Getting Started
===============

1. `Install Hail <https://hail.is/docs/0.2/getting_started.html#installation>`_::

    pip install hail

2. Use ``hailctl`` to start a `Google Dataproc <https://cloud.google.com/dataproc/>`_ cluster with the
   ``gnomad`` package installed (see `Hail on the Cloud <https://hail.is/docs/0.2/hail_on_the_cloud.html>`_ for more detail on ``hailctl``)::

    hailctl dataproc start cluster-name --packages gnomad

3. Connect to a `Jupyter Notebook <https://jupyter-notebook.readthedocs.io/en/stable/notebook.html>`_ on the cluster::

    hailctl dataproc connect cluster-name notebook

4. Import gnomAD data in `Hail Table <https://hail.is/docs/0.2/hail.Table.html>`_ format:

    * gnomAD v2.1.1 variants::

        from gnomad.resources.grch37 import gnomad

        gnomad_v2_exomes = gnomad.public_release("exomes")
        exomes_ht = gnomad_v2_exomes.ht()
        exomes_ht.describe()

        gnomad_v2_genomes = gnomad.public_release("genomes")
        genomes_ht = gnomad_v2_genomes.ht()
        genomes_ht.describe()

    * gnomAD v3 variants::

        from gnomad.resources.grch38 import gnomad
        gnomad_v3_genomes = gnomad.public_release("genomes")
        ht = gnomad_v3_genomes.ht()
        ht.describe()

5. Shut down the cluster when finished with it::

    hailctl dataproc stop cluster-name