Package: varfish-cli
VarFish Command Line InterfaceCommand line interface forbihealth/varfish-server.[!NOTE]
This repository focuses on the command line interface programvarfish-cli.
If you are new to VarFish, you may want to start at the repositorybihealth/varfish-server.User Manual:varfish-cli user manualInstallationYou can installvarfish-clifrombioconda:To create a new conda environment namedvarfish-cliwith the package:mamba create -y -n varfish-cli -c bioconda varfish-cli
conda activate varfish-cli
varfish-cli --helpTo get help with individual sub commands:varfish-cli importer
# OR
varfish-cli importer --helpYou 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"
EOFDeveloper InformationDevelopment SetupPreqrequisites:Python >=3.10Clone the repository:git clone git@github.com:bihealth/varfish-cli.git
cd varfish-cli-ngNow, 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"
EOFGitHub Project Management with Terraformexport 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 applyChangelog0.6.3(2024-01-24)Bug Fixeswrite out .sample_data in dragen-to-bam-qc (#101) (#102) (638c294)Documentationfix link to pypi in README (#97) (8f25193)0.6.2(2024-01-23)Bug Fixesproperly assign version in release-please (#91) (3037f7a)version for release-please in CI (#89) (2aedb64)Documentationadd pypi and bioconda badges (#96) (88c7f79)0.6.1(2024-01-23)Continuous Integrationinstall setuptools to fix "python sdist" in release-please (#87) (9b03c68)0.6.0(2024-01-23)Featuresadd "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)Documentationinstallation instructions in manual (#69) (0afb87c)updating README, adding terraform docs (#68) (f6dd1bf)0.5.3(2023-07-17)Featuresforce release of 0.6 (#46) (f003be8)Bug Fixesallow varfish upload without SV effects (#43) (4aead65)fixing issue with logging (ab62f24)0.5.2(2023-07-17)Bug Fixesallow varfish upload without SV effects (#43) (4aead65)Fixing case list API (#37) (ccaccfc)0.5.2(2023-06-12)Bug FixesFixing case list API (#37) (ccaccfc)0.5.1(2023-02-09)Bug Fixesmanifest for readme and changelog (#35) (f14d647)0.5.0(2023-02-09)Featuresreplace python-Levenshtein with polyleven (#26) (#32) (73703bd)Documentationfixing CI status badge (#34) (9967bbd)0.4.0Adding support for varannos REST API (#24).0.3.5Allowing to upload per-case gene annotation file (#20).Adding client endpoint for retrieving case from API (#18).0.3.4Adding support for latest varfish-annotator output for svs (#16).0.3.3Case importer distinguished smallvar and SV DB info files (#13).0.3.2Fixing structuring/unstructuring of genomic region0.3.1Allow disabling ofverify_sslin CLI0.3.0Adding implementation of REST API (#7).0.2.8Adding support to specify genome build on import (defaulting to GRCh37).0.2.7Fix reading of non-compressed genotypes TSV file.0.2.6Fixes to linting.0.2.5Switching build system to Github ActionsAdding many testsFixingverify_sslfor case list.0.2.4Added--no-verify-ssl.0.2.3Added state field toVariantSetImportInfoclass.Added endpoint for updating variant set import info.0.2.2MoreMANIFEST.infixes.0.2.1Fixing package (MANIFEST.in).0.2.0Adjusted to upstream REST API changes.Cases with all files can now be uploaded.0.1.0everything is new