🐢> Shelley Bio

A bioinformatics tool finder and module builder for CVMFS-hosted containers on the (to be renamed) bioimage

Shelley-bio helps researchers using (to be renamed) bioimage virtual machine image on Nirin and Nectar research cloud platforms. They can use shelley-bio to discover, query, and deploy bioinformatics software from CVMFS (CernVM File System) repositories. It provides both interactive and programmatic interfaces for finding tools, building Lmod modules, and managing containerised workflows.

Features

• Tool Discovery: Search for bioinformatics tools by name or function
• Container Management: Query available container versions from CVMFS
• Module Building: Automatically generate Lmod modules for tools
• Interactive CLI: User-friendly command-line interface
• Batch Operations: Build multiple modules simultaneously
• MCP Integration: Model Context Protocol server for AI assistants

Quick Start

Installation

shelley-bio is installed as part of the BioShell.

# Clone the repository
git clone https://github.com/Sydney-Informatics-Hub/shelley-bio.git
cd shelley-bio

# Install dependencies
pip install -r requirements.txt

Basic Usage

# Find a specific tool
shelley-bio find fastqc

# Search by function
shelley-bio search "quality control"

# List available versions
shelley-bio versions samtools

# Build an Lmod module
shelley-bio build samtools

# Build a specific version
shelley-bio build samtools/1.21

# Interactive mode
shelley-bio interactive

Batch Operations

# Build multiple modules at once
shelley-bio-batch samtools fastqc bowtie2

# Build specific versions
shelley-bio-batch samtools/1.21 fastqc/0.12.1

Documentation

• Command Reference - Complete CLI documentation
• Developer Reference - API and development guide
• Query Guide - Advanced search techniques

Architecture

Shelley Bio is organised as a modular Python package:

shelley_bio/
├── client/          # CLI interface and client logic
├── server/          # MCP server for AI integration
├── builder/         # CVMFS module building functionality
├── scripts/         # Batch operations and utilities
└── utils.py         # Shared utilities and constants

Requirements

• Python 3.8+
• Access to CVMFS repositories (typically /cvmfs/singularity.galaxyproject.org/)
• Lmod (for module management)
• Singularity/Apptainer (for container execution)

TODO Migration from bio-finder

This is a migration from the original bio-finder codebase, the core functionality remains the same with these improvements:

• Professional packaging: Installable via pip
• Improved CLI: Better user experience and error handling
• Modular design: Clean separation of concerns
• Enhanced documentation: Comprehensive guides and references
• Batch operations: Efficient multi-tool module building

Command Changes

bio-finder	shelley-bio
./biofinder find fastqc	shelley-bio find fastqc
./biofinder build samtools	shelley-bio build samtools
./build-modules.sh tool1 tool2	shelley-bio-batch tool1 tool2