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Update ambient install docs to specify Python version #202

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Apr 30, 2024
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4 changes: 3 additions & 1 deletion src/install.rst
Original file line number Diff line number Diff line change
Expand Up @@ -213,7 +213,9 @@ Set up a Nextstrain runtime

The ambient runtime does not require a particular setup method; it will work as long as the programs you wish to use are available.

The following describes how to accomplish this using a custom Conda environment as an example. You should be familiar with the `basics of Conda <https://conda.io/projects/conda/en/latest/user-guide/getting-started.html>`__ before proceeding.
.. Suggest Python ≤3.10 because Augur on Bioconda won't resolve dependencies on Python ≥3.11: <https://github.com/nextstrain/augur/issues/1334>

The following describes how to accomplish this by creating a new custom Conda environment, as an example. You should be familiar with the `basics of Conda <https://conda.io/projects/conda/en/latest/user-guide/getting-started.html>`__ before proceeding. If you want to add Nextstrain to an existing Conda environment, please make sure you're using Python ≤3.10 and activate that environment instead of creating a new one.

.. tabs::

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17 changes: 9 additions & 8 deletions src/snippets/ambient-setup.rst
Original file line number Diff line number Diff line change
@@ -1,19 +1,20 @@
1. Activate a Conda environment that you wish to use:
1. Create a new Conda environment and install all the necessary software:

.. code-block:: bash

conda activate <your-environment-name>

2. Install all the necessary software:

.. code-block:: bash

conda install --override-channels --strict-channel-priority \
conda create -n <your-environment-name> \
--override-channels --strict-channel-priority \
-c conda-forge -c bioconda --yes \
augur auspice nextclade \
snakemake git epiweeks pangolin pangolearn \
ncbi-datasets-cli csvtk seqkit tsv-utils

2. Activate the runtime:

.. code-block:: bash

conda activate <your-environment-name>

3. Set the runtime:

.. code-block:: none
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