Installation
Using Pip
Install varfish-cli
into a new virtualenv:
virtualenv venv
source venv/bin/activate
pip install varfish-cli
varfish-cli --help
Using Conda
You can install VarFish via bioconda
## OR use "conda" below instead of mamba
mamba create -y -n varfish-cli varfish-cli
conda activate varfish-cli
varfish-cli --help
Creating Configuration
You must create a configuration file at ~/.varfishrc.toml
with the URL to the server and the API token that you previously created.
The following Bash snippet creaets such a file:
… code-block:: bash
cat >~/.varfishrc.toml <<EOF [global]
# URL to VarFish server. varfish_server_url = “https://varfish.example.com/” # API token to use for VarFish API. varfish_api_token = “XXX” EOF