oxo-call 0.11.0

Model-intelligent orchestration for CLI bioinformatics — call any tool with LLM intelligence
Documentation
# Installation

oxo-call can be installed through multiple channels depending on your needs.

## From GitHub Releases (Pre-built Binaries) — Recommended

Pre-built binaries are the easiest way to get started. Download from the [Releases page](https://github.com/Traitome/oxo-call/releases):

1. Download the archive for your platform:

| Platform | Architecture | File |
|----------|-------------|------|
| Linux | x86_64 | `oxo-call-vX.Y.Z-x86_64-unknown-linux-gnu.tar.gz` |
| Linux | aarch64 | `oxo-call-vX.Y.Z-aarch64-unknown-linux-gnu.tar.gz` |
| Linux (musl) | x86_64 | `oxo-call-vX.Y.Z-x86_64-unknown-linux-musl.tar.gz` |
| Linux (musl) | aarch64 | `oxo-call-vX.Y.Z-aarch64-unknown-linux-musl.tar.gz` |
| macOS | x86_64 (Intel) | `oxo-call-vX.Y.Z-x86_64-apple-darwin.tar.gz` |
| macOS | aarch64 (Apple Silicon) | `oxo-call-vX.Y.Z-aarch64-apple-darwin.tar.gz` |
| Windows | x86_64 | `oxo-call-vX.Y.Z-x86_64-pc-windows-msvc.zip` |
| Windows | aarch64 | `oxo-call-vX.Y.Z-aarch64-pc-windows-msvc.zip` |
| WebAssembly | wasm32-wasip1 | `oxo-call-vX.Y.Z-wasm32-wasip1.tar.gz` (advanced) |

2. Extract and move to your PATH:

```bash
# Linux / macOS
tar xzf oxo-call-vX.Y.Z-x86_64-unknown-linux-gnu.tar.gz
sudo mv oxo-call /usr/local/bin/

# Or add to your user bin directory
mv oxo-call ~/.local/bin/
```

## From Bioconda (Conda/Mamba)

If you use conda for bioinformatics package management, oxo-call is available from [Bioconda](https://bioconda.github.io/):

```bash
# First-time bioconda setup (if not already configured)
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

# Install
conda install oxo-call
```

Or with mamba (faster dependency resolution):

```bash
mamba install oxo-call -c bioconda -c conda-forge
```

> **Note:** Bioconda support is new. Please report any issues at [GitHub Issues]https://github.com/Traitome/oxo-call/issues.

## From crates.io (Cargo)

If you have Rust installed, install via cargo:

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

This downloads, compiles, and installs the latest published version. Requires [Rust](https://rustup.rs/) to be installed.

## From Source (Git Clone)

For the latest development version or to contribute:

```bash
cargo install --git https://github.com/Traitome/oxo-call oxo-call
```

To build a release-optimized binary:

```bash
cargo build --release
# Binary is at target/release/oxo-call
```

## Verifying Installation

After installation, verify it works:

```bash
oxo-call --version
oxo-call --help
```

## Updating

```bash
# From GitHub Releases — re-download the latest binary

# From Bioconda
conda update oxo-call
# or
mamba update oxo-call

# From crates.io
cargo install oxo-call --force

# From source
cd oxo-call
git pull
cargo install --path .
```

## System Requirements

- **Operating System**: Linux, macOS, or Windows
- **Rust**: 2024 edition (if building from source)
- **LLM Access**: A valid API token for at least one supported LLM provider
- **License**: A valid `license.oxo.json` file (free for academic use)

## Shell Completion (Recommended)

After installation, set up shell completion for tab-completion support:

```bash
# Bash
mkdir -p ~/.local/share/bash-completion/completions
oxo-call completion bash > ~/.local/share/bash-completion/completions/oxo-call

# Zsh
mkdir -p ~/.zfunc
oxo-call completion zsh > ~/.zfunc/_oxo-call
```

See the [completion command reference](../commands/completion.md) for detailed setup instructions for all supported shells (bash, zsh, fish, PowerShell, elvish).