Installation

The pipeline is available as a Docker image, a conda package, or can be installed from source after resolving dependencies via conda.

Via Docker

Images are published to quay.io/artic/fieldbioinformatics for both amd64 and aarch64 in two variants:

Tag	Clair3 models	Use when
latest / vX.Y.Z	Not included	You will mount a pre-downloaded model directory
latest-models-included / vX.Y.Z-models-included	Bundled	You want a fully self-contained image

With models pre-bundled

docker pull quay.io/artic/fieldbioinformatics:latest-models-included

docker run --rm \
  -v $(pwd):/data \
  -w /data \
  quay.io/artic/fieldbioinformatics:latest-models-included \
  artic minion \
    --scheme-name artic-inrb-mpox \
    --scheme-version v1.0.0 \
    --scheme-length 2500 \
    --read-file my_sample.fastq \
    my_sample

Without models (bring your own)

Download models first (see Clair3 Models), then mount the directory at run time:

docker pull quay.io/artic/fieldbioinformatics

docker run --rm \
  -v $(pwd):/data \
  -v /path/to/models:/models \
  -w /data \
  quay.io/artic/fieldbioinformatics:latest \
  artic minion \
    --model-dir /models \
    --scheme-name artic-inrb-mpox \
    --scheme-version v1.0.0 \
    --scheme-length 2500 \
    --read-file my_sample.fastq \
    my_sample

Via conda

conda create -n artic -c bioconda artic
conda activate artic

After installation, download the Clair3 models:

artic_get_models

Via source

1. Install dependencies

The pipeline has several software dependencies. Use the provided conda environment file to resolve them. We strongly recommend conda >= 23.10.0 (which uses the libmamba solver by default):

git clone https://github.com/artic-network/fieldbioinformatics
cd fieldbioinformatics
conda env create -f environment.yml

2. Install the pipeline

conda activate artic
pip install .

3. Download Clair3 models

artic_get_models

4. Verify the installation

Check the pipeline can be called:

artic -v

To verify all dependencies are present, run the pipeline integration tests:

./test-runner.sh clair3

For further tests see Tests.