CLI Reference

Vaibify provides two equivalent entry points: vaibify and the shorthand vaib. All commands accept a --config flag to specify an alternate vaibify.yml path.

Global Options

Flag	Description
--config PATH	Path to vaibify.yml (default: ./vaibify.yml)
--version	Print the installed version and exit
--help	Show the help message and exit

When invoked with no subcommand, Vaibify starts in hub mode – a browser-based dashboard for managing multiple projects.

Project Targeting

Note: When you are in a directory containing vaibify.yml, the --project flag defaults to that project. When only one project is registered globally, the flag can be omitted entirely. When multiple projects exist, --project is required unless you are in a project directory. Projects are registered automatically when you run vaibify init.

Project Setup

vaibify init

Create a new project from a template.

vaibify init [--template NAME] [--force]

Option	Description
--template	Template name: sandbox or workflow
--force	Overwrite existing configuration files

Creates vaibify.yml, container.conf, and workflow.json in the current directory.

vaibify register

Register an existing project directory in the global registry so it can be targeted with --project/-p from any directory. Unlike vaibify init, this does not create or overwrite any files.

vaibify register [DIRECTORY]

Argument	Description
DIRECTORY	Path to the project directory (default: .)

The directory must contain a vaibify.yml file.

vaibify setup

Launch the interactive setup wizard in a browser (port 8051). The wizard walks through configuration fields and writes the result to vaibify.yml.

vaibify setup

vaibify config

Edit, export, or import configuration.

vaibify config edit                         # Open vaibify.yml in $EDITOR
vaibify config export [-p NAME] <file>      # Write current config to a file
vaibify config import <file>                # Load config from a file

Container Lifecycle

vaibify build

Build the Docker image from vaibify.yml and container.conf.

vaibify build [--no-cache] [--project/-p NAME]

Option	Description
--no-cache	Force a clean rebuild of all layers
--project, -p	Target project name (optional if only one exists)

vaibify start

Start the container in the background.

vaibify start [--gui] [--jupyter] [--project/-p NAME]

Option	Description
--gui	Launch the pipeline viewer after starting
--jupyter	Start JupyterLab inside the container
--project, -p	Target project name (optional if only one exists)

vaibify stop

Stop the running container. The workspace volume persists.

vaibify stop [--project/-p NAME]

vaibify destroy

Remove the container and optionally delete the workspace volume.

vaibify destroy [--volumes] [--project/-p NAME]

Option	Description
--volumes	Also remove the workspace volume
--project, -p	Target project name (optional if only one exists)

vaibify status

Report the state of the container, image, and workspace volume.

vaibify status [--project/-p NAME]

Working with the Container

These commands work from any directory on the host. If you have multiple projects, specify which one with --project/-p. If only one project is registered, the flag can be omitted.

vaibify connect

Open an interactive shell inside the running container.

vaibify connect [--project/-p NAME]

Option	Description
--project, -p	Target project name (optional if only one exists)

vaibify push

Copy files from the host into the container workspace.

vaibify push [--project/-p NAME] <source> <destination>

Option	Description
--project, -p	Target project name (optional if only one exists)

vaibify pull

Copy files from the container workspace to the host.

vaibify pull [--project/-p NAME] <source> <destination>

Option	Description
--project, -p	Target project name (optional if only one exists)

vaibify verify

Run the isolation security audit inside the container. The audit checks for Docker socket access, privilege escalation paths, exposed ports, and mounted secrets.

vaibify verify [--project/-p NAME]

GUI and Pipeline

vaibify gui

Launch the pipeline viewer in a browser (port 8050). When run without a project, the landing page opens and displays all registered containers. Use the + button to add an existing project or create a new one. See Workflow Viewer for details.

vaibify gui [--project/-p NAME]

Publishing

vaibify publish workflow

Generate a GitHub Actions workflow from workflow.json and vaibify.yml. The output is written to .github/workflows/vaibify.yml.

vaibify publish workflow

vaibify publish archive

Package pipeline outputs and upload them to Zenodo (or the Zenodo sandbox). Returns a DOI on success.

vaibify publish archive