varfish-cli


Namevarfish-cli JSON
Version 0.6.3 PyPI version JSON
download
home_pagehttps://github.com/bihealth/varfish-cli
SummaryCommand line interface client for VarFish Server.
upload_time2024-01-24 12:50:06
maintainer
docs_urlNone
authorManuel Holtgrewe
requires_python
licenseMIT license
keywords varfish_cli
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls. 
            [![CI](https://github.com/bihealth/varfish-cli/actions/workflows/main.yml/badge.svg)](https://github.com/bihealth/varfish-cli/actions/workflows/main.yml)
[![codecov](https://codecov.io/gh/bihealth/varfish-cli/branch/main/graph/badge.svg?token=9ZX53MPEJT)](https://codecov.io/gh/bihealth/varfish-cli)
[![Pypi](https://img.shields.io/pypi/pyversions/varfish-cli.svg)](https://pypi.org/project/varfish-cli)
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/varfish-cli/README.html)
[![Documentation Status](https://readthedocs.org/projects/varfish-cli/badge/?version=latest)](https://varfish-cli.readthedocs.io/en/latest/?badge=latest)
[![MIT license](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)

# VarFish Command Line Interface

Command line interface for [bihealth/varfish-server](https://github.com/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](https://github.com/bihealth/varfish-server).

- **User Manual:** [varfish-cli user manual](https://varfish-cli.readthedocs.io/en/latest/)

## Installation

You can install `varfish-cli` from [bioconda](https://bioconda.github.io/):

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](https://github.com/varfish-org/varfish-cli/compare/v0.6.2...v0.6.3) (2024-01-24)


### Bug Fixes

* write out .sample_data in dragen-to-bam-qc ([#101](https://github.com/varfish-org/varfish-cli/issues/101)) ([#102](https://github.com/varfish-org/varfish-cli/issues/102)) ([638c294](https://github.com/varfish-org/varfish-cli/commit/638c2945d1ea8c4951c5d235f3aef231dcc604c6))


### Documentation

* fix link to pypi in README ([#97](https://github.com/varfish-org/varfish-cli/issues/97)) ([8f25193](https://github.com/varfish-org/varfish-cli/commit/8f25193f5fd313def2457f03e338992aa04eaf9f))

## [0.6.2](https://github.com/bihealth/varfish-cli/compare/v0.6.1...v0.6.2) (2024-01-23)


### Bug Fixes

* properly assign version in release-please ([#91](https://github.com/bihealth/varfish-cli/issues/91)) ([3037f7a](https://github.com/bihealth/varfish-cli/commit/3037f7a44ec4a6a1be641d4ee8c327c11bfacaa2))
* version for release-please in CI ([#89](https://github.com/bihealth/varfish-cli/issues/89)) ([2aedb64](https://github.com/bihealth/varfish-cli/commit/2aedb6465237211133625ef19be601e43d47be9b))


### Documentation

* add pypi and bioconda badges ([#96](https://github.com/bihealth/varfish-cli/issues/96)) ([88c7f79](https://github.com/bihealth/varfish-cli/commit/88c7f79150ca921fe21116fa4c8523840c8d22b2))

## [0.6.1](https://github.com/bihealth/varfish-cli/compare/v0.6.0...v0.6.1) (2024-01-23)


### Continuous Integration

* install setuptools to fix "python sdist" in release-please ([#87](https://github.com/bihealth/varfish-cli/issues/87)) ([9b03c68](https://github.com/bihealth/varfish-cli/commit/9b03c687e34f9e94533fbd04f02b2d4baa65e759))

## [0.6.0](https://github.com/bihealth/varfish-cli/compare/v0.5.3...v0.6.0) (2024-01-23)


### Features

* add "projects project-list" command ([#50](https://github.com/bihealth/varfish-cli/issues/50)) ([057abd5](https://github.com/bihealth/varfish-cli/commit/057abd56667e2b089ee2d30a4c761fd4b67a7278))
* conversion from DRAGEN QC to legacy varfish format ([#85](https://github.com/bihealth/varfish-cli/issues/85)) ([#86](https://github.com/bihealth/varfish-cli/issues/86)) ([043dbc3](https://github.com/bihealth/varfish-cli/commit/043dbc3437dfc2d938a3ba5a4a4ea91ffa12be4f))
* migrate argparse code to typer ([#48](https://github.com/bihealth/varfish-cli/issues/48)) ([#61](https://github.com/bihealth/varfish-cli/issues/61)) ([d1c86d4](https://github.com/bihealth/varfish-cli/commit/d1c86d43be19b66c5f3429c62772e2febadf119c))
* migration from attrs to pydantic ([#49](https://github.com/bihealth/varfish-cli/issues/49)) ([#65](https://github.com/bihealth/varfish-cli/issues/65)) ([2c9e402](https://github.com/bihealth/varfish-cli/commit/2c9e402b66731e35f2214eaca52d3ae49069613b))


