Installing the Virtual Servers

Install VirtualBox

To run the virtual servers you will need to install VirtualBox.

On Ubuntu, type in the Ubuntu Software store "VirtualBox" or in the 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:

File > Import Appliance...

Setting up the Virtual Servers

Setting up the VirtualBox network adapter

• On the VirtualBox top menu, at the far right, go to the tab Global Tools, click the drop down and select Host Network manager.
  
  • Ensure the Adapter tab at the bottom of the screen has the following settings:
    
    • IPv4 address: 192.168.56.1
    • IPv4 Network Mask: 255.255.255.0
    • IPv6 Prefix Length: 0
  • And ensure the DHCP Server tab, next to Adapter, at the bottom of the screen:
    • Has Enable Server unchecked.
  • Click "Apply" to save any changed settings.
• Now click on Machine Tools at the top of the screen, next to "Global Tools", and select from drop down Details.
  • Selecting each VM in turn, check that under the Network tab, the following options are fulfilled:
    
    • Adapter 1: Intel PRO/1000 MT Desktop (NAT)
    • Adapter 2: Intel PRO/1000MT Desktop (Host-only Adapter, 'vboxnet0')

Once the machines have been started you can login directly, for tasks such as reviewing logs produced on the server, instructions here.

Connect to the Virtual Servers

Starting the Opal test servers

To start an Opal server just open VirtualBox click on a server and click on the green arrow that says start (or just double click on the Opal server name).

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

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

Opal web access

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 for the non-secure connection
• https://192.168.56.100:8443 for the secured connection

username: administrator
password: datashield_test&

Shutting down the Opal servers

If no changes to Opal servers (e.g. for general users), when 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:
• 

• Select Power off the machine.

  Turing off a VM "abruptly" can cause problems, hence the specific shutdown instructions.

Setting up your local machine to use the VMs

Installing R in Ubuntu

Use:

$ sudo -i

to run the following commands as root.

Add a CRAN R repository

Add the following to the /etc/apt/sources.list file, this gives a newer version of R than the one that is in Ubuntu's repositories. Note: the CRAN R repository you add depends on the Ubuntu release you are running:

• If you are running Ubuntu 18.04 "Bionic Beaver":

# add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'

• If you are running Ubuntu 16.04 "Xenial Xerus":

# add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/'

You may wish to select a different CRAN mirror, closer to your location.

You can find further details about installing R in Ubuntu on the CRAN website.

Add the public key for the CRAN R repository to your list of keys

# apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9

Install R

(Plus one dependency, needed for installing R packages)

• "apt-get install r-base" will install the latest version of R

# apt-get update
# apt-get install r-base r-base-dev libcurl4-openssl-dev

# apt-get install libxml2-utils
# apt-get install libxml2-dev
# apt-get install libssl-dev
# apt-get install libgit2-dev

Set-up R for DataSHIELD analysis

You shouldn't do this as root, instead run command:

# exit

or use the ctrl + D hotkey combination.

Install the Opal packages

Do this either in R environment of terminal (see below), or by getting the RStudio app through the ubuntu application store, then running the below commands prefixed with ">" in the terminal.

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

Install the DataSHIELD client packages

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

> q()

DataSHIELD R Package Manuals

See: Current release

Keeping up to date

If you have installed the DataSHIELD client packages using the method above (that is, within R using install.packages and specifying the Obiba repository), then you can update those client packages as follows:

# R
> update.packages(repos='http://cran.obiba.org')