Model-intelligent
orchestration for
CLI bioinformatics

# Import a built-in SLURM template and run it
$ oxo-call job list --builtin --tag slurm
$ oxo-call job import squeue-me
$ oxo-call job run squeue-me

# Generate a job from a plain-English description
$ oxo-call job generate "show Docker containers over 1 GB memory"

# View execution history and status
$ oxo-call job status
$ oxo-call job history squeue-me

# List all built-in templates
$ oxo-call workflow list

# Preview the RNA-seq pipeline (no execution)
$ oxo-call workflow dry-run rnaseq

# Run a workflow (native engine — no Snakemake/Nextflow needed)
$ oxo-call workflow run my_rnaseq.toml

# Export to Snakemake for HPC submission
$ oxo-call workflow export wgs.toml --to snakemake -o Snakefile

# Generate a custom ChIP-seq workflow with LLM
$ oxo-call workflow generate \
    "ChIP-seq H3K27ac: QC → Bowtie2 → MACS3 peaks vs input control" \
    -o chipseq.toml

# Install the latest release from crates.io
cargo install oxo-call

# Download pre-built binary (Linux x86_64 example)
curl -LO https://github.com/Traitome/oxo-call/releases/latest/download/oxo-call-VERSION-x86_64-unknown-linux-gnu.tar.gz
tar xzf oxo-call-*-x86_64-unknown-linux-gnu.tar.gz
sudo mv oxo-call /usr/local/bin/

# Available for: Linux (x86_64/aarch64), macOS (Intel/Apple Silicon), Windows, WASM

# Clone and build from source (latest development version)
cargo install --git https://github.com/Traitome/oxo-call oxo-call

# GitHub Copilot (default — free for Copilot subscribers)
oxo-call config set llm.api_token YOUR_GITHUB_TOKEN

# OpenAI
oxo-call config set llm.provider openai
oxo-call config set llm.api_token sk-...

# Local Ollama (no token needed)
oxo-call config set llm.provider ollama
oxo-call config set llm.model llama3.2

# Preview — no execution
oxo-call dry-run samtools "sort input.bam by coordinate and output to sorted.bam"

# Execute immediately
oxo-call run bwa "align reads.fastq to reference.fa using 8 threads, output SAM"

# Confirm before running
oxo-call run --ask bcftools "call variants from my.bam against ref.fa"

# Variable substitution with --var
oxo-call run --var SAMPLE=NA12878 samtools "index {SAMPLE}.bam"
# → samtools index NA12878.bam

# Batch processing with {item} placeholder
oxo-call run samtools "flagstat {item}" \
    --input-items s1.bam,s2.bam,s3.bam --jobs 4

# Process files from a list with path placeholders
# {stem} = filename without extension, {ext} = extension
oxo-call run samtools "sort {item} -o {stem}.sorted.{ext}" \
    --input-list bam_files.txt --jobs 8

# Combine variables and batch input
oxo-call run bwa "mem -t {THREADS} {REF} {item} > {stem}.sam" \
    --var THREADS=16 --var REF=hg38.fa \
    --input-list samples.txt --jobs 4

# Download the .wasm binary from the GitHub Releases page, then:
wasmtime oxo-call.wasm -- dry-run samtools "sort input.bam by coordinate"

# Step 1: Copy this JSON and save it as license.oxo.json
{
  "schema": "oxo-call-license-v1",
  "license_id": "6548e181-e352-402a-ab72-4da51f49e7b5",
  "issued_to_org": "Public Academic Test License (any academic user)",
  "license_type": "academic",
  "scope": "org",
  "perpetual": true,
  "issued_at": "2026-03-12",
  "signature": "duKJcISYPdyZkw1PbyVil5zTjvLhAYsmbzRpH0n6eRYJET90p1b0rYiHO0cJ7IGR6NLEJWqkY1wBXUkfvUvECw=="
}

# Step 2: Move the file to the config directory
# Linux:
mkdir -p ~/.config/oxo-call && mv license.oxo.json ~/.config/oxo-call/

# macOS:
mkdir -p ~/Library/Application\ Support/io.traitome.oxo-call && mv license.oxo.json ~/Library/Application\ Support/io.traitome.oxo-call/

# Windows (PowerShell):
New-Item -ItemType Directory -Force -Path $env:APPDATA\oxo-call; Move-Item license.oxo.json $env:APPDATA\oxo-call\

# Step 3: Verify the license works
oxo-call license verify

# Step 4: Try your first command
oxo-call dry-run samtools "sort input.bam by coordinate"