diff --git a/src/install.rst b/src/install.rst index 7b564991..c966305c 100644 --- a/src/install.rst +++ b/src/install.rst @@ -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 `__ before proceeding. + .. Suggest Python ≤3.10 because Augur on Bioconda won't resolve dependencies on Python ≥3.11: + + 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 `__ 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:: diff --git a/src/snippets/ambient-setup.rst b/src/snippets/ambient-setup.rst index eebd5421..c863e2da 100644 --- a/src/snippets/ambient-setup.rst +++ b/src/snippets/ambient-setup.rst @@ -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 - -2. Install all the necessary software: - - .. code-block:: bash - - conda install --override-channels --strict-channel-priority \ + conda create -n \ + --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 + 3. Set the runtime: .. code-block:: none