To do

Create a separate virtual disk for the data, and explain how to mount it on the virtual machine.
Understand when and why the file /etc/bash_completion.d/grub appears in the folder /etc/bash_completion.d/. This config file creates warnings (see https://askubuntu.com/questions/778439/have-command-not-found), and I don’t need it since grub is not installed.

Requirements

Downloads

Before starting the installation process, we recommend to download the following files

Virtualbox: https://www.virtualbox.org/wiki/Downloads

Ubuntu Desktop: ubuntu-17.04-desktop-amd64 (1.5Gb).

Lighter alternative (without graphical Ubuntu interface): Ubuntu Server Version 17.04: ubuntu-17.04-server-amd64 (685Mb).

Installation of the virtual machine

Creating a new virtual machine

Open VirtualBox
Click on the New button.
Parameters

Name and operating system
- Name: RSAT-VM-2017-04
- Type: Linux
- Version: Ubuntu (64 bits)
Memory size: 2048 Mb (this can be modified afterwards).
Hard drive: Create a virtual hard drive now.
Hard drive file type: VMDK (Virtual Machine Disk).

I chose this option because it ensures a wider compatibility with other OS and Virtual Machine management systems.

Another potential advantage of VMDK is that it enables to split virtual disks into files <=2Gb, which is convenient to store them on FAT partitions. However, for the distribution I avoid to activate this option because it is simpler to put a single dwnloable file on the server.
Storage on physical hard drive
- Select Dynamically allocated
- Depending on your storage device, you may activate the option Split into files less than 2Gb, which allows to store the VM on FAT partitions for Windows host machines.
File location and size
- name of virtual hard drive file: RSAT-VM-2017-04_HDD
- max size of virtual hard drive: 18GB
  
  Beware: the size has to be larger than you real needs, because Ubuntu will automatically create some big partitions (/dev and /run/shm). Since we allow dynamical memory allocation, it is fine to set the max size to 18Gb, which will be grossly assigned as follows:
  - max 14Gb for the root partition /
  - 2Gb for /dev
  - 2Gb for /run/user

At this stage, the VM has been created and needs to be configured before installing the operating system.

General configuration of the network for your VirtualBox program

Before configuring the virtual machine, we need to tell VirtualBox how it will enable your local virtual machines to interact with their host (the operating system of the machine on which the VM is running).

Open VirtualBox Preferences
Open the tab Network > Host-only Networks
- Click on the “+” icon.
- This creates a network vboxnet0.
- Select this network, click on the screw driver icon (edit host-only network), and set the following options:
- Adapter tab
  - IPv4 Address: 192.168.56.1
  - IPv4 Network Mask: 255.255.255.0
  - IPv6 Adress: blank
  - IPv6 Network Mask Length: 0
- DHCP Server tab
  - Check Enable Server
  - Server Address: 192.168.56.100
  - Server Mask: 255.255.255.0
  - Lower Address Bound: 192.168.56.101
  - Upper Address Bound: 192.168.56.254

Network configuration of the virtual machine

In the VirtualBox main window, select the newly created virtual machine.
Click on the Settings button.
In the VM settings, select tne Network tab.

VirtualBox enables you to specify several adapters, each corresponding to one separate network acces (e.g. using an ethernet card + wi-fi connection). Note that you will have the possibility to modify the network settings later.

VirtualBox offers alternative ways to configure network communications between the virtual machine, the host machine, and the external network. To get more information about network settings:

VirtualBox manual page: https://www.virtualbox.org/manual/ch06.html
An excellent tutorial: http://christophermaier.name/blog/2010/09/01/host-only-networking-with-virtualbox

We present here one possible way to configure your Virtual machine, but this should be adapted to the particular security/flexibility requirements of the network where the maching has to run.

Adapter 1: Host-only adapter

The first network adapter is the safest: the only possible communication is from the host to the guest. This is sufficient to enable you to use the RSAT VM from your computer and only from there. Besides, your VM has no possibility to establish a connection to the external work.

click on the tab Adapter 1,
check Enable Network Adapter
Attached to: Host-only Adapter
Name: vboxnet0 (this network must have been created beforehand)

Adapter 2: NAT

We strongly recommend to specify a NAT as second adaptor, since this allows your VM to establish connections (browser, ssh) to the world outside the host machine (your computer).

click on the tab Adapter 2,
check Enable Network Adapter
Attached to: NAT

Additional networks (optional)

BEWARE! If you activate the adaptor described below your VM will be visible from external computers in the same network as the host machine.

See information at: https://www.virtualbox.org/manual/ch06.html#network_bridged

click on the tab Adapter 3,
check Enable Network Adapter
Attached to : Bridged Adapter
Name: choose an option corresponding to the actual internet connection of the host machine (e.g. ethernet cable, Wi-Fi, …).

