Minor edits to setup docs
Link full text instead of the word "here" and add a line break to `mamba
install` command to prevent package names from being cut off by the code
block box. Also, simplify headings to avoid strange appearance of
numbered lists inside the table of contents unordered list.
@@ -6,25 +6,23 @@ The following steps will prepare you to run complete analyses of SARS-CoV-2 data
.. contents:: Table of Contents
:local:
-1. Install Nextstrain components
+Install Nextstrain components
--------------------------------
-Follow instructions to install Nextstrain components :doc:`here <docs.nextstrain.org:install>`.
+:doc:`Follow instructions to install Nextstrain components <docs.nextstrain.org:install>`.
.. note::
- If using the :term:`native runtime <docs.nextstrain.org:runtime>`, install these additional packages necessary to run the ncov workflow. Make sure the correct conda environment is activated.
+ If using the :term:`native runtime <docs.nextstrain.org:runtime>`, install these additional packages necessary to run the ncov workflow. Make sure to activate the correct conda environment.
.. code:: bash
- mamba install -c conda-forge -c bioconda epiweeks nextclade nextalign pangolin pangolearn
+ mamba install -c conda-forge -c bioconda \
+ epiweeks nextclade nextalign pangolin pangolearn
-2. Download the ncov workflow
+Download the ncov workflow
-----------------------------
-Download the workflow
-~~~~~~~~~~~~~~~~~~~~~
-
Use Git to download a copy of the ncov repository containing the workflow and this tutorial.
.. code:: bash
