Pipeline Builder

bio-pype-builder is an interactive web-based UI for building and editing bio-pype pipelines. It provides a visual interface to browse available snippets, inspect their arguments, and construct pipeline YAML files — without needing to write YAML by hand.

Note

bio-pype-builder is a separate package. Install it independently from bio-pype:

pip install bio-pype-builder

Once PYPE_MODULES is set to a workflow directory (e.g., via pype registry path), bio-pype-builder reads the available snippets and pipelines from that directory and exposes them through the UI.

Starting the Builder

After activating a workflow module:

export PYPE_MODULES=$(pype registry path somatic==2026.03.11-1)

Start the builder:

bio-pype-builder

Or with custom host/port:

bio-pype-builder --host 0.0.0.0 --port 8000

Then open your browser at http://localhost:8000.

What the Builder Provides

• Snippet browser — view all available snippets, their arguments, requirements, and expected results

• Pipeline editor — load existing pipeline YAML files, edit arguments and step definitions, and save back to disk

• Dry-run — execute a dry-run to preview the DAG (execution graph) of a pipeline before actually running it

• Argument inspection — all argument metadata (types, defaults, choices, nargs) is displayed directly in the UI, derived from the snippet’s argparse definitions

The builder uses PYPE_PIPELINES (from PYPE_MODULES) to discover and edit pipeline YAML files, and PYPE_SNIPPETS to populate the snippet browser.

Refreshing Snippets

If you add or modify snippets while the builder is running, use the refresh endpoint (or button in the UI) to reload the snippet cache without restarting the server.