Installing q2-classo

Conda environment

q2-classo installs into the same QIIME 2 2026.7 environment as q2-gglasso — if you have already created it, activate it and start at the clone step.

Note

Two upstream renames landed in QIIME 2 2026.4: the amplicon distribution is now called qiime2 (so paths contain /qiime2/, not /amplicon/), and the environment files are named rachis-* because the framework package was rebranded from qiime2 to rachis. A compatibility shim keeps import qiime2 working.

# Create the QIIME 2 2026.7 environment if you do not already have it
# (linux-64 shown; osx-64 also available, osx-arm64 is not)
conda env create \
  --name qiime2-2026.7 \
  --file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2026.7/qiime2/released/rachis-qiime2-linux-64-conda.yml

# Activate the environment
conda activate qiime2-2026.7

# Clone and install q2-classo
git clone https://github.com/Vlasovets/q2-classo.git
cd q2-classo
python -m pip install --no-cache-dir -r requirements.txt
pip install -e .

# Refresh QIIME 2 cache
qiime dev refresh-cache

Note

Older instructions pointed at a repository called q2-classo-latest under the bio-datascience organisation. The canonical repository is now Vlasovets/q2-classo. Likewise, python setup.py install is deprecated and redundant with pip install -e ..

Docker installation

A q2-classo image is published on Docker Hub:

# Pull the Docker image
docker pull ovlasovets/q2-classo:latest

# Run q2-classo container with volume mapping for data
docker run -it -v $(pwd):/data ovlasovets/q2-classo:latest

# Alternative: Run specific analysis with data directory
docker run -it -v /path/to/your/data:/data ovlasovets/q2-classo:latest qiime classo --help

Note

The published :latest image is built on the retired amplicon base image and has not yet been rebuilt for 2026.7. Use the conda instructions above until it has been.

Verification

Confirm that q2-classo is registered:

# Check that classo is available
qiime classo --help

You should see eight actions: add-covariates, add-taxa, classify, generate-data, predict, regress, summarize and transform-features.

Note

In releases before this one, classify was registered under the name regress, so qiime classo --help listed two actions with the same name. If you see that, your q2-classo predates the fix.