OmicsBox Engine · CLI · Early Access

OmicsBox on the command line

The OmicsBox Engine CLI runs the analyses of OmicsBox from a terminal, on a server or inside a container. Script them, automate them and plug them into Nextflow or Snakemake pipelines, with the same tools, account and cloud storage as OmicsBox Desktop.

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One command, three steps

Every analysis of the desktop application is available as a subcommand of a single omicsbox command. The tool list and parameters always match your installed version of OmicsBox.

Step 1

Discover

List the available tools, or filter them by module.

omicsbox list
omicsbox list --group <module>

Step 2

Inspect

See a tool's inputs, parameters and defaults, or save them as a reusable configuration file.

omicsbox describe fasta-splitter
omicsbox describe kraken2 --save-template

Step 3

Run

Run the tool on local files or cloud paths. Detach long cloud jobs and reconnect later with the run ID.

omicsbox fasta-splitter \
  --i-input-files-single-end ./sequences.fasta \
  --filter parts --split-value-parts 4 \
  --local-folder ./results

Workflow managers

Built for Nextflow and Snakemake pipelines

Because every analysis is a plain shell command, an OmicsBox step fits into any workflow manager. Call it from a Nextflow process or a Snakemake rule, and keep the rest of your pipeline as it is.

Nextflow

Example: an OmicsBox step inside a Nextflow process.

process SPLIT_FASTA {
  input:  path fasta
  output: path 'results/*'
  script:
  """
  omicsbox fasta-splitter \
    --i-input-files-single-end ${fasta} \
    --filter parts --split-value-parts 4 \
    --local-folder results
  """
}

Snakemake

Example: the same step as a Snakemake rule.

rule split_fasta:
    input: "sequences.fasta"
    output: directory("results")
    shell:
        "omicsbox fasta-splitter "
        "--i-input-files-single-end {input} "
        "--filter parts --split-value-parts 4 "
        "--local-folder {output}"

  • JSON output: add --output-format json to get a machine-readable run manifest with every output path.
  • Scriptable exit codes: 0 success, 1 error, 2 bad arguments, 3 authentication, 4 cloud or transport.
  • Cloud-to-cloud chaining: pass one step's cloud outputs straight into the next step, without intermediate downloads.
  • Detach and reconnect: submit long cloud jobs with --detach and collect the results later with the run ID.

Installation

Installation overview

The Engine will ship as native packages that put the omicsbox command on your PATH and enable shell auto-completion for bash and zsh. Packages are released to Early Access members first.

Linux

.deb package for Debian and Ubuntu, plus other common package formats.

Windows

.exe installer.

macOS

To be confirmed.

Activate once, then run

Activate the Engine with your OmicsBox subscription key, then sign in to OmicsCloud in your browser. On headless servers, sign in with --no-browser. In CI systems and containers, provide the key as the OMICSBOX_SKEY environment variable.

omicsbox activate <your-subscription-key>
omicsbox whoami

# headless server
omicsbox activate <key> --no-login
omicsbox login --no-browser

Downloads

Download the OmicsBox Engine

The installation packages are not public yet. Early Access members receive them first, together with installation instructions for their platform.

Request Early Access

Version history

Release notes

  • Early Access preview: in preparation.
Release notes for each Engine version will be published here.

Early Access program

Be among the first to use the Engine CLI

Tell us about your pipelines and servers, and we will contact you as soon as your access is ready.

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Documentation

Engine overview · Installation & Activation · Running Tools · Built-in Commands · Global Options