oxo-call 0.3.0

Model-intelligent orchestration for CLI bioinformatics — call any tool with LLM intelligence
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<div align="center">

# oxo-call

**Model-intelligent orchestration for CLI bioinformatics**

[![CI](https://github.com/Traitome/oxo-call/actions/workflows/ci.yml/badge.svg)](https://github.com/Traitome/oxo-call/actions/workflows/ci.yml)
[![Crates.io](https://img.shields.io/crates/v/oxo-call.svg)](https://crates.io/crates/oxo-call)
[![License](https://img.shields.io/badge/license-Academic%20%7C%20Commercial-blue.svg)](#license)
[![Rust](https://img.shields.io/badge/rust-2024_edition-orange.svg)](https://www.rust-lang.org/)
[![Platform](https://img.shields.io/badge/platform-Linux%20%7C%20macOS%20%7C%20Windows-lightgrey.svg)](#data-storage)
[![Docs](https://img.shields.io/badge/docs-guide-blue.svg)](https://traitome.github.io/oxo-call/documentation/)

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](https://traitome.github.io/oxo-call/documentation/)**

</div>

---

## 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

```bash
cargo install oxo-call
```

See the [Installation guide](https://traitome.github.io/oxo-call/documentation/tutorials/installation.html) for pre-built binaries and source builds.

### 2. Get a license

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

```bash
# 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

```bash
# 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](https://traitome.github.io/oxo-call/documentation/tutorials/configuration.html).

---

## 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](https://traitome.github.io/oxo-call/documentation/tutorials/installation.html) | Install, configure, and run your first command |
| [Tutorials](https://traitome.github.io/oxo-call/documentation/tutorials/first-command.html) | Hands-on walkthroughs: BAM processing, RNA-seq, workflows |
| [How-to Guides](https://traitome.github.io/oxo-call/documentation/how-to/add-tool-docs.html) | Practical recipes for common tasks |
| [Command Reference](https://traitome.github.io/oxo-call/documentation/commands/run.html) | All commands, options, and examples |
| [Architecture](https://traitome.github.io/oxo-call/documentation/reference/architecture.html) | 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](LICENSE-ACADEMIC) | **Free** — signed license file required |
| Commercial / production | [LICENSE-COMMERCIAL](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**.