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

Changelog

0.6.3 (2024-01-24)

Bug Fixes

• write out .sample_data in dragen-to-bam-qc (#101) (#102) (638c294)

Documentation

• fix link to pypi in README (#97) (8f25193)

0.6.2 (2024-01-23)

Bug Fixes

• properly assign version in release-please (#91) (3037f7a)
• version for release-please in CI (#89) (2aedb64)

Documentation

• add pypi and bioconda badges (#96) (88c7f79)

0.6.1 (2024-01-23)

Continuous Integration

• install setuptools to fix "python sdist" in release-please (#87) (9b03c68)

0.6.0 (2024-01-23)

Features

• add "projects project-list" command (#50) (057abd5)
• conversion from DRAGEN QC to legacy varfish format (#85) (#86) (043dbc3)
• migrate argparse code to typer (#48) (#61) (d1c86d4)
• migration from attrs to pydantic (#49) (#65) (2c9e402)

Documentation

• installation instructions in manual (#69) (0afb87c)
• updating README, adding terraform docs (#68) (f6dd1bf)

0.5.3 (2023-07-17)

Features

• force release of 0.6 (#46) (f003be8)

Bug Fixes

• allow varfish upload without SV effects (#43) (4aead65)
• fixing issue with logging (ab62f24)

0.5.2 (2023-07-17)

Bug Fixes

• allow varfish upload without SV effects (#43) (4aead65)
• Fixing case list API (#37) (ccaccfc)

0.5.2 (2023-06-12)

Bug Fixes

• Fixing case list API (#37) (ccaccfc)

0.5.1 (2023-02-09)

Bug Fixes

• manifest for readme and changelog (#35) (f14d647)

0.5.0 (2023-02-09)

Features

• replace python-Levenshtein with polyleven (#26) (#32) (73703bd)

Documentation

• fixing CI status badge (#34) (9967bbd)

0.4.0

• Adding support for varannos REST API (#24).

0.3.5

• Allowing to upload per-case gene annotation file (#20).
• Adding client endpoint for retrieving case from API (#18).

0.3.4

• Adding support for latest varfish-annotator output for svs (#16).

0.3.3

• Case importer distinguished smallvar and SV DB info files (#13).

0.3.2

• Fixing structuring/unstructuring of genomic region

0.3.1

• Allow disabling of verify_ssl in CLI

0.3.0

• Adding implementation of REST API (#7).

0.2.8

• Adding support to specify genome build on import (defaulting to GRCh37).

0.2.7

• Fix reading of non-compressed genotypes TSV file.

0.2.6

• Fixes to linting.

0.2.5

• Switching build system to Github Actions
• Adding many tests
• Fixing verify_ssl for case list.

0.2.4

• Added --no-verify-ssl.

0.2.3

• Added state field to VariantSetImportInfo class.
• Added endpoint for updating variant set import info.

0.2.2

• More MANIFEST.in fixes.

0.2.1

• Fixing package (MANIFEST.in).

0.2.0

• Adjusted to upstream REST API changes.
• Cases with all files can now be uploaded.

0.1.0

• everything is new