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