Skip to content

cli_guide.md

Latest commit

 

History

History
156 lines (108 loc) · 2.78 KB

cli_guide.md

File metadata and controls

156 lines (108 loc) · 2.78 KB
Raw

GenomeMCP CLI Guide

A beautiful command-line interface for genomic analysis.

Installation

# Quick install
./install.sh

# Or with pip
pip install genomemcp[cli]

# Development mode
./setup-dev.sh
source .venv/bin/activate

Commands

🔍 search — Search ClinVar

genomemcp search BRCA1
genomemcp search "Lynch Syndrome" --limit 20

📋 variant — Variant Report

genomemcp variant 12345
genomemcp variant 12345 --literature --max-articles 10

🧬 gene — Gene Information

genomemcp gene TP53
genomemcp gene BRCA1

📍 context — Genomic Context

genomemcp context BRCA1 150
# Returns: Position 150 falls within: Exon 2

🔬 pathway — Pathway Analysis

genomemcp pathway TP53
genomemcp pathway EGFR --visualize

👥 population — gnomAD Frequencies

genomemcp population 1-55516888-G-GA
genomemcp population 17-41245466-C-T

🔗 discover — Gene Discovery

genomemcp discover "Lynch Syndrome"
genomemcp discover "Cardiomyopathy" --max-genes 10

📚 evidence — Research Evidence

genomemcp evidence "Breast Cancer"
genomemcp evidence "Lynch Syndrome" --max-genes 5

🖥️ tui — Interactive Mode

genomemcp tui

TUI Keyboard Shortcuts:

  • s — Focus search
  • q — Quit
  • r — Refresh
  • ? — Help
  • Esc — Clear search

Global Options

genomemcp --version              # Show version
genomemcp --theme cyberpunk ...  # Set theme
genomemcp --no-banner ...        # Hide header

Themes

  • default — Balanced colors
  • cyberpunk — Magenta/cyan accents
  • professional — Blue tones
  • minimal — Subtle styling

🤖 chat — Local LLM Chat

Interact with GenomeMCP using natural language and local AI models (via Ollama).

# Start chat with default model (qwen2.5:7b)
genomemcp chat

# Use specific model
genomemcp chat --model llama3.1:8b

# Show tool calls (verbose mode)
genomemcp chat --verbose

Required: Ollama running locally.

📋 models — List Models

List available models in Ollama.

genomemcp models

🔬 research — Scientific Research (Denario)

End-to-end scientific research workflows powered by Denario agents. Note: Requires Python 3.12+.

# Initialize a new research project
genomemcp research init --phenotype "Lynch Syndrome"

# Generate novel research idea
genomemcp research idea

# Generate experimental methodology
genomemcp research method

# Run analysis and generate results/plots
genomemcp research analyze

# Write full LaTeX paper
genomemcp research paper --journal Nature

# Interactive guided mode
genomemcp research interactive

See the Research Guide for detailed workflows.