Note: you can also activate a fourth adapter, for example to support both an ethernet card (Adapter 3) and a Wi-Fi connection (Adapter 4). This is particularly useful for laptop computers, whose network parameters vary from place to place.

Starting the server for installation

Once the settings have been specified, you can click on the Start icon (big fluo green array in VurtualBox).
A dialog box may appear “Please select a virtual optic disk …”. Click on the small folder icon and locate the disk image of Ubuntu that was downloaded in a previous step. Then click the Start button.

Ubuntu is now starting from the installation disk. The next section explains how to configure it.

Linux operating system installation

Ubuntu desktop version

The desktop version of Ubuntu presents the advantage of letting users work directly in the graphical environment of the Ubuntu virtual machine, which is convenient to open non-text result files for visualization (web pages, images) and to analyze the results in other graphical packages (R, openOffice, CytoScape, …).

Start the default installation: Click the button: Install Ubuntu

Install Ubuntu

Dialog box Preparing to install Ubuntu.
- Make sure the option Download updates while installing Ubuntu is unchecked (we will update the packages after installation).
- Leave the other parameters unchanged and click Continue.

Preparing to install Ubuntu

Installation type:
- Check Erase disk and install Ubuntu
- Uncheck Encrypt new Ubuntu installation for security
- Leave all other options unchanged.
- Click Install Now.
- There will be a warning message Write the changes to disk?. Click Continue.

Installation type

In the dialog box Write the changes to disk? click Continue.

Write changes on disk

Where are you?

If you VM has a suitable Internet connexion, your location should be detected automatically. If not, choose the right location.

Where are you?

Keyboard layout: make your choice¹

NOTE CLAVIER FRANÇAIS: for the French Macintosh keyboard, I spent a lot of time to find the solution to use the 3-component keys (e.g. alt-shit-L for the pipe character |). The simplest solution: use the alt key on the RIGHT side of the space bar.

Who are you?

Field	Value
Your name	RSAT admin
Your computer’s name	rsat-vb-2017-04
Pick a username	rsat
Password	rsat1704²
Log in automatically	I activate it because this will greatly facilitate the use of the Destkop version
	Click Continue

Who are you?

Ubuntu now installs the system, this should take a few minutes³.

Ubuntu installation

After installation, Ubuntu displays a message “Installation is complete. You need to restart …”. Click Restart now.
When rebooting, Ubuntu warns you that you need to remove the installation media and close the tray. In our case, the installation media is the iso disk. To remove it, go in the menu Devices -> Optical Drives -> Remove Disk from Optical Drive. If this does not work, close the window with the virtual machine, and restart this virtual machine from VirtualBox.
After reboot, you will automatically log in as RSAT admin user.
For the sake of convenience, I disactivate the lock screen and password prompt options. Indeed, since the VM is running under my account on the hosting system, there is no need to double the security options. For this, click on the Settings icon (toothed wheels) on the top-right corner of the Ubuntu display. Select All Settings and click on the panell Brightness and Lock. Set Lock to off and uncheck Require my password when waking from suspend.

Disactivate lock screen and password prompt after suspend.

Screen resolution (for Desktop version 14.04)

Note: If you are using Ubuntu version 17.04 you can skip this section which was useful to fix a problem with version 14.04.

With Ubuntu 14.05, at your first log in, the screen resolution is restricted to 640x480 pixels.

I found a solution to increase the screen resolution here: http://www.juanrubio.me/2014/02/ubuntu-trusty-virtualbox-guest-additions/

Open a terminal and run the following commands:

sudo apt-get install virtualbox-guest-utils
sudo apt-get install virtualbox-guest-dkms

You need to restart the Virtual machine for the changes to apply.
After rebooting, the VM has a resizable screen: if you increase the VM window, the Ubunutu desktop will adapt its size accordingly.

Ubuntu Server version (still for version 14.04, to be checked and adapted for 16.04)

The server version is less comfortable than the desktop version, but it should be more economic in terms of hard drive (and CPU/RAM for graphical resources ?).

Language English

Home page: choose “Install Ubuntu Server”

Language (again): English

Country, territory or area: other > Europe > France

Country to base the default locale setting: United Kingdom (there is apparently no setting for France !)

Detect keyboard layout: No > French > French - French (Macintosh)

Your system has multiple network interfaces (I guess this corresponds tothe 3 adapters specified in VirtualBox preferences). Primary network interface: eth0

host name: rsat-vb-ub14s

Full name of new user: RSAT admin

Username for your account: rsat

Password for new user: the classical (only for RSAT team members)

Encrypt home directory ? No

Time: Europe/Paris

Partitioning method: (default) Guided - use entire disk and set up LVM

 Next partitioning options: I say "continue" to all with default values

… Installing the sysem … (takes some time)

Configure the package manager Leave the HTTP proxy blank -> … configuring apt (takes some time)

Configuration taskse1

Install security updates automatically

Software selection : I just install the OpenSSH server, in order to be able connecting, but I don’t install anything else since I want to use the RSAT bash file with apt-get packages etc. -> … Select and install software (takes some time)

Install the GRUB boot loader Yes

Convenient settings (not necessary)

Remote log in to the VM

So far the virtual machine does not support remote access. To add support for ssh access, we need to install the appropriate package.

