Install Linux on Windows

If you’re using Windows, it’s highly recommended to set up a Linux environment (such as Ubuntu) through the Windows Subsystem for Linux (WSL). Follow these steps to get started:

Step 1: Open Command Prompt and Run WSL Installation

wsl --install
  

• Follow the instructions to install the WSL virtual machine.
• You’ll be required to restart your computer during this process.
• After restarting, a terminal should appear.
• Set up a username and password for your new Ubuntu environment.

If you need more details, visit the official website: Install WSL

Step 2: Install Required Software Elements

Run the following commands to set up your session:

Add a complete library repository for Ubuntu

sudo add-apt-repository universe
sudo apt update
  

Install the needed libraries

Use the following commands to install git, bzip2, bwa, samtools, and blast:

sudo apt install git-all -y
sudo apt install bzip2 -y
sudo apt install bwa -y
sudo apt install samtools -y
sudo apt install ncbi-blast+ -y
  

You are all set. Continue to the Workflow page to begin the Worked Example.

Program Installation on a Mac using Homebrew

Step 1: Install Homebrew

Homebrew ("brew" for short) is an open-source software package management system that simplifies the installation of software on MacOS. For more details visit Homebrew. To install Homebrew on your Mac, run the following command:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
  

Once installed, Homebrew will encourage you to "add it to your path". Use the commands provided by Homebrew, which look similar to these:

echo 'eval "$(/opt/homebrew/bin/brew shellenv)"' >> /Users//.zprofile
eval "$(/opt/homebrew/bin/brew shellenv)"
  

Step 2: Program Installation

You can now install `samtools`, `blastn`, and `bwa` using the following commands:

brew install samtools
brew install blast
brew install bwa
  

To manually install BLAST, download the latest disk image (dmg) from the following link: NCBI BLAST+ Download

You are all set. We will begin the Worked Example in the field starting on the Workflow page.