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Setup Guide

Before You Arrive

Complete these setup steps at least one week before the course begins.

1. System Requirements

Minimum Specifications

  • RAM: 8GB (16GB recommended)
  • Storage: 50GB free space
  • OS: Linux, macOS, or Windows 10/11
  • Internet: Stable broadband connection

Operating System Setup

# Update package list
sudo apt update && sudo apt upgrade -y

# Install essential tools
sudo apt install -y git curl wget build-essential

# Install Homebrew (if not already installed)
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

# Install essential tools
brew install git curl wget
  1. Install Git Bash: Download from git-scm.com
  2. Enable WSL2 (optional but recommended): 
    wsl --install
  3. Install Windows Terminal from Microsoft Store

2. Git Configuration

Configure Git with your information:

git config --global user.name "Your Name"
git config --global user.email "your.email@example.com"
git config --global init.defaultBranch main

Verify configuration: 

git config --list

3. SSH Setup

Generate SSH key for secure connections:

# Generate SSH key pair
ssh-keygen -t ed25519 -C "your.email@example.com"

# Start SSH agent
eval "$(ssh-agent -s)"

# Add key to agent
ssh-add ~/.ssh/id_ed25519

# Display public key (copy this for later use)
cat ~/.ssh/id_ed25519.pub

4. Text Editor

Choose and install a text editor:

# For vim users
sudo apt install vim  # Linux
brew install vim      # macOS

# For nano users (usually pre-installed)
which nano

5. Test Your Setup

Basic Command Line Test

# Check versions
git --version
curl --version
wget --version

# Test directory operations
mkdir test_setup
cd test_setup
echo "Hello World" > test.txt
cat test.txt
cd ..
rm -rf test_setup

Git Test

# Clone a test repository
git clone https://github.com/CIDRI-Africa/microbial-genomics-training.git
cd microbial-genomics-training
ls -la
cd ..
rm -rf microbial-genomics-training

6. Course-Specific Setup

HPC Access (If Provided)

You will receive: - SSH connection details - Username and login instructions - VPN setup (if required)

Docker/Singularity (Optional)

For local analysis (advanced users):

# Linux
sudo apt install docker.io
sudo usermod -aG docker $USER

# macOS
# Download Docker Desktop from docker.com

# Test installation
docker --version
docker run hello-world

# Linux (Ubuntu/Debian)
sudo apt install singularity-container

# Test installation
singularity --version

7. Download Course Materials

One week before the course:

# Create course directory
mkdir -p ~/microbial-genomics-course
cd ~/microbial-genomics-course

# Clone course repository
git clone https://github.com/CIDRI-Africa/microbial-genomics-training.git

# Check repository contents
cd microbial-genomics-training
ls -la

8. Pre-course Data Download

Large datasets will be provided via: - Shared storage on HPC systems - Cloud storage links (Google Drive/Dropbox) - Direct download scripts (provided before course)

9. Connectivity Test

SSH Connection Test

# Test SSH connectivity (replace with provided details)
ssh -T username@hostname

# If successful, you should see a welcome message

Internet Speed Test

Ensure you have adequate bandwidth: - Minimum: 10 Mbps download - Recommended: 50+ Mbps download - Upload: 5+ Mbps for video calls

10. Backup and Recovery

Create Backups

# Backup SSH keys
cp ~/.ssh/id_ed25519* ~/backup_location/

# Backup Git configuration
git config --list > ~/git_config_backup.txt

Recovery Commands

Keep these handy in case of issues: 

# Reset Git configuration
git config --global --unset-all user.name
git config --global --unset-all user.email

# Regenerate SSH keys
rm ~/.ssh/id_ed25519*
ssh-keygen -t ed25519 -C "your.email@example.com"

Troubleshooting

Common Issues

Git Issues

# Fix permission issues (Linux/macOS)
sudo chown -R $USER ~/.ssh/

# Reset SSH agent
eval "$(ssh-agent -k)"
eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_ed25519

Network Issues

# Test connectivity
ping google.com
curl -I https://github.com

# Check proxy settings (if behind firewall)
echo $http_proxy
echo $https_proxy

Permission Issues (Linux)

# Fix common permission problems
sudo chown -R $USER:$USER ~/
chmod 755 ~/.ssh
chmod 600 ~/.ssh/id_ed25519
chmod 644 ~/.ssh/id_ed25519.pub

Getting Help

Before the Course

Documentation

Final Checklist

Before the course starts, verify:

  • Git installed and configured
  • SSH key generated and working
  • Text editor installed and functional
  • Course repository cloned
  • HPC access tested (if provided)
  • Internet connection stable
  • Backup of important configurations created

Day 1 Preview

On the first day (September 1, 2025), we'll: 1. Course introductions and welcome session 2. Overview of clinical pathogens and genomic surveillance 3. Sequencing technologies and data types overview 4. Hands-on PubMLST database exploration 5. Command line interface basics and R environment setup

Come prepared with your laptop and the software installed above. Don't worry if you encounter setup problems – we'll troubleshoot together during the session!