vm_setup.md

Setting up the Linux VM

This process should take 15-20 minutes.

Step 1. Install the virtual machine image

There is a file called Genomics Ubuntu VM.ova in the C:\temp folder. Double click it, it will open up VirtualBox and ask if you want to Import the Virtual Appliance. Click Import.

This will take a few minutes to import.

If you don't have that file on your computer it can be downloaded from here.

Step 2. Configuration

We will be running some heavy analyses, so we want to make sure adequate computational resources are being provided to the virtual machine. Once it's imported select the new VM and click Settings.

We want to check that the number of processors available is set to 2:

And we want to make sure that 5 GB RAM are being allocated to the vitual machine:

Step 3. Login to the VM

The VM should load up. In normal use you will use the User1 login. But to setup we will use the admin login:

Username: admin

Password: Atlanta$Moon

You are now logged in! It should look like this:

You can make this 'full screen' by pressing right ctrl + f. You can get out of the fullscreen by pressing right ctrl + f again.

Step 4. Getting data and software

We need to download a script that will perform our setup.

This script will be downloaded the the Downloads directory.

wget https://gist.githubusercontent.com/explodecomputer/bbcfe22cce1658a717b30419b2d311d7/raw/f6c74718872b323646af71d4d937d4f742b00a45/setup.sh

Copy the above command by highlighting it, right click, select 'Copy'. Next, open up the the Terminal programme (it's in the side bar), and paste the command (right click in the window, select 'Paste').

Once it has been pasted into the command line, press enter. Once that is finished, run the following command:

sudo bash setup.sh

It will ask for your password. Type in Atlanta$Moon and press enter. This script will then run for about 10 minutes (depending on how fast your internet connection is). It is downloading the data files (less than 1GB), and installing some software.

Step 5. Restart the VM and log back in as 'user1'

Click the cog shaped button in the top right, choose 'Shutdown'.

Now login as 'user1'. The password is Florida$Sun. See the instructions here if you are unsure how to do this.

Step 6. Configure Atom

Atom and Konsole can talk to each other if you install the screen-send package. You can do this as follows:

1. Open Atom
2. Click 'Install a Package', then 'Open Installer'.
3. In the new tab search for screen-send, it should find the package. Click 'Install'.
4. Once installed click on the Packages tab on the left bar, find the 'screen-send' package, click settings, and change the 'Terminal Type' from iTerm 2 to Konsole. Now restart Atom.