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MetaGEAR

MetaGEAR Tools (CLI)

MetaGEAR Tools is a small command-line wrapper (metagear) that installs the pipeline, configures defaults for your machine, manages reference databases, and launches workflows — so you can run a full metagenomic analysis without writing Nextflow.

→ schirmer-lab/metagear-tools ↗ — installer, CLI source, configuration templates, and full reference.

Why a wrapper

Nextflow and nf-core are powerful but have a learning curve. MetaGEAR Tools removes it by:

  • Detecting your hardware (CPUs, RAM) and setting resource limits to roughly 80% of available capacity, capped at 48 CPUs and 80 GB.
  • Installing the matching pipeline version alongside itself, so you don’t have to coordinate Nextflow + pipeline versions yourself.
  • Centralizing configuration under ~/.metagear/ with editable defaults.
  • Wrapping every workflow behind a one-word subcommand.

Prerequisites

Install

1. Run the installer.

Terminal window
curl -L http://get-metagear.schirmerlab.de | bash

Latest stable release, installed to ~/.metagear/.

2. (Optional) Pin a specific pipeline version.

Terminal window
curl -L http://get-metagear.schirmerlab.de | bash -s -- --pipeline 1.0

3. Review generated configuration in ~/.metagear/metagear.config and ~/.metagear/metagear.env. Adjust paths or resource limits if needed.

Basic usage

Terminal window
# Install reference databases (one-time, per machine)
metagear download_databases


# Run workflows
metagear qc_dna --input samples.csv
metagear microbial_profiles --input samples.csv


# Generate the launch script without executing it (useful for HPC)
metagear qc_dna --input samples.csv -preview

Input samplesheet:

sample,fastq_1,fastq_2
SAMPLE-01,/path/to/sample1_R1.fastq.gz,/path/to/sample1_R2.fastq.gz
SAMPLE-02,/path/to/sample2_R1.fastq.gz,/path/to/sample2_R2.fastq.gz

Where to go next