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 `__ (optional alternative)
- `FastTree `__ (optional alternative)
-- ``augur merge`` requires ``sqlite3``, the `SQLite `__ CLI (version ≥3.39).
+- ``augur merge`` requires ``sqlite3`` (the `SQLite `__ CLI (version ≥3.39)) for metadata and ``seqkit`` for sequences.
- Bacterial data (or any VCF usage) requires `vcftools `__
@@ -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 `__:
.. 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.