Installing q2-gglasso

Conda environment

Create a dedicated conda environment for q2-gglasso.

Note

Two upstream renames landed in QIIME 2 2026.4 and change every install command written for an earlier release:

• the amplicon distribution is now called qiime2, so the channel and file paths contain /qiime2/ rather than /amplicon/;

• the environment files are named rachis-* rather than qiime2-*, because the framework package was rebranded from qiime2 to rachis. A compatibility shim keeps import qiime2 working, so existing scripts need no change.

Pick the file matching your platform. linux-64 and osx-64 are available. There is no osx-arm64 build of this distribution, so on Apple Silicon run the osx-64 build under Rosetta or use Docker.

# Create the QIIME 2 2026.7 environment (linux-64 shown)
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-gglasso
git clone https://github.com/Vlasovets/q2-gglasso.git
cd q2-gglasso
python -m pip install --no-cache-dir -r requirements.txt
pip install -e .

# Refresh QIIME 2 cache
qiime dev refresh-cache

Note

If conda env create fails with

package deblur-1.1.1 requires sortmerna 2.0, but none of the providers
can be installed

you have hit a known defect in the upstream 2026.7 linux-64 file: it pins zlib=1.3.2 while every sortmerna 2.0 build requires zlib <1.3. Nothing in this book uses deblur. Download the environment file, delete the deblur, q2-deblur and sortmerna lines, and create the environment from your edited copy.

Note

Older instructions ran python setup.py install. It is deprecated and redundant with pip install -e . — use the latter alone.

Docker installation

A q2-gglasso image is published on Docker Hub:

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

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

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

# Check that gglasso is available
qiime gglasso --help

You should see six actions: build-groups, calculate-covariance, pca, solve-problem, summarize and transform-features.

If all six appear, the installation is complete.