In the virtual machine, open a terminal and type the following command.

sudo apt-get install --quiet --assume-yes ssh
sudo apt-get install --quiet --assume-yes net-tools

The package net-tools includes the ifconfig command, which will be useful to get the IP addresses of your VM.

From the host machine, open a terminal and type the following command.

ssh rsat@192.168.56.101

Note: the IP address above may be different on your computer, depending on the network settings of your VirtualBox and on the number of Virtual Machines currently running.

You are now connected to your virtual machine via an ssh session from the host machine.

At this stage, the machine is able to boot and get a dynamic IP from the network. I login as rsat user and type

ifconfig

to get the IP address. I then open a terminal on the host machine, and run

ssh rsat@[IP_OF_MY_VM]

so I can run the rest of the installation in my familiar environment (terminal, keyboard, …)

Useful commands to manage VirtualBox

It is useful to install some VirtualBox accompanying software on your Ubuntu virtual machine.

sudo apt-get install virtualbox
sudo apt-get install virtualbox-dkms

List running VMs

VBoxManage list runningvms

Get IDs of the virtual machines

VBoxManage list runningvms | awk -F"[{}]" '{print $2}'

For convenience, we store the IP of the machine of interest in an environment variable VMID. VMID=VBoxManage list runningvms | awk -F"[{}]" '{print $2}'

Get properties of the VM

VBoxManage guestproperty enumerate ${VMID}

List information about a given virtual machine

VBoxManage showvminfo ${VMID}

Note: that command returns the MAC address, but no IP address.

VBoxManage showvminfo ${VMID} | grep '^NIC'

Create a generic user for the virtual machine

We create two separate users:

vmuser is a simple user of RSAT, has no right to administrate it (e.g. add new genomes, …)
rsat is the administrator for the Web site.

Both users (vmuser and rsat) have an initial password provided with the distribution (tochng), but which must be changed at the first login.

################################################################
## Create a user for the virtual machine
##
## This VM user is separate from the rsat user, which only serves to
## manage the RSAT software suite and related packages.
##
## For the sake of security, we force this user to change password at
## first login

## First delete this user (in case it was previously defined)
##  sudo userdel --remove vmuser

sudo useradd --password `openssl passwd -1 -salt xyz tochng`\
    --home /home/vmuser \
    --create-home \
    --shell /bin/bash \
    --comment "VM user" \
    vmuser

## Force vmuser to change password at first login
sudo chage -d 0 vmuser

## Force rsat user to change password at first login
sudo usermod --password `openssl passwd -1 -salt xyz tochng` rsat
sudo chage -d 0 rsat

## Add sudoer rights to vmuser and rsat users
sudo chmod 644 /etc/sudoers
sudo nano /etc/sudoers
## Find the following line
##     # User privilege specification
##     root    ALL=(ALL:ALL) ALL
## Below it, add the following line:
##     rsat    ALL=(ALL:ALL) ALL
##     vmuser  ALL=(ALL:ALL) ALL
## Type "Ctrl-X" to exit from the nano editor, then "Y" to save your changes.

Install Ubuntu packages and RSAT distribution

The instructions to install Ubuntu packages are in a separate file

$RSAT/doc/howto/install_rsat_ubuntu16.bash

PROBLEMS TO BE FIXED

Ethernet: optimize solution for a simple setting in the classroom.
Problem of disk occupancy: Ubuntu shared memory occupies 2Gb. This can be modified as explained here.

http://www.cyberciti.biz/tips/what-is-devshm-and-its-practical-usage.html
For the desktop version, I should try to use the Advanced installation in order to use less disk without loosing too much confort. For example, I could inactivate the support for all the languages that are installed by default (downloading language packs).

Customizing your instance of the VM

## Set up time zone, date and time (source:
## https://help.ubuntu.com/community/UbuntuTime).
sudo dpkg-reconfigure tzdata

To set up the keyboard (may vary between users who download the VirtualBox VM)

sudo apt-get install console-data
sudo dpkg-reconfigure console-data
## (for my laptop, mac / Unknown / French /Standard / New)

For the Virtualbox VM: mount the virtual disk rsat_data

Export appliance

Once the Virtual Machine is working fine, it can be exported to an appliance.

