Installation

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 https://github.com/artic-network/fieldbioinformatics
cd fieldbioinformatics
python setup.py 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:

./test-runner.sh nanopolish
./test-runner.sh medaka

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