From c099e16755c59e8f793ba9eab66ffd080ceb0937 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Tue, 27 Aug 2024 10:41:59 -0700
Subject: [PATCH] =?UTF-8?q?=F0=9F=9A=A7=20add=20seqkit=20as=20external=20d?=
 =?UTF-8?q?ependency?=
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---
 .github/workflows/ci.yaml                     | 2 +-
 augur/merge.py                                | 4 ++++
 docs/installation/non-python-dependencies.rst | 8 ++++----
 3 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 89285e166..8671de526 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -63,7 +63,7 @@ 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/augur/merge.py b/augur/merge.py
index 1ce3a9495..a69125057 100644
--- a/augur/merge.py
+++ b/augur/merge.py
@@ -272,6 +272,10 @@ def cat(filepath: str):
 
 
 def merge_sequences(args):
+    # Confirm that seqkit is installed.
+    if which("seqkit") is None:
+        raise AugurError("'seqkit' is not installed! This is required to merge sequences.")
+
     # Parse --sequences arguments
     if not len(args.sequences) >= 2:
         raise AugurError(f"At least two sequence inputs are required for merging.")
diff --git a/docs/installation/non-python-dependencies.rst b/docs/installation/non-python-dependencies.rst
index 30f520b10..a1cba1fdb 100644
--- 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.