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Jordan Tucker

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Aug 3, 2024, 11:10:55 AM8/3/24

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Oracle VirtualBox is a cross-platform virtualization application. It installs on your existing Intel or AMD-based computers, whether they are running Windows, Mac, Linux or Solaris operating systems. VirtualBox can create and run a "guest" operating system (virtual machine) in a window of the host operating system. The virtual machine provides a self-contained environment in which to experiment with new software without risking damaging changes to the host operating system.

We will give an instruction with step-by-step screenshots to show how to install VirtualBox with an example of installing Ubuntu OS as a guest machine. We also explain how to share files between the host and guest operating systems.

Note the instruction here is based on the latest version of the VirtualBox. If you have already installed an earlier version of VirtualBox, your experience may be different. It is recommended to use the latest version of VirtualBox to avoid issues. The VirtualBox forum is a good place to find a solution if you see any problems.

Go to VirtualBox website here to download the binary for your current operating system. Since our host machine is running on Windows, I'll choose 'x86/amd64' from Windows hosts. When download is finished, run the executable file. Continue with the installation of VirtualBox with the defaults. This will open VirtualBox at the end of the installation.

Type a name for the new virtual machine. Since I am planning to install Ubuntu 14.04, I'll enter 'ubuntu1404'. Note that VirtualBox automatically changes 'Type' to Linux and 'Version' to 'Ubuntu (64 bit)'. These two options are exactly what we need.

The memory size depends on your host machine memory size. In my case, I have 12GB physical RAM. I like to allocate as much as possible for Ubuntu but leave some for my Windows host machine. I pick 8192 MB for my Ubuntu. Note that VirtualBox will create a swap partition with the same amount space as base memeory you have entered here. So later when you are selecting the size of the virtual hard drive, make sure it is large enough since the hard drive will be splitted into root (/)and swap partitions. The root partition contains by default all your system files, program settings and documents.

For the virtual hard drive space, the default value is 8GB which is too little for RNA-Seq analysis. I'll pick 100GB since I have plenty of space in my hard disk. You want to choose a good size for your RNA-Seq analysis. If you realize the drive space is not large enough, you'll need to go over these steps again to create another virtual machine.

Now the virtual machine is created. We are ready to install Ubuntu in this virtual machine. Select your new virtual machine and click 'Settings' button. Click on 'Storage' category and then 'Empty' under Controller:IDE. Click "CD/DVD" icon on right hand side and select the ubuntu ISO file to mount.

Note that if you have not downloaded 64-bit Ubuntu ISO file, you can check out this page for more information. When downloading Ubuntu ISO file, make sure to selecte 64-bit version. Also make sure the VT-x/Virtualization Technology has been enabled in your computer's BIOS/Basic Input Output System.

Since Tophat program can take an advantage of multiple processors/threads, it is a good idea to specify a large number of processors in virtual machine (default value is 1). You can change this number by clicking on 'System' category. In this case, I change the number of CPUs to 4 since 4 is the largest value shown on the green bar in my case. Now you can click 'OK' button to continue.

Back to Oracle VM VirtualBox Manager, click on the new Ubuntu virtual machine and hit 'Start' button. Now you shall see a 'Welcome' screen. Click 'Install Ubuntu' button. Note that the installation process may differ a little bit from version to version. The screenshots here are based on Ubuntu 14.04.1.

After installation is complete, click 'Restart Now' button. When you see a screen with a black background saying 'Please remove installation media and close the tray (if any) then press ENTER:', just follow it.

Before we proceed to install Guest Additions, make sure the current user has sudo/root privilege. If the current user does not have sudo/root privilege or it is not sure, run the following terminal command from an account (such as the user created when Ubuntu was first created; see the screenshot of 'Who are you?' above) with root privileges to enable the root privilege for the current usersudo adduser USERNAME sudo where USERNAME should be replaced by the current user's name.

Type the following line in the Terminal to add a user to 'vboxsf' group. This step is necessary in order to use the VB's 'Shared Folder' feature.sudo adduser brb vboxsfReplace 'brb' with your account name in Ubuntu.When you are done, restart the Ubuntu guest machine and go to /media/ directory. From Nautilus (file manager in Ubuntu), click Computer > File System > Media folder and inside it you will see a folder beginning with sf_ (the folder name is sf_Downloads in our example). Now you can transfer files between the Ubuntu guest machine and the Windows host machine in Nautilus.

Although Shared Folder system in VirtualBox is a nice feature, using VirtualBox shared folder directly for fastq data, annotation or output directorycan significantly reduce the performance compared to a native (Ubuntu) system or VirtualBox native system.

The previous blog post of our VirtualBox series covered VirtualBox update. After updating VirtualBox, it is recommended to update VirtualBox Extension Pack on a host machine and VirtualBox Guest Additions on guest machines (VMs). If you have not installed VirtualBox Extension Pack yet, it is time to install it in order to unlock advanced VirtualBox features.

Support for USB 2.0 and USB 3.0 devices. USB devices such as network adapters, flash drives, hard disks, web cams etc., that are inserted into physical USB ports of a host machine can be attached to a virtual machine running on VirtualBox. As a result, you can use a physical USB device in a guest operating system (OS).

Host webcam pass-through. With this feature you can connect your host webcam to a guest machine. The advantage is that you can use a webcam which is not supported by the guest operating system of your VM. Imagine that you are using a webcam on a Windows-based host machine (you have all official Windows drivers for the webcam). You can use this webcam on a macOS-based VM (while this webcam is not supported on macOS and there are no macOS drivers for this webcam) thanks to the Host webcam pass-through feature.

VirtualBox Remote Desktop Protocol (VRDP). This feature allows you to control virtual machines remotely via the VirtualBox interface even if you cannot connect directly to a VM (for example, if the virtual network of a VM is not configured properly or disabled). You must have connectivity with a host machine to use this feature.

Disk image encryption with AES algorithm. Data stored on virtual disk images can be encrypted transparently for a guest OS. As a result, your VM data is encrypted even if the VM is copied from your protected storage to another location. The XTS encryption mode is used with 128-bit or 256-bit data encryption keys.

Intel PXE Boot ROM. PXE is a pre-boot execution environment that is used for network booting. A VM can boot using emulated PXE boot ROM (Read-Only Memory) to install an operating system. You must prepare PXE boot configuration files in your /VirtualBox/TFTP folder before using this feature.

Go to the download page of the official VirtualBox site and open the download link for the VirtualBox Extension Pack for all supported platforms. A single extension pack file is suitable for multiple supported host operating systems on which VirtualBox can work, and is installed using the VirtualBox interface. You can download the single file and use it to install VirtualBox Extension pack on Windows, Mac OS X, Linux, and Solaris. Save the downloaded Extension Pack file to a custom location. The name of the file used in this example is Oracle_VM_VirtualBox_Extension_Pack-6.0.8.vbox-extpack and this file is saved to C:\VirtualBox\ in this example. You can also download appropriate extension pack versions for older versions of VirtualBox.

In the Preferences window, go to the Extensions section. After a fresh installation of VirtualBox, there are no extensions packages installed. Click the Add a new package button (the icon with a green plus) to add the extension pack.

Read the license agreement and hit Agree to continue installation. Wait a few seconds while the files are being copied. If everything is OK, you will get the message that Oracle VM VirtualBox Extension Pack was installed successfully. After closing this notification window, you will see VirtualBox Extension pack in the list of extension packages.

The process of Installing VirtualBox Extension Pack on macOS is quite similar to that required for the extension pack on other operating systems. Open Launchpad, run VirtualBox, then go to Tools > Preferences and select the Extensions tab. Click the add icon to install VirtualBox Extension Pack.

Read and accept the license agreement. Then enter your password to continue installation and wait for a few seconds while VirtualBox Extension Pack is being installed on your mac. After finishing installation, you should see the notification message: Oracle VM VirtualBox Extension Pack was installed successfully. Hit OK and look for your VirtualBox extension pack in the list of installed extension packages.

In Windows, go to the VirtualBox installation directory. The default installation directory is C:\Program files\VirtualBox\. If you do not wish to change the directory in the command line manually every time you need to use VBoxManage, add your VirtualBox installation directory to the PATH environment variable in the advanced system settings of your Windows system.