Amina CLI

Run autonomous protein engineering workflows via AminoAnalytica's Amina CLI.

Documentation: CLI | Tools

Reference Loading

This skill uses progressive disclosure. Load references based on context:

At Session Start

When starting a new Amina session or first protein engineering request:

1. Read references/setup.md — Run through session initialization
2. Read references/usage.md — Load execution guidance for the session

Mid-Session Refresh

When you need a reminder on CLI usage, execution patterns, or agent behavior:

• Read references/usage.md only

When to Load References

Trigger	Action
Session start, first Amina request	Load both setup.md and usage.md
"How do I use amina...", CLI questions	Load usage.md
Job submission, workflow execution	Load usage.md if not already loaded
Environment issues, auth problems	Load setup.md

Quick Reference

# Essential commands
amina tools list                              # List all tools
amina run <tool> --help                       # Show parameters
amina run <tool> [params] -o <dir>            # Sync execution
amina run <tool> --background --job-name <n>  # Async execution
amina jobs cancel <id>                          # Cancel job (full refund)
amina jobs wait <id> && amina jobs download <id> -o ./

Key principle: Run commands automatically, complete workflows end-to-end, never ask unnecessary questions.