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.