List of Software and Web Applications

1. Plink

Plink can be downloaded from here.

Download the binary distribution for your system from the "Binaries" table, "Stable build" column. Then unzip the folder and move it to the training directory.

Direct links (as of 2024-06-06):

• Linux binary to use in WSL2
• Windows binary to use in cmd.exe / PowerShell
• MacOS users need Mac binary

Note: PLINK is not a regular app to be installed into Program Files. It is just a command-line executable. You only need to download it and make sure you have privileges to execute it (i.e. admin privileges).

To check installation, open PowerShell, navigate to the folder containing plink.exe and type:

			.\plink.exe --help
		

Alternatively, you can use cmd in the address bar:

1. From the Plink folder, go to the address bar and highlight the address.
2. Type cmd in the address bar.
3. Type .\plink.exe --help

Watch a video on how to install on Windows.

2. R

R can be downloaded from here.

For the mirror, use this link.

To install "source-only" packages on Windows:

You'll need Rtools from here.

• If your version of R is R-4.2.xx, install Rtools42.
• If your version of R is R-4.3.xx, install Rtools43.

3. R Packages on R-Studio

Install the following R packages in R-Studio:

• install.packages("qqman")
• install.packages("ggplot2")
• install.packages(c("dplyr", "glue", "reshape2"))
• install.packages(c("readr", "vroom", "openxlsx"))
• install.packages("BEDMatrix")
• install.packages("BiocManager") - To install packages from Bioconductor
• BiocManager::install("snpStats")
• install.packages(c("shinydashboard", "DT", "bslib", "rmarkdown"))

4. Optional Software

The following software are optional, but may be useful:

• Admixture
• GEMMA
• SnpEff and SnpSift

Post-Installation Check

1. Java

Check the version of Java by opening a PowerShell or Terminal and typing:

			java -version
		

2. TASSEL

Open TASSEL and use the tutorial dataset packaged within the Tassel folder.

3. RStudio

Open RStudio, and run the version command in the console.

Install the qqman package using the menu.

4. Powershell/Terminal

Open PowerShell (Windows) or Terminal (Mac) and note the current working directory by typing pwd then pressing Enter.

5. WSL

If you are on Windows, check the WSL version:

			wsl --version
		

			wsl --list
		

Software Installation Guide

WSL2

Helpful links:

• WSL Installation Guide
• About WSL

Make sure Windows is up to date. It is recommended to run Windows 10 version 2004 and higher (Build 1904 and higher) or Windows 11.

1. Go to Turn Windows feature on or off in the Control Panel.

2. Enable Windows Subsystem for Linux and Virtual Machine Platform.

3. Restart the computer.
4. Download the latest WSL2 kernel here.
5. Follow the instructions in the link for installation.

Ubuntu Installation

1. Go to the Microsoft store and search for Ubuntu.
2. Install Ubuntu 24.04.1 LTS.

Software (Install in Ubuntu)

FastQC

			sudo apt-get install fastqc
		

FastP

			sudo apt-get install fastp
		

BWA

			sudo apt-get install bwa
		

SAMtools

			sudo apt-get install samtools
		

BCFtools

			sudo apt install bcftools
		

JAVA Installation

Download the latest package (JDK24) for Linux / MacOS or use the following command:

			wget https://download.oracle.com/java/24/latest/jdk-24_linux-x64_bin.tar.gz
		

Place the file in your home directory or any directory you prefer (e.g., `/home/riza/`).

Unpack the tarball and set the environment variables as follows:

			tar zxvf jdk-24_linux-x64_bin.tar.gz
		

			nano ~/.bashrc
		

Add the following lines at the end of your ~/.bashrc file (edit the code according to the location of the file on your machine)

			export JAVA_HOME='/home/riza/jdk-24'
		

			export PATH=$JAVA_HOME/bin:$PATH
		

PICARD Installation

Download the latest jar file here or use:

			wget https://github.com/broadinstitute/picard/releases/download/3.3.0/picard.jar
		

Place the file in your home directory or any directory you prefer (e.g., `/home/riza/`).

Set the environment variable:

			nano ~/.bashrc
		

Add the following lines at the end of your ~/.bashrc file (edit the code according to the location of the file on your machine)

			export PICARD='/home/riza/picard.jar'
		

Verify installation:

			java -jar $PICARD
		

GATK4 Installation

Download the latest file here or use:

			wget https://github.com/broadinstitute/gatk/releases/download/4.6.1.0/gatk-4.6.1.0.zip
		

Place the file in your home directory or any directory you prefer (e.g., `/home/riza/`).

Set the environment variable:

			nano ~/.bashrc
		

Add the following lines at the end of your ~/.bashrc file (edit the code according to the location of the file on your machine)

			export GATK='/home/riza/gatk-4.6.1.0/gatk-package-4.6.1.0-local.jar'
		

Verify installation:

			java -jar $GATK
		

MacOS-specific

• Homebrew
• Follow installation instructions at the homepage of Homebrew
• Or on the Terminal app
• /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
• Run these two commands in your terminal to add Homebrew to your PATH:
• (echo; echo 'eval "$(/usr/local /bin/brew shellenv)"')
• eval "$(/usr/local/bin/brew shellenv)"
• In the terminal app
• brew install bwa
• brew install fastp
• brew install fasqc
• brew install samtools
• brew install bcftools
• brew install picard-tools