### Documentation

* installation instructions in manual ([#69](https://github.com/bihealth/varfish-cli/issues/69)) ([0afb87c](https://github.com/bihealth/varfish-cli/commit/0afb87c377ebda2f50892afff4ab857bce34e4a9))
* updating README, adding terraform docs ([#68](https://github.com/bihealth/varfish-cli/issues/68)) ([f6dd1bf](https://github.com/bihealth/varfish-cli/commit/f6dd1bf850d3f1ac8637f15d165ac262d1f93b2b))

## [0.5.3](https://github.com/bihealth/varfish-cli/compare/v0.5.2...v0.5.3) (2023-07-17)


### Features

* force release of 0.6 ([#46](https://github.com/bihealth/varfish-cli/issues/46)) ([f003be8](https://github.com/bihealth/varfish-cli/commit/f003be8b1f953ff4ab22f7d274264747dd39870d))


### Bug Fixes

* allow varfish upload without SV effects ([#43](https://github.com/bihealth/varfish-cli/issues/43)) ([4aead65](https://github.com/bihealth/varfish-cli/commit/4aead65054e97adf7564f8fb3d3a3e0db755c34f))
* fixing issue with logging ([ab62f24](https://github.com/bihealth/varfish-cli/commit/ab62f242445150c2472aa45ea0c0f6d7782a7b8c))

### [0.5.2](https://www.github.com/bihealth/varfish-cli/compare/v0.5.1...v0.5.2) (2023-07-17)


### Bug Fixes

* allow varfish upload without SV effects ([#43](https://www.github.com/bihealth/varfish-cli/issues/43)) ([4aead65](https://www.github.com/bihealth/varfish-cli/commit/4aead65054e97adf7564f8fb3d3a3e0db755c34f))
* Fixing case list API ([#37](https://www.github.com/bihealth/varfish-cli/issues/37)) ([ccaccfc](https://www.github.com/bihealth/varfish-cli/commit/ccaccfcbec7fb209492f1855b5e740f20ac60bbc))

### [0.5.2](https://www.github.com/bihealth/varfish-cli/compare/v0.5.1...v0.5.2) (2023-06-12)


### Bug Fixes

* Fixing case list API ([#37](https://www.github.com/bihealth/varfish-cli/issues/37)) ([ccaccfc](https://www.github.com/bihealth/varfish-cli/commit/ccaccfcbec7fb209492f1855b5e740f20ac60bbc))

### [0.5.1](https://www.github.com/bihealth/varfish-cli/compare/v0.5.0...v0.5.1) (2023-02-09)


### Bug Fixes

* manifest for readme and changelog ([#35](https://www.github.com/bihealth/varfish-cli/issues/35)) ([f14d647](https://www.github.com/bihealth/varfish-cli/commit/f14d6472728995b9e18726fbfb7c36e86319c999))

## [0.5.0](https://www.github.com/bihealth/varfish-cli/compare/v0.4.0...v0.5.0) (2023-02-09)


### Features

* replace python-Levenshtein with polyleven ([#26](https://www.github.com/bihealth/varfish-cli/issues/26)) ([#32](https://www.github.com/bihealth/varfish-cli/issues/32)) ([73703bd](https://www.github.com/bihealth/varfish-cli/commit/73703bd73796b066de689954caa19a5767f97d76))


### Documentation

* fixing CI status badge ([#34](https://www.github.com/bihealth/varfish-cli/issues/34)) ([9967bbd](https://www.github.com/bihealth/varfish-cli/commit/9967bbd7a706d8338c188468a67a8bbebdb7a330))

