Before the workshop, we require that all students have a working Unix command line interface. Additionally, we ask that students install the IGV Genome Browser software for the visualization portion of the workshop. Without these two requirements, it will be impossible for students to carry out the exercises and practicals of the workshop.

We have prepared this brief guide so students can install the required software in advance. This tutorial will be mostly focused on Windows users, since MacOS and Linux already a working Unix command line installed by default. However, all users should download and install IGV before the workshop.

If you have any problem installing these tools, please come to one of our open-door sessions on Thursdays from 3-4pm. Otherwise, we will also be hosting a troubleshooting session on the first day of the workshop, from 8-9am, so if you still have issues, be sure to arrive early to the workshop.

IGV Install Guide

The Integrative Genomics Viewer (IGV) is a graphical, high-performance visualization tool for genomics data. It supports many types of files, including BAM and BigWig which are some of the most common file types for NGS. It is developed and maintained by the Broad Institute and is Open-Source and released under an MIT License, which means it can be used for free. To install, follow these instructions:

  1. Make sure you have Java 8 installed in your computer. IGV will not work with Java 9 or above. If you don’t have Java 8, use the following link to download and install it, before you try to install IGV.

  2. Go to the IGV download page and follow the instructions depending on your OS:
    • MacOS users: download the first file. Unzip it, and move it to the Applications folder. Double-click the icon to run the program.
    • Windows users: download the second file. Unzip it and double click the igv.bat file to start IGV. A black console window will open, follwed by the IGV application.
    • Linux users: download the third file. Unzip it, and launch IGV from the command line by following the instructions in the README file. Additionally, a development version can be cloned from the following GitHub Repository using the command git clone https://github.com/igvteam/igv.git.

If you run into problems installing IGV, please try a different installation method or come to one of our Open-Door sessions.

Command Line Install Guide for Windows Users

Windows users have three main options to get a working Unix command line, you should chose one and install it before the workshop:

Installing Ubuntu on Windows

This feature is only available for 64-Bit Windows 10 users. If you are running an older version of Windows, or if you are running the 32-Bit version of Windows 10, please chose one of the other two options available below. This tutorial is a summarized version of the guide by HowToGeek.com.

  1. Go to Control Panel > Programs > Turn Windows Features On Or Off and click on the Windows Subsystem for Linux option to enable it. Then click the OK button.
Windows Features Panel

  1. Restart your computer.

  2. After your computer has restarted, click the Start Menu to go to the Microsoft Store and from there search for “Linux”.

  3. You should see a result called Linux on Windows, select it and click Get the apps.

Windows Store Search Result
  1. A new window will open displaying all the available Linux environments. Chose Ubuntu and then click the Get or Install button, to install the application just as you would any other application.
Install Ubuntu

  1. An Ubuntu shortcut will now appear in the Start Menu. Click it to open the Ubuntu command line.

  2. The fisrt time you open Ubuntu, you will be prompted to create a username and password for your Ubuntu account. These can be the same as your Windows credentials, or they can be completely different, it is up to you. However, you need to remember your Ubuntu username and password to use the command line.
    • When typing your password, it is normal not to see anything displayed on the screen. Don’t worry, your keystrokes are being recorded, but passwords are never displayed in the command line for your privacy and protection.

  3. We also recommend updating the Ubuntu installation once you have installed it, to make sure all packages are up-to-date. To do that, open the Ubuntu command line and type (you might be prompted to write your Ubuntu password):

    sudo apt update
sudo apt upgrade

If you run into any issues when installing or updating Ubuntu on Windows, please consult this troubleshooting guide provided by Microsoft.

Installing Cigwin

Cigwin is a good alternative to Ubuntu on Windows, especially for older systems or systems running a 32-bit version of Windows. It is a program that collects a large number of Unix tools so that they can be run on Windows. It comes with a pre-defined set of tools, which cannot be modified, so it will not allow users to install custom Unix software. However, for the purposes of this workshop it should be more than enough. To install Cigwin, follow these instructions:

  1. Download the appropriate setup...exe file from the Cigwin download page. Make sure that the version being downloaded is the appropriate one based on the version of Windows (64-bit or 32-bit).

  2. After downloading, double-click on the setup...exe file to run the installer, follow its instructions. By default, Cigwin will do a minimal base package install, which means that only a small portion of important tools are installed, taking up only about 100Mb. Additional packages can be selected by category during the setup, but the minimal base installation is enough for the purposes of this workshop. Do not install all the packages included in the setup, since most of them are not required and doing this will result in a download of tens of Gigabytes of data.
    • Be warned that some old anti-virus software can prevent Cigwin from installing properly. If you have installation problems, consider disabling your anti-virus during the Cigwin setup.

  3. Once the setup is finished, click on the Cigwin icon in the Start Menu to open and run Cigwin.

If you have any issues installing or running Cigwin, we recommend that you check their troubleshooting site.

Installing PuTTY

If you just want an SSH client to connect to a remote machine, a simple option is to install PuTTY. To clarify, PuTTY will not install a fully working command line, it will just let you connect to another server where you can run Unix tools. If you want to be able to run Unix tools in your local machine, a better solution might be to install an actual command line interface such as the ones explained above. However PuTTY should be enough to carry out the exercises of this workshop. To install PuTTY follow these instructions:

  1. Download the most recent version of the PuTTY package files (MSI or Windows Installer) from the PuTTY website. Make sure you are downloading the version that is appropriate for your version of Windows (32-bit or 64-bit).

  2. Once you have downloaded the .msi file, double click on it and follow the instructions on the Installer.

  3. When opening PuTTY for the first time, you will see a dialog box. From this dialog, you can control the connection to a server using a few basic parameters:
    • In the “Host Name” box, enter the server address of the host you want to connect to (for example mp2.ccs.usherbrooke.ca).
    • In the “Connection Type” menu, select SSH. This will automatically change the “Port” box, so you don’t need to change the Port setting yourself.
    • Press the “Open” button and PuTTY will begin trying to connect you to the server.
    • If it is the first time you connect to a server, you will probably see a message that says The server's host key is not cached in the registry..., if you are connected to a trusted server (such as the Compute Canada servers), type Yes to continue with the connection.
    • After this, you will be prompted for your username and password. Use the username and passwords assigned to you by the owner of the host server (in the case of Compute Canada, these will be your Compute Canada username and password).
      • If you make a mistake typing your username, you will need to close PuTTY and try again. You will have several attempts to write your password, so if you make a mistake once, you can try again.

If you have any issues installing or running PuTTY, we recommend you check their troubleshooting site.