🚧 add seqkit as external dependency

nextstrain · Oct 23, 2024 · 4e40e48 · 4e40e48
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -69,7 +69,7 @@ jobs:
     - name: Install dependencies from Conda
       uses: mamba-org/setup-micromamba@v1
       with:
-        create-args: mafft raxml fasttree iqtree vcftools sqlite tsv-utils biopython=${{ matrix.biopython-version }} python=${{ matrix.python-version }}
+        create-args: mafft raxml fasttree iqtree vcftools seqkit sqlite tsv-utils biopython=${{ matrix.biopython-version }} python=${{ matrix.python-version }}
         condarc: |
           channels:
             - conda-forge

diff --git a/docs/installation/non-python-dependencies.rst b/docs/installation/non-python-dependencies.rst
@@ -8,7 +8,7 @@ Augur uses some external bioinformatics programs that are not available on PyPI:
    - `RAxML <https://cme.h-its.org/exelixis/web/software/raxml/>`__ (optional alternative)
    - `FastTree <http://www.microbesonline.org/fasttree/>`__ (optional alternative)
 
-- ``augur merge`` requires ``sqlite3``, the `SQLite <https://sqlite.org>`__ CLI (version ≥3.39).
+- ``augur merge`` requires ``sqlite3`` (the `SQLite <https://sqlite.org>`__ CLI (version ≥3.39)) for metadata and ``seqkit`` for sequences.
 
 - Bacterial data (or any VCF usage) requires `vcftools <https://vcftools.github.io/>`__
 
@@ -20,19 +20,19 @@ If you use Conda, you can install them in an active environment:
 
 .. code:: bash
 
-   conda install -c conda-forge -c bioconda mafft raxml fasttree iqtree vcftools sqlite --yes
+   conda install -c conda-forge -c bioconda mafft raxml fasttree iqtree vcftools seqkit sqlite --yes
 
 On macOS using `Homebrew <https://brew.sh/>`__:
 
 .. code:: bash
 
    brew tap brewsci/bio
-   brew install mafft iqtree raxml fasttree vcftools sqlite
+   brew install mafft iqtree raxml fasttree vcftools seqkit sqlite
 
 On Debian/Ubuntu:
 
 .. code:: bash
 
-   sudo apt install mafft iqtree raxml fasttree vcftools sqlite3
+   sudo apt install mafft iqtree raxml fasttree vcftools seqkit sqlite3
 
 Other Linux distributions will likely have the same packages available, although the names may differ slightly.