## 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

Raw data

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    "platform": null,
    "description": "[![CI](https://github.com/bihealth/varfish-cli/actions/workflows/main.yml/badge.svg)](https://github.com/bihealth/varfish-cli/actions/workflows/main.yml)\n[![codecov](https://codecov.io/gh/bihealth/varfish-cli/branch/main/graph/badge.svg?token=9ZX53MPEJT)](https://codecov.io/gh/bihealth/varfish-cli)\n[![Pypi](https://img.shields.io/pypi/pyversions/varfish-cli.svg)](https://pypi.org/project/varfish-cli)\n[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/varfish-cli/README.html)\n[![Documentation Status](https://readthedocs.org/projects/varfish-cli/badge/?version=latest)](https://varfish-cli.readthedocs.io/en/latest/?badge=latest)\n[![MIT license](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)\n\n# VarFish Command Line Interface\n\nCommand line interface for [bihealth/varfish-server](https://github.com/bihealth/varfish-server).\n\n> [!NOTE]\n> This repository focuses on the command line interface program `varfish-cli`.\n> If you are new to VarFish, you may want to start at the repository [bihealth/varfish-server](https://github.com/bihealth/varfish-server).\n\n- **User Manual:** [varfish-cli user manual](https://varfish-cli.readthedocs.io/en/latest/)\n\n## Installation\n\nYou can install `varfish-cli` from [bioconda](https://bioconda.github.io/):\n\nTo create a new conda environment named `varfish-cli` with the package:\n\n```\nmamba create -y -n varfish-cli -c bioconda varfish-cli\nconda activate varfish-cli\nvarfish-cli --help\n```\n\nTo get help with individual sub commands:\n\n```\nvarfish-cli importer\n# OR\nvarfish-cli importer --help\n```\n\nYou will also need to create a configuration file in your home folder with the server address:\n\n```\n$ cat >~/.varfishrc.toml <<EOF\n[global]\n\n# URL to VarFish server.\nvarfish_server_url = \"https://varfish.example.com/\"\n# API token to use for VarFish API.\nvarfish_api_token = \"XXX\"\nEOF\n```\n\n## Developer Information\n\n### Development Setup\n\nPreqrequisites:\n\n- Python >=3.10\n\nClone the repository:\n\n```\ngit clone git@github.com:bihealth/varfish-cli.git\ncd varfish-cli-ng\n```\n\nNow, create a virtualenv and install the software and its development requirements:\n\n```\nvirtualenv venv\nsource venv/bin/activate\n\npip install -r requirements/develop.txt\npip install -e .\n```\n\nFinally, create the configuration file:\n\n```\n$ cat >~/.varfishrc.toml <<EOF\n[global]\n\n# URL to VarFish server.\nvarfish_server_url = \"https://varfish.example.com/\"\n# API token to use for VarFish API.\nvarfish_api_token = \"XXX\"\nEOF\n```\n\n### GitHub Project Management with Terraform\n\n```\nexport GITHUB_OWNER=bihealth\nexport GITHUB_TOKEN=ghp_<thetoken>\n\ncd utils/terraform\nterraform init\nterraform import github_repository.varfish-cli varfish-cli\nterraform validate\nterraform fmt\nterraform plan\nterraform apply\n```\n\n\n# Changelog\n\n## [0.6.3](https://github.com/varfish-org/varfish-cli/compare/v0.6.2...v0.6.3) (2024-01-24)\n\n\n### Bug Fixes\n\n* write out .sample_data in dragen-to-bam-qc ([#101](https://github.com/varfish-org/varfish-cli/issues/101)) ([#102](https://github.com/varfish-org/varfish-cli/issues/102)) ([638c294](https://github.com/varfish-org/varfish-cli/commit/638c2945d1ea8c4951c5d235f3aef231dcc604c6))\n\n\n### Documentation\n\n* fix link to pypi in README ([#97](https://github.com/varfish-org/varfish-cli/issues/97)) ([8f25193](https://github.com/varfish-org/varfish-cli/commit/8f25193f5fd313def2457f03e338992aa04eaf9f))\n\n## [0.6.2](https://github.com/bihealth/varfish-cli/compare/v0.6.1...v0.6.2) (2024-01-23)\n\n\n### Bug Fixes\n\n* properly assign version in release-please ([#91](https://github.com/bihealth/varfish-cli/issues/91)) ([3037f7a](https://github.com/bihealth/varfish-cli/commit/3037f7a44ec4a6a1be641d4ee8c327c11bfacaa2))\n* version for release-please in CI ([#89](https://github.com/bihealth/varfish-cli/issues/89)) ([2aedb64](https://github.com/bihealth/varfish-cli/commit/2aedb6465237211133625ef19be601e43d47be9b))\n\n\n### Documentation\n\n* add