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.
conda install -c bioconda artic
1. installing the pipeline
git clone https://github.com/artic-network/fieldbioinformatics cd fieldbioinformatics python setup.py install
2. installing dependencies
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:
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.