1. Introduction to Linux and R

2. Justification for Linux
Linux is one of several variants of Unix; Linux, Solaris, MacOS
Several “flavours” of Linux: eg Ubuntu, Debian, Fedora, RedHat
Many Bioinformatics tools are only available for Linux
All large computers that are analysing large data sets run Unix
There are many commands and programs for managing large files
You can run a linux machine from anywhere,
If you have a large dataset that you cannot analyse on your laptop you can run it on a linux machine on another continent from your laptop

3. Learning Linux
Graphical interfaces available but we use the command line
Can access remote Linux machines from a Windows machine with ”putty” available from
Much to learn but a lot of help on the internet

4. Virtual Machines Windows Host Operating System
Docker provides a way to run applications securely isolated in a container, packaged with all its dependencies and libraries.
Virtual Box Virtual machine
Xubuntu Guest Operating System
Docker is free from
Docker Container
H3 Africa project is developing workflows for GWAS for distribution on the Cloud in Docker Containers
Python Workflow for fastStructure
Other software eg: Beagle, Plink, vcftools etc

5. Cut and Paste Between Windows and Linux
The most recent set linux installation notes has instructions for enabling cut and paste between Windows and Linux
If you have already done the installation but not enabled cat andpaste between Windows andLinux then Google “virtualbox cut and paste between host and guest” to get instructions

6. Getting a terminal To get the Application menu
Right click on the desktop Or
Alt-F1

7. R R is a programming language popular with statisticians
Many Bioinformatics packages written in R
As a programming language R is complex to learn
A very little knowledge of R is sufficient to run many R packages
We will mainly use R because it can generate good graphics
You should have installed R on your computers
There is a lot of help online
Plink is one program with many options R is a programming language in which anyone can write a program

8. Lists, Arrays and Vectors
Used for storing sets of similar information
Zero based index 1 2 3 4 5 6 7
Array of Integers
672
242
530
501
972
417
180
One based index (R) 8
Array of Strings
Apple
orange
mango
melon
banana
pineapple
guava
lemon
If I enter Fruit[2] the program will return orange
If I enter Fruit[2] = “melon” the program will change the contents of cell 2 to melon
The R tutorial will teach you how to create vectors and extract data from them in R.
Arrays can have many dimensions.
In R multi-dimensional vectors are called matrices.
Other languages use the same concept but different syntax

9. Bash scripting
The shell is an application that allows users to communicate with the computer.
The “bash” shell is the most widely used shell for Linux
The shell can be used to write simple programs or shell scripts
We will use a couple of scripts to run the same command many times each time with different parameters.
Scripts are very fussy about exact use of capitals and punctuation
Bad things can happen if you copy from word documents into linux commands. Punctuation may need to be reentered.

10. Example bash shell script
eucalypt="eucalypt.clean3"
#Begininging of loop
for first in bh br cr dr kh lj lr qv rt do
grep $first ${eucalypt}.ped | awk '{print $1, $2, $1}' > within.txt
plink --file $eucalypt --fst --within within.txt --allow-no-sex --out temp
done
To learn how to write loops in the bash shell Google ‘bash loops’

11. Excercises
Do the online Linux tutorials 1-6 at
Complete the Rpractical.doc