Welcome to the DataSHIELD installation instructions for Linux. Click below for the table of contents, specifying all the stages needed to get set up and ready to go.

Installing the Virtual Servers

Install VirtualBox

To run the virtual servers you will need to install VirtualBox (click here for more about what Virtualbox is).

There are three ways to install.

• Via web browser: go to the download page for linux distributions and choose the one corresponding to your machine.
• Via Ubuntu Software app: in the applications search, type "Ubuntu Software" (called "software store" in Ubuntu 18), then click on "install".
• Via terminal:

$ sudo apt-get install virtualbox

Download the Virtual Servers

Two virtual servers are available for you to test DataSHIELD with. The virtual servers require 4GB RAM each and about 5GB hard-disk space each.
You can download the VMs from google drive:

Import the Virtual Servers into VirtualBox

You will need to import the VMs into Virtualbox. Open Virtualbox, and in the top menu, on the left:

• File > Import Appliance...
• Navigate to the directory the VM files were saved to (e.g. Downloads...)
• Click "Next", to move onto "Appliance Settings"
• Nothing needs to be changed here, so click "Import"
  • the import should take around 1 minute
• Repeat for the second downloaded VM file.

Setting up the Virtual Servers

Setting up the VirtualBox network adapter

• On the VirtualBox "Tools" bar at the top of the list of Virtual Machines on the left hand side, left click Network and click Create
• Ensure the Adapter tab at the bottom of the screen has the following settings:
  • • Configure Adapter Manually options checked
    • IPv4 address: 192.168.56.1
    • IPv4 Network Mask: 255.255.255.0
    • IPv6 Prefix Length: 0
  • And ensure the DHCP Server tab at the bottom of the screen, next to Adapter;
    • Has Enable Server unchecked.
  • Click "Apply" to save any changed settings.
  • You can now safely close this Host Network Manager popup window
• Now on each of your imported Virtual Machines, one at a time, right click the VM and click on "Settings" at the top of the right click menu (icon is orange in colour):
  • Check that under the Network tab on the left hand side, the following options are set:
    
    • Adapter 1:  Attached to: NAT
    • Adapter 2: Attached to: Host-only Adapter
      • Name:  'vboxnet0'

Connect to the Virtual Servers

Boot the Virtual Machines

Now that the two virtual machines have been downloaded, imported and configured, it's time to launch them. What is happening when the VM launches is that it is booting up a mini-computer (within your computer) which plays the role of an Opal server as if it were online and you were remotely connecting to the data stored on it.

To start a VM (i.e. a Virtual Opal Server):

• When in VirtualBox:
• left-click on a server
• click on the green arrow that says start
  • (or just double click on the Opal server name).
• Repeat for the second VM

Depending on how powerful your computer is, the Opal servers may take a few minutes to boot and for Opal to start.

Now that your VMs are launched you should check they are ready to be used before getting set up in R.

Virtual Servers' IP addresses

By default, machines on the host-only network can be found at 192.168.56.xxx:

Your computer (the host) will be at 192.168.56.1
The virtual servers have been configured as follows:

• dstesting-100 – 192.168.56.100
• dstesting-101 – 192.168.56.101

Web Access to the Opal Server (How to look inside the VM)

The opal web interface is accessed in you browser. Simply type the IP address of the VM, followed by the port number.

For example: to access the web interface for dstesting-100, go to:

• http://192.168.56.100:8080

username: administrator
password: datashield_test&

When finished: Shutting down the Opal servers

Assuming no changes have been applied to the Virtual Opal Servers (which will be the case for general users) after you have finished your analysis, to shutdown the Opal server:

• click the cross at the top right of the window. This will give you a list of options for how to shutdown the machine:
• 

• Choose: Send the shutdown signal.

  Turing off a VM "abruptly" can cause problems, so please follow the specific shutdown instructions.

Setting up your R Session

Installing R in Ubuntu

How to check your Ubuntu version:

Open your Terminal, and past command

lsb_release -a

And take note of the number (20, 18, 16) next to "Release".

Now install R using the following instructions:

• If you are running Ubuntu 20.04 "Focal Fossa":
  • Open this link in a NEW TAB (right click → new tab, or middle mouse click) https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-20-04
• If you are running Ubuntu 18.04 "Bionic Beaver":
  • Open this link in a NEW TAB (right click → new tab, or middle mouse click) https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-18-04
• If you are running Ubuntu 16.04 "Xenial Xerus":
  • Open this link in a NEW TAB (right click → new tab, or middle mouse click) https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-16-04-2

Set-up R for DataSHIELD analysis

Install the Opal packages

Open an R Session (whether in terminal, RGui or RStudio), then run:

R
install.packages('DSI')
install.packages('DSOpal')
install.packages('DSLite')

install.packages(c('fields', 'metafor', 'ggplot2', 'gridExtra', 'data.table'))

Install the DataSHIELD client packages

install.packages('dsBaseClient', repos=c(getOption('repos'), 'http://cran.obiba.org'), dependencies=TRUE)

DataSHIELD R Package Manuals

See: Current release

Keeping up to date

Please see our keeping up to date wiki page in the user/analyst support section.

What's next?