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Remove basic example in setup page
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This will be replaced by the "example data" tutorial.
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victorlin committed Mar 23, 2022
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24 changes: 0 additions & 24 deletions docs/src/tutorial/setup.rst
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Expand Up @@ -66,27 +66,3 @@ Alternately, download a specific version of the workflow that you know works for
# Change into the workflow's directory.
cd ncov-7/
3. Run a basic analysis with example data
-----------------------------------------

Run a basic workflow with example data, to confirm that your :term:`Nextstrain runtime <docs.nextstrain.org:runtime>` is properly configured.

.. code:: bash
nextstrain build . --cores 4 \
--configfile ./my_profiles/getting_started/builds.yaml
The ``nextstrain build`` command runs a :term:`pathogen workflow <docs.nextstrain.org:workflow>` defined using Snakemake. Since our ``Snakefile`` is in the current directory, we specify the directory as ``.``. All other arguments pass through to Snakemake.

The ``getting_started`` build produces a minimal global phylogeny for visualization in :term:`docs.nextstrain.org:Auspice`. This workflow should complete in about 5 minutes on a MacBook Pro (2.7 GHz Intel Core i5) with four cores.

4. Visualize the phylogeny for example data
-------------------------------------------

`Open auspice.us <https://auspice.us>`__ in your browser. Drag and drop the :term:`JSON file <docs.nextstrain.org:JSONs>` ``auspice/ncov_global.json`` anywhere on the landing page, to visualize the resulting phylogeny. The resulting phylogeny should look something like this:

.. figure:: ../images/getting-started-tree.png
:alt: Phylogenetic tree from the “getting started” build as visualized in Auspice

Phylogenetic tree from the “getting started” build as visualized in Auspice

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