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Introduction#

oxo-call is an AI-powered command orchestration tool for bioinformatics. Instead of memorizing hundreds of flags across dozens of tools, you describe what you want to accomplish — and oxo-call translates that into a grounded command you can preview, explain, audit, and reproduce.

# You write:
oxo-call dry-run samtools "sort input.bam by coordinate using 4 threads"

# oxo-call generates:
samtools sort -@ 4 -o sorted.bam input.bam

This is not a simple LLM chat. oxo-call fetches the tool's actual --help output, injects curated expert knowledge (called a skill), and only then asks the LLM — making command generation substantially easier to trust in real research and engineering settings.

How It Works#

Command Generation Pipeline

The docs answer "what flags exist?" The skill answers "which flags should I use, and what mistakes should I avoid?" Together, they produce commands that are both syntactically correct and semantically appropriate.

Core Capabilities#

Capability What it means for you
159 built-in skills Start from domain-aware guidance for samtools, STAR, BWA, GATK, bcftools, fastp, and 150+ more tools
Auto documentation Reuse real --help text automatically instead of hunting through man pages before every task
Dry-run mode Inspect commands safely before they touch data or consume compute time
Workflow engine Move from one-off commands to reusable DAG pipelines with Snakemake/Nextflow export
History with provenance Keep auditable records of the generated command, tool version, model, and docs context
Local LLM support Run with Ollama when data governance, offline work, or latency matter
Job library Turn recurring commands into named, schedulable assets with history and LLM-assisted generation

Why It Feels Easier To Use#

  • Plain-language in, exact flags out — describe the biology or data task instead of remembering syntax
  • Preview before execution — use dry-run to learn and verify before spending cluster time
  • Explanations included — generated commands come with reasoning, which helps onboarding and review
  • Consistent from laptop to cluster — the same interface works for local tools, remote docs, workflows, and HPC targets
  • Evidence-backed — the docs-first + skill-first design is benchmarked at scale, not just marketed as a prompt trick

Who Is This For?#

Bioinformaticians working with many CLI tools daily — oxo-call handles flag lookup so you can focus on biology, not man pages.

Researchers who need reproducible pipelines — every generated command is logged with the documentation and model that produced it.

Core facility staff supporting multiple assay types — a single tool covers NGS, single-cell, metagenomics, and more.

Students learning bioinformatics for the first time — describe tasks in plain language and learn by reading the generated explanations.

How to Use This Guide#

This documentation is organized to get you productive quickly and still support deep technical inspection when you need it:

If you are new to oxo-call#

Start with Getting Started:

  1. Installation — install the binary
  2. License Setup — get your free academic license
  3. Configuration — connect your LLM
  4. Your First Command — run something real in 10 minutes

If you want hands-on practice#

Work through the Tutorials in order:

If you need to accomplish a specific task#

Jump to How-to Guides:

If you need the full details#

See Command Reference and Architecture & Design for complete specifications.

Quick Example#

Here is what a five-minute oxo-call session looks like:

# 1. Install
cargo install oxo-call

# 2. Set up (license + LLM token assumed)
export OXO_CALL_LICENSE=~/.config/oxo-call/license.oxo.json
oxo-call config set llm.api_token ghp_...

# 3. Enable shell completion (optional but recommended)
oxo-call completion bash > ~/.local/share/bash-completion/completions/oxo-call
# See: https://traitome.github.io/oxo-call/documentation/commands/completion/

# 4. Preview a command
oxo-call dry-run samtools "sort input.bam by coordinate and output to sorted.bam"
# → samtools sort -o sorted.bam input.bam

# 5. Execute it
oxo-call run samtools "sort input.bam by coordinate and output to sorted.bam"

# 6. Review what ran
oxo-call history list

Ready to begin? → Installation

Join the Community#

oxo-call is a user-driven, feedback-driven project. Every bug report, feature request, and real-world use case you share directly influences what gets built next.

We actively welcome early adopters and testers — from students running their first RNA-seq pipeline to seasoned bioinformaticians automating complex workflows.

How to contribute Link
🐛 Report a bug Bug report
💡 Request a feature Feature request
🎯 Request a skill for a new tool Skill request
🤝 Contribute code or skills Contributing guide

Try it, break it, and tell us what happened. Even a one-line comment on what went wrong — or right — helps us improve the tool for the whole community.