oxo-call

Model-intelligent orchestration for CLI bioinformatics

Describe your task in plain language — oxo-call fetches the tool's documentation, grounds the request with a built-in skill, and asks your LLM backend to generate the exact flags you need.

→ Full documentation, tutorials, and how-to guides: traitome.github.io/oxo-call/documentation

What is oxo-call?

oxo-call is an AI-powered CLI assistant for bioinformatics. Instead of memorizing hundreds of flags across dozens of tools, you describe what you want to accomplish — oxo-call translates that into a correct, grounded command.

  Natural-language task  ──▶  Documentation + Skill  ──▶  LLM  ──▶  Exact command

🧠 LLM-powered — GitHub Copilot, OpenAI, Anthropic, or local Ollama
📚 Docs-grounded — tool --help output is cached and injected before every LLM call
🎯 Skill system — built-in expert knowledge for 150+ bioinformatics tools
🔄 Workflow engine — native DAG-based pipelines with Snakemake/Nextflow export
🔍 Dry-run mode — preview every command before it runs
📜 History — every execution is logged with provenance metadata

Quick Start

1. Install

cargo install oxo-call

See the Installation guide for pre-built binaries and source builds.

2. Get a license

A signed license is required for core commands. Academic licenses are free.

# Apply at: https://github.com/Traitome/oxo-call#license
# Then place your license file or set the environment variable:
export OXO_CALL_LICENSE=/path/to/license.oxo.json

3. Configure your LLM and run

# GitHub Copilot (default)
oxo-call config set llm.api_token <your-github-token>

# Preview a command without running it
oxo-call dry-run samtools "sort input.bam by coordinate and output to sorted.bam"
# → samtools sort -o sorted.bam input.bam

# Execute a command
oxo-call run bwa "align reads.fastq to reference.fa using 8 threads"

# Run a built-in workflow pipeline
oxo-call workflow dry-run rnaseq

For OpenAI, Anthropic, Ollama, and full configuration details, see the Configuration guide.

Documentation

The full documentation is a hands-on tutorial book covering everything from first steps to advanced workflow design:

Section	What you'll learn
Getting Started	Install, configure, and run your first command
Tutorials	Hands-on walkthroughs: BAM processing, RNA-seq, workflows
How-to Guides	Practical recipes for common tasks
Command Reference	All commands, options, and examples
Architecture	How oxo-call works under the hood

License

Dual License — Academic Free / Commercial Per-Organization

Use case	License	Cost
Academic research, education, personal non-commercial	LICENSE-ACADEMIC	Free — signed license file required
Commercial / production	LICENSE-COMMERCIAL	USD 200 — per-org, one-time fee

Apply for an academic license or contact w_shixiang@163.com for commercial licensing.

A public test license for evaluation is available at docs/public-academic-test-license.oxo.json.

Skill files contributed to the community registry are licensed under CC-BY-4.0.

oxo-call 0.4.0