VarFish Command Line Interface

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

Installation

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

Developer Information

Development Setup

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

GitHub Project Management with Terraform

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