diff --git a/src/tutorials/creating-a-workflow.rst b/src/tutorials/creating-a-workflow.rst index 8985d227..77643af4 100644 --- a/src/tutorials/creating-a-workflow.rst +++ b/src/tutorials/creating-a-workflow.rst @@ -33,15 +33,27 @@ Setup mkdir -p results/ -3. Additionally, if you installed Nextstrain with the :term:`Docker 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 Run a Nextstrain Build ======================