Installing Ubuntu Linux for running genetic analysis software

Jurg Ott / 4 June 2016

Many software packages for genetic analysis (sequence analysis, GWAS, etc.) run better under Linux than Windows, or run only in Linux. Ubuntu is a convenient desktop implementation of Linux suitable for these programs (personally, I like Kubuntu better than plain Ubuntu). This document provides guidelines on how to install the current Ubuntu version on a Windows laptop or desktop PC. For courses, please use an Ubuntu version in English. Below, the terms folder and directory are used equivalently. It is assumed that you use the Firefox web browser (default in Ubuntu Linux).

1. Installing Ubuntu

1.1 Running Ubuntu as a Windows program

The easiest and strongly recommended approach is to install Ubuntu under Windows. If you ever make a terrible mistake and cannot correct it, it will be easy to remove Ubuntu (via “Installed Programs” in the Control Panel) and re-install it. You can switch between Windows and Ubuntu by rebooting.

To prepare your laptop (or desktop) for installation, make sure you have sufficient space (> 10 GB) on your installation disk. This may be (1) an internal disk (any disk is fine) or (2) an external disk like a USB disk of 8 GB or preferably 16 GB disk space. Option (2) may be slightly slower than option (1), but option (2) has the advantage that you have access to all your other disks from within Ubuntu. For example, if your Ubuntu system will reside on disk C:, with option (1), you will be unable to “see” your files on disk C:. Also, run your disk defragmenter prior to installing Ubuntu.

The recommended installation approach is to download the wubi.exe file to your PC and run it by double-clicking on it. It will download all necessary files from the internet. Make certain you are connected to the internet with a cable connection rather than wireless; wifi is ok if your laptop connects to wifi automatically after rebooting. On the initial screen, the wubi program will ask you for the installation disk. Here is where you decide whether to follow option (1) or (2). You will also be asked to provide a user name and password. The program will propose a user name based on information in your PC – it is recommended that you accept this proposed user name rather than inserting another name. If you do the latter, you will have two user names but the one originally proposed by the system will be invisible. Underneath your user name, the program will propose a name for the Ubuntu system; choose a short name because in terminal windows you will be identified as username@system.

It is also convenient to have the system log you in automatically. Do this by clicking on System Settings (one of the items on the left side panel), then click on User Accounts, and Unlock. Then change automatic login to ON.

1.2 Running Ubuntu in a virtual drive

Installing virtualbox by Oracle in Windows allows you to run other operating systems at the same time as Windows (or install virtualbox in Linux to run Windows). This is probably the most efficient solution and you don't need to reboot for switching between Windows and Ubuntu, but it requires quite a bit of computing power.

1.3 Running Ubuntu from a USB flash disk

You may want to download an Ubuntu iso file and “burn” it to a USB (memory) stick. Then try running Ubuntu from the USB stick. This may be the simplest solution and will not make changes to your lapop but whatever you in that Ubuntu session will be lost after you exit, and some programs cannot be installed in Ubuntu while it is being run from a USB flash drive.

2. Software

plink 1.07

While in Ubuntu, visit http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml#download and click on plink-1.07-i686.zip to download the installation package. By default, Firefox will save the file in the ~/Downloads folder. To see this file, click on Home Folder (left side panel, second from the top), then double-click on Downloads. Now double-click on the downloaded file name, which will open a new window showing you the contents of the zip file, that is, a folder called plink-1.07-i686. Drag this folder back into the Downloads folder and close the newly opened window. Open a terminal session (ctrl-alt-T), type cd Downloads, then cd plink-1.07-i686, and ls. You should then see the plink program in green. Type sudo mv plink /usr/local/bin, which will require password confirmation. Now type plink; you should see messages by the plink program on the screen but it will not do anything as there is no input file.

plink 1.9

This program version, sometimes called plink2, is much faster than plink 1.07. Also, a few analyses run slightly different in version 1.9 than 1.07. It is recommended to only use plink 1.9 (plink2).