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Update runtime-dependent setup step
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The step now applies to all runtime setups. Previously, it relied on
inaccurate assumptions:

1. It only supported 2 runtimes, Docker and ambient.
2. If using the ambient runtime, it already had tools available (e.g. a
   Conda environment is already active).
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victorlin committed Jun 15, 2023
1 parent 15a4b54 commit 98d8a5e
Showing 1 changed file with 17 additions and 5 deletions.
22 changes: 17 additions & 5 deletions src/tutorials/creating-a-workflow.rst
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Expand Up @@ -33,15 +33,27 @@ Setup
mkdir -p results/
3. Additionally, if you installed Nextstrain with the :term:`Docker runtime<runtime>`, start Docker and enter the runtime.
3. Enter a prompt with Nextstrain tools available. This varies by runtime.

.. code-block:: bash
.. tabs::

.. group-tab:: Docker, Conda

.. code-block:: bash
nextstrain shell .
.. note::

The dot (``.``) as the last argument indicates that your current directory (``zika-tutorial/``) is the working directory. Your command prompt will change to indicate you are in a Nextstrain shell, which provides access to commands such as ``augur`` and ``auspice``. If you want to leave the Nextstrain shell, run the command ``exit``.

.. group-tab:: Ambient (advanced)

nextstrain shell .
This varies depending on how your ambient runtime is set up. If you've installed tools into a custom Conda environment, activate it.

.. note::
.. code-block:: bash
The dot (``.``) as the last argument indicates that your current directory (``zika-tutorial/``) is the working directory. Your command prompt will change to indicate you are in the Docker runtime. If you want to leave the runtime, run the command ``exit``.
conda activate <your-environment-name>
Run a Nextstrain Build
======================
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