This PR transforms the OCEAN repository into a comprehensive template system that enables researchers to quickly create genomic data platforms for any species. The original OCEAN platform was specifically designed for Ostrea chilensis research, but this implementation generalizes it while preserving all existing functionality.

Key Features

🔧 Template Configuration System

• YAML-based configuration: Single template-config.yml file controls all species-specific content
• Automated file generation: setup-template.py script processes Jinja2 templates to generate complete projects
• Flexible customization: Easy modification of species names, data sources, branding, and population studies

📁 Template Components

• Quarto page templates: Homepage, about page, data exploration, and genome browser pages
• JBrowse configuration template: Customizable genome assemblies and track configurations
• Website configuration template: Navigation, themes, and GitHub integration
• Example configurations: Working Arabidopsis thaliana example demonstrates plant genomics adaptation

🧬 Species Adaptation Demo

The template system successfully generates platforms for different organisms:

# Original: Ostrea chilensis (marine)
species:
  scientific_name: "Ostrea chilensis"
  common_name: "Chilean flat oyster"

# Template adaptation: Arabidopsis thaliana (plant)  
species:
  scientific_name: "Arabidopsis thaliana"
  common_name: "thale cress"

Generated websites automatically update:

• Species-specific branding and terminology
• Custom data source URLs
• Tailored population/study information
• JBrowse genome browser configurations

📖 Comprehensive Documentation

• README.md: Complete setup and usage instructions
• TEMPLATE-GUIDE.md: Detailed customization guide with examples
• Example configurations: Arabidopsis thaliana demonstrates cross-kingdom adaptation

Usage

Creating a new genomic platform is now a simple 3-step process:

# 1. Customize configuration
cp template-config.yml my-species-config.yml
# Edit species information, data URLs, etc.

# 2. Generate project files  
python setup-template.py my-species-config.yml

# 3. Build and deploy
cd quarto && quarto render

Impact

This template system dramatically reduces the barrier to creating sophisticated genomic data platforms. Research groups can now leverage OCEAN's proven architecture (Quarto + JBrowse + R integration) for their own species without starting from scratch, enabling faster scientific discovery and data sharing across the genomics community.

All original OCEAN functionality is preserved and the platform continues to work exactly as before for Ostrea chilensis research.

Fixes #1.

💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.