Stargazer¶

Stargazer is a bioinformatics pipeline framework built on Flyte v2. It provides a library of composable tasks for common bioinformatics operations and exposes them through an MCP server that any AI-powered client can consume.

How It Works¶

1. Assets carry structured metadata that describes every file's role in the system — reference genomes, read pairs, alignments, variant calls
2. Tasks are atomic operations that fetch assets, run bioinformatics tools, and produce new assets
3. Workflows compose tasks into end-to-end pipelines (e.g., germline variant calling for a cohort)
4. MCP server exposes tasks, workflows, and storage as tools that LLM clients can invoke

Interface¶

Stargazer is used through the MCP server — bring your own MCP-compatible client (Claude Code, OpenCode, Cursor, etc.) and connect to stargazer serve. Tasks and workflows can also be managed directly via the Flyte CLI.

Documentation¶

• Getting Started — go from zero to running your first workflow
• Architecture — how the system is designed and why
• Guides — step-by-step walkthroughs for common tasks
• API Reference — auto-generated from docstrings