As of release 1.1.0, it is probably easiest to install the artic pipeline using conda. Alternatively, you can install the pipeline itself via source/pip but you will have to also satisfy the pipeline dependencies.

Via conda

conda install -c bioconda artic

Via source

1. installing the pipeline

git clone
cd fieldbioinformatics
python install

2. installing dependencies

The artic pipeline has several software dependencies. You can solve these dependencies using the minimal conda environment we have provided:

conda env create -f environment.yml
conda activate artic

3. testing the pipeline

First check the pipeline can be called:

artic -v

To check that you have all the required dependencies, you can try the pipeline tests with both workflows:

./ nanopolish
./ medaka

For further tests, such as the variant validation tests, see here.