Introduction to Linux and R Justification for Linux

Introduction to Linux and R

Justification for Linux • Linux is one of several variants of Unix; Linux, Solaris, Mac. OS • Several “flavours” of Linux: eg Ubuntu, Debian, Fedora, Red. Hat • 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

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

Virtual Machines Windows Host Operating System Virtual Box Virtual machine Xubuntu Guest Operating System Docker Container Python Workflow for fast. Structure Other software eg: Beagle, Plink, vcftools etc Docker provides a way to run applications securely isolated in a container, packaged with all its dependencies and libraries. Docker is free from https: //docs. docker. com/ H 3 Africa project is developing workflows for GWAS for distribution on the Cloud in Docker Containers http: //h 3 abionet. org/17 -h 3 abionetcourses/h 3 abionet-coursesupcoming/266 -h 3 abionet-cloudcomputing-hackathon

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 and. Linux then Google “virtualbox cut and paste between host and guest” to get instructions

Getting a terminal To get the Application menu Right click on the desktop Or Alt-F 1

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

Lists, Arrays and Vectors Used for storing sets of similar information Zero based index Array of Integers One based index (R) Array of Strings 0 672 1 242 2 530 3 1 4 501 5 972 6 417 7 180 1 2 3 4 5 6 7 8 Apple orange mango melon banana pineapple guava 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 lemon

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.

Example bash shell script eucalypt="eucalypt. clean 3" #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. txt --allow-no-sex --out temp done To learn how to write loops in the bash shell Google ‘bash loops’

Excercises • Do the online Linux tutorials 1 -6 at http: //www. ee. surrey. ac. uk/Teaching/Unix/ • Complete the Rpractical. doc