:tocdepth: 3

aoutools (workbench)
====================

Helpers for setting up a Hail session on the *All of Us* Researcher Workbench.
None of these is required to use the rest of the library -- they exist so that
the Workbench-specific boilerplate (requester-pays billing, the reference
genome, the Google billing project, and the locations of the VariantDataset and
the workspace bucket) lives in one place rather than being copied into every
notebook.

.. note::

   The current *All of Us* platform (Verily) no longer exports the
   ``WGS_VDS_PATH`` and ``WORKSPACE_BUCKET`` environment variables that the
   older Workbench guaranteed. Code that reads them directly fails on a fresh
   workspace. These helpers resolve both without them.

   Exporting a variable from a Jupyter **terminal** does not reach the
   notebook: the terminal and the kernel are sibling children of the Jupyter
   server, which captured its environment at startup, so the kernel never sees
   it -- even after a restart. Set it from inside a notebook cell instead, or
   put it in ``~/.ipython/profile_default/startup/00-aou-env.py``.

.. autofunction:: aoutools.init_hail

.. autofunction:: aoutools.get_vds_path

.. autofunction:: aoutools.get_workspace_bucket

.. autofunction:: aoutools.get_google_project

.. autodata:: aoutools.DEFAULT_VDS_PATH
   :annotation: