Start VirtualMachine

1 How to install VirtualBox and VirtualBox Extension Pack

Before you can use the virtual machine of sRNAtoolbox (sRNAtoolboxVM) you need to download and install a hypervisor or a virtual machine monitor, i.e. a computer software that creates and runs virtual machines. There are many hypervisors that are compatible with the Open Virtualization Format (OVF or OVA), like VirtualBox, VMware and XenServer, among others. OVA is the format that we use to distribute sRNAtoolboxVM. We recommend using VirtualBox (version 5 or higher) because it is free, open source and user friendly.

To install VirtualBox visit this website.

Download the version for your operating system (Windows, OS X, Linux and Solaris) and the VirtualBox Extension Pack (is the same for all supported platforms). Install VirtualBox and then double-click on the VirtualBox Extension Pack file to install it. If the double click does not work, open VirtualBox and go to

File ➜ Preferences ➜ Extensions
to add the VirtualBox Extension Pack file. Once installed, restart VirtualBox.

2 Download Virtual Machine

Download the sRNAtoolboxVM OVA file here.

Then open VirtualBox and go to

File ➜ Import Appliance
to import the sRNAtoolboxVM. Select the OVA file and leave the default options (later we will change these options). Import the OVA file.

3 Configure Virtual Machine

Once imported, you will see sRNAtoolboxVM in the VirtualBox interface (left menu). Now click on sRNAtoolboxVM to select it for configuration.

To change the memory allocation, go to

Settings (orange gear) ➜ System ➜ Motherboard ➜ Base Memory
We recommend using 1.5 GB of memory per Gb of the reference assembly. For example, the human genome has roughly 3Gb and therefore the recommended memory would be 4.5.

To change the number of CPUs assigned, go to

Settings (orange gear) ➜ System ➜ Processor ➜ Processor(s)
You must use at least 4 CPUs for proper functioning.

4 Use a shared folder

It is highly recommended to use a shared folder to store the datasets, assemblies and results. If you do not use a shared folder, the performance of sRNAtoolbox will be considerably lower and the virtual disk will grow undesirably. Please use a shared folder.

To select the shared folder in the host machine:

Settings (orange gear) ➜ Shared Folders
In order to ‘activate’ a shared folder, two pieces of information are needed:

  1. The name and path of the folder in the host machine.
  2. The name of the shared folder for the virtual machine.

Note that it is important to activate the auto-mount feature.

Within the virtual machine, the shared folder will be on /media and the name of the folder will be the name you entered, preceded by sf_. For example, /media/sf_mydata. Please note that the path of the shared folder on the host and the virtual machine are different.

5 Launch the virtual machine

After closing the configuration window, in the VirtualBox interface, select sRNAtoolboxVM and click on Start button (green arrow). sRNAtoolboxVM will start in a new window. To log into the VM, enter your credentials:

  • User: srna
  • Password: srna

Optionally, you can change the password, by typing in a terminal:


Note that the virtual machine can access internet if the host machine is connected to the web. However, the VM is not accessible from outside and therefor a lax password should be not security issue.

6 Change keyboard layout and time zone

To change the keyboard layout, type the following command in a terminal of the sRNAtoolboxVM:

sudo dpkg-reconfigure keyboard-configuration

You will be asked the password for your user in the sRNAtoolboxVM (default: srna). Select your keyboard layout and ready.

To change your time zone, type the following command in a terminal of the sRNAtoolboxVM:

sudo tzselect

You will be asked the password for your user in the sRNAtoolboxVM (default: srna). Select your time zone and ready.