Command line interface for bihealth/varfish-server.
Note
This repository focuses on the command line interface program varfish-cli.
If you are new to VarFish, you may want to start at the repository bihealth/varfish-server.
- User Manual: varfish-cli user manual
You can install varfish-cli from bioconda:
To create a new conda environment named varfish-cli with the package:
mamba create -y -n varfish-cli -c bioconda varfish-cli
conda activate varfish-cli
varfish-cli --help
To get help with individual sub commands:
varfish-cli importer
# OR
varfish-cli importer --help
You will also need to create a configuration file in your home folder with the server address:
$ 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
Preqrequisites:
- Python >=3.10
Clone the repository:
git clone git@github.com:bihealth/varfish-cli.git
cd varfish-cli-ng
Now, create a virtualenv and install the software and its development requirements:
virtualenv venv
source venv/bin/activate
pip install -r requirements/develop.txt
pip install -e .
Finally, create the configuration file:
$ 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
export GITHUB_OWNER=bihealth
export GITHUB_TOKEN=ghp_<thetoken>
cd utils/terraform
terraform init
terraform import github_repository.varfish-cli varfish-cli
terraform validate
terraform fmt
terraform plan
terraform apply