In VirtualBox, open “File -> Export Appliance …”, and select the VM.
- Save as: rsat-vm-2017-04.ova
- Files of Type: Open Virtualization Format Archive (.ova)
- Storage Settings
- Format: OVF 1.0
- Check this option: v Write Manifest File

Appliance Settings

Parameter	Value
Name	rsat-vm-2017-04
Product	Regulatory Sequences Analysis Tools
Product-URL	http://rsat.eu/
Vendor	Jacques van Helden
Vendor URL	http://jacques.van-helden.perso.luminy.univ-amu.fr/
Version	2017-04
Description	Regulatory Sequence Analysis Tools (RSAT, http://rsat.eu/), installed on an Ubuntu 14.04 Virtual Machine.
License	Free of use for academic users, non-commercial and non-military usage.

Transfer Appliance to USB key

Prepare the VM + accompanying material on a USB key, to ensure distribution in the teaching room. We use ScanDisk 64Gb USB3.0 keys, which have a high transfer rate (190Mbps write / 250Mbps read).

SOURCE_DIR=/no_backup/VirtualBox_VMs/appliances
VERSION=2017-04

## Specification of the target location
KEY_NB=02
TARGET_DIR=/Volumes/RSAT-VM_${KEY_NB}/
time rsync -ruptvl ${SOURCE_DIR} ${TARGET_DIR}

Split the VM into smaller files (optional)

This can be useful for two purposes.

To transfer files to a FAT-formatted drive for distribution (FAT cannot hold files >4Gb). Note that the final installation drive will have to support files >4Gb for the server version of the VM.
To facilitate synchronization between local and remote machines.

SPLIT_SIZE=3999m
mkdir -p ${TARGET_DIR}/appliances
time split -b ${SPLIT_SIZE} ${SOURCE_DIR}/rsat-vm-2017-04_${VERSION}.ova ${TARGET_DIR}/appliances/rsat-vm-2017-04_${VERSION}.ova.split${SPLIT_SIZE}_

Centos 6.8

I downloaded the install disk from here:

http://centos.mirrors.ovh.net/ftp.centos.org/6.8/isos/x86_64/CentOS-6.8-x86_64-LiveCD.iso

Installation steps:

Install
Skip media testing
Language: English
Keyboard: fr-pc
Installation media: Local CD/DVD

I have a French - French Macintosh, so I use it for installation, but I will later add an English keybord for the distribution.↩
This password is obviously not safe, but it will be changed at the end of the installation↩
Note if you did activate the option to update Ubuntu packages in the previous window, the installation can take several minutes↩

Creating an Ubuntu VM under Virtualbox

Jacques van Helden

Last update: 2017-04-22

To do

Requirements

Downloads

Installation of the virtual machine

Creating a new virtual machine

General configuration of the network for your VirtualBox program

Network configuration of the virtual machine

Adapter 1: Host-only adapter

Adapter 2: NAT

Additional networks (optional)

Starting the server for installation

Linux operating system installation

Ubuntu desktop version

Screen resolution (for Desktop version 14.04)

Ubuntu Server version (still for version 14.04, to be checked and adapted for 16.04)

Convenient settings (not necessary)

Remote log in to the VM

Useful commands to manage VirtualBox

List running VMs

Get IDs of the virtual machines

Create a generic user for the virtual machine

Install Ubuntu packages and RSAT distribution

PROBLEMS TO BE FIXED

Customizing your instance of the VM

To set up the keyboard (may vary between users who download the VirtualBox VM)

For the Virtualbox VM: mount the virtual disk rsat_data

Export appliance

Appliance Settings

Transfer Appliance to USB key

Split the VM into smaller files (optional)

Centos 6.8

Creating an Ubuntu VM under Virtualbox

Jacques van Helden

Last update: 2017-04-22

To do

Requirements

Downloads

Installation of the virtual machine

Creating a new virtual machine

General configuration of the network for your VirtualBox program

Network configuration of the virtual machine

Adapter 1: Host-only adapter

Adapter 2: NAT

Additional networks (optional)

Starting the server for installation

Linux operating system installation

Ubuntu desktop version

Screen resolution (for Desktop version 14.04)

Ubuntu Server version (still for version 14.04, to be checked and adapted for 16.04)

Convenient settings (not necessary)

Clipboard sharing between guest and host

Remote log in to the VM

Useful commands to manage VirtualBox

List running VMs

Get IDs of the virtual machines

Create a generic user for the virtual machine

Install Ubuntu packages and RSAT distribution

PROBLEMS TO BE FIXED

Customizing your instance of the VM

To set up the keyboard (may vary between users who download the VirtualBox VM)

For the Virtualbox VM: mount the virtual disk rsat_data

Export appliance

Appliance Settings

Transfer Appliance to USB key

Split the VM into smaller files (optional)

Centos 6.8