NGS Runtime Environment

Use this skill whenever an NGS workflow needs package checks, install planning, or runtime validation.

Existence Check Order

1. Check executables on PATH with command -v or shutil.which.
2. Check Python imports for Python-backed tools.
3. Check active package managers with conda list, mamba list, micromamba list, or pip show.
4. If requested, check package indexes or container registries.
5. Emit an install plan before installing.
6. Install only when explicitly requested by the user.

Do not modify system Python. Prefer isolated conda/mamba environments or containers.

Script

From the repo root: