose docker
+
+# start gnome display manager
+service gdm start
+
+# set the current locale, otherwise the gnome-terminal doesn't start
+sudo locale-gen en_GB.UTF-8
+sudo locale-gen en_US.UTF-8
+sudo locale-gen de_DE.UTF-8
+sudo locale-gen fr_FR.UTF-8
+sudo locale-gen es_ES.UTF-8
+sudo locale-gen it_IT.UTF-8
+sudo locale-gen pt_PT.UTF-8
+sudo locale-gen pt_BR.UTF-8
+sudo locale-gen ja_JP.UTF-8
+sudo locale-gen zh_CN.UTF-8
+sudo update-locale LANG=en_GB.UTF-8
+sudo localectl set-x11-keymap uk
+sudo localectl status
+
+
+# To hide vagrant from login screen:
+#  1. Log-in as vagrant
+#  2. In /var/lib/AccountsService/users/vagrant change 'SystemAccount=true'
+sudo echo '[User]' > vagrant
+sudo echo 'SystemAccount=true' >> vagrant
+sudo cp -v vagrant /var/lib/AccountsService/users/vagrant
+
+  # To remove the Ubuntu user from VM:
+#sudo deluser --remove-home ubuntu
+# Could add custom logos here: /etc/gdm3/greeter.dconf-defaults 
+
+userHOME=/home/$SIRFUSERNAME
+
+if [ ! -d $userHOME/devel ]; then
+  mkdir $userHOME/devel 
+fi
+cd $userHOME/devel
+
+if [ ! -d $userHOME/devel/SyneRBI_VM ]; then
+  git clone https://github.com/SyneRBI/SyneRBI_VM.git
+  cd SyneRBI_VM
+else
+  cd SyneRBI_VM
+  git pull
+fi
+
+if [ ! -d $userHOME/devel/SIRF-SuperBuild ]; then
+  git clone https://github.com/SyneRBI/SIRF-SuperBuild.git
+  cd SIRF-SuperBuild
+else
+  cd SIRF-SuperBuild
+  git pull
+fi
+
+
+
+#bash $userHOME/devel/SyneRBI_VM/scripts/INSTALL_prerequisites_with_apt-get.sh
+#bash $userHOME/devel/SyneRBI_VM/scripts/INSTALL_CMake.sh /usr/local
+#bash $userHOME/devel/SyneRBI_VM/scripts/INSTALL_python_packages.sh
+
+# port 8888 is forwarded to 8888 so the user can use the host browser
+# Therefore no browser is installed on the VM
+
+chown -R $SIRFUSERNAME:users $userHOME
+# sudo -u $SIRFUSERNAME -H bash $userHOME/devel/SyneRBI_VM/scripts/UPDATE.sh -t origin/master
+
+
+# add sirfuser to the group docker
+sudo groupadd docker
+sudo usermod -aG docker ${SIRFUSERNAME}