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AGOUTIC Launchpad: Dogme/Nextflow Job Execution Engine

Docs Current For: AGOUTIC 3.6.6
Service Version: 0.3.0
Status: Active Development

Overview

Launchpad is the execution engine for the AGOUTIC bioinformatics platform. It receives job requests from Cortex (the Agent Engine) and manages the execution of Dogme/Nextflow pipelines for genomic analysis.

Key Responsibilities

  • 🚀 Job Submission: Receive and queue Dogme pipeline jobs (DNA/RNA/cDNA)
  • 📊 Job Monitoring: Track job progress in real-time
  • 📝 Logging: Capture detailed execution logs
  • 🔍 Status Tracking: Maintain persistent job state in database
  • 📤 Result Retrieval: Return analysis outputs and reports
  • 🤝 Dual Interface: REST API + MCP Protocol for LLM agents

Architecture: Dual Interface

Launchpad provides both interfaces, allowing flexible integration patterns:

1. REST API (HTTP)

  • Port: 8003 (default)
  • Location: launchpad/app.py
  • Use Case: Web dashboards, external scripts, periodic polling.
  • Endpoints:
    • POST /jobs/submit - Submit job
    • GET /jobs - List jobs
    • GET /jobs/{uuid} - Get details
    • GET /jobs/{uuid}/logs - Stream logs

2. MCP Protocol (Model Context Protocol)

  • Port: 8002 (MCP-over-HTTP)
  • Location: launchpad/mcp_server.py
  • Use Case: LLM Agents (Cortex) directly controlling tools.
  • Tools:
    • submit_dogme_job: Generic submission wrapper
    • submit_dogme_nextflow: Low-level submission with config generation
    • check_nextflow_status: Query database for status
    • find_pod5_directory: Locate data files

Installation & Setup

Prerequisites

  • Python 3.10+
  • Nextflow (installed and in PATH)
  • Java 11+ (for Nextflow)

Quick Start

  1. Environment Setup:

    cd /path/to/agoutic
source load_env.sh

  2. Start the Server:

    # Starts both REST (8003) and MCP (8002) interfaces
./agoutic_servers.sh start launchpad

  3. Verify Status:

    curl http://localhost:8003/health
# Expected: {"status":"ok","version":"0.3.0",...}

Project Structure

  • app.py: FastAPI application entry point (REST).
  • mcp_server.py: FastMCP application (MCP-over-HTTP). Exposes /tools/schema endpoint for Cortex to fetch tool contracts.
  • mcp_tools.py: Logic for MCP tools integration.
  • nextflow_executor.py: Core logic for spawning and monitoring Nextflow processes.
  • models.py: SQLAlchemy models for DogmeJob and JobLog.
  • db.py: Database connection and CRUD operations.
  • config.py: Configuration for paths, reference genomes, and pipelines.

Development

Running Tests

pytest tests/launchpad -q

Manual Ops Scripts

Manual Launchpad helpers now live under scripts/launchpad/:

python scripts/launchpad/submit_real_job.py --url http://localhost:8001 --input /path/to/data --mode DNA
python scripts/launchpad/debug_job.py <run_uuid>