pypi and bioconda badges ([#96](https://github.com/bihealth/varfish-cli/issues/96)) ([88c7f79](https://github.com/bihealth/varfish-cli/commit/88c7f79150ca921fe21116fa4c8523840c8d22b2))\n\n## [0.6.1](https://github.com/bihealth/varfish-cli/compare/v0.6.0...v0.6.1) (2024-01-23)\n\n\n### Continuous Integration\n\n* install setuptools to fix \"python sdist\" in release-please ([#87](https://github.com/bihealth/varfish-cli/issues/87)) ([9b03c68](https://github.com/bihealth/varfish-cli/commit/9b03c687e34f9e94533fbd04f02b2d4baa65e759))\n\n## [0.6.0](https://github.com/bihealth/varfish-cli/compare/v0.5.3...v0.6.0) (2024-01-23)\n\n\n### Features\n\n* add \"projects project-list\" command ([#50](https://github.com/bihealth/varfish-cli/issues/50)) ([057abd5](https://github.com/bihealth/varfish-cli/commit/057abd56667e2b089ee2d30a4c761fd4b67a7278))\n* conversion from DRAGEN QC to legacy varfish format ([#85](https://github.com/bihealth/varfish-cli/issues/85)) ([#86](https://github.com/bihealth/varfish-cli/issues/86)) ([043dbc3](https://github.com/bihealth/varfish-cli/commit/043dbc3437dfc2d938a3ba5a4a4ea91ffa12be4f))\n* migrate argparse code to typer ([#48](https://github.com/bihealth/varfish-cli/issues/48)) ([#61](https://github.com/bihealth/varfish-cli/issues/61)) ([d1c86d4](https://github.com/bihealth/varfish-cli/commit/d1c86d43be19b66c5f3429c62772e2febadf119c))\n* migration from attrs to pydantic ([#49](https://github.com/bihealth/varfish-cli/issues/49)) ([#65](https://github.com/bihealth/varfish-cli/issues/65)) ([2c9e402](https://github.com/bihealth/varfish-cli/commit/2c9e402b66731e35f2214eaca52d3ae49069613b))\n\n\n### Documentation\n\n* installation instructions in manual ([#69](https://github.com/bihealth/varfish-cli/issues/69)) ([0afb87c](https://github.com/bihealth/varfish-cli/commit/0afb87c377ebda2f50892afff4ab857bce34e4a9))\n* updating README, adding terraform docs ([#68](https://github.com/bihealth/varfish-cli/issues/68)) ([f6dd1bf](https://github.com/bihealth/varfish-cli/commit/f6dd1bf850d3f1ac8637f15d165ac262d1f93b2b))\n\n## [0.5.3](https://github.com/bihealth/varfish-cli/compare/v0.5.2...v0.5.3) (2023-07-17)\n\n\n### Features\n\n* force release of 0.6 ([#46](https://github.com/bihealth/varfish-cli/issues/46)) ([f003be8](https://github.com/bihealth/varfish-cli/commit/f003be8b1f953ff4ab22f7d274264747dd39870d))\n\n\n### Bug Fixes\n\n* allow varfish upload without SV effects ([#43](https://github.com/bihealth/varfish-cli/issues/43)) ([4aead65](https://github.com/bihealth/varfish-cli/commit/4aead65054e97adf7564f8fb3d3a3e0db755c34f))\n* fixing issue with logging ([ab62f24](https://github.com/bihealth/varfish-cli/commit/ab62f242445150c2472aa45ea0c0f6d7782a7b8c))\n\n### [0.5.2](https://www.github.com/bihealth/varfish-cli/compare/v0.5.1...v0.5.2) (2023-07-17)\n\n\n### Bug Fixes\n\n* allow varfish upload without SV effects ([#43](https://www.github.com/bihealth/varfish-cli/issues/43)) ([4aead65](https://www.github.com/bihealth/varfish-cli/commit/4aead65054e97adf7564f8fb3d3a3e0db755c34f))\n* Fixing case list API ([#37](https://www.github.com/bihealth/varfish-cli/issues/37)) ([ccaccfc](https://www.github.com/bihealth/varfish-cli/commit/ccaccfcbec7fb209492f1855b5e740f20ac60bbc))\n\n### [0.5.2](https://www.github.com/bihealth/varfish-cli/compare/v0.5.1...v0.5.2) (2023-06-12)\n\n\n### Bug Fixes\n\n* Fixing case list API ([#37](https://www.github.com/bihealth/varfish-cli/issues/37)) ([ccaccfc](https://www.github.com/bihealth/varfish-cli/commit/ccaccfcbec7fb209492f1855b5e740f20ac60bbc))\n\n### [0.5.1](https://www.github.com/bihealth/varfish-cli/compare/v0.5.0...v0.5.1) (2023-02-09)\n\n\n### Bug Fixes\n\n* manifest for readme and changelog ([#35](https://www.github.com/bihealth/varfish-cli/issues/35)) ([f14d647](https://www.github.com/bihealth/varfish-cli/commit/f14d6472728995b9e18726fbfb7c36e86319c999))\n\n## [0.5.0](https://www.github.com/bihealth/varfish-cli/compare/v0.4.0...v0.5.0) (2023-02-09)\n\n\n### Features\n\n* replace python-Levenshtein with polyleven ([#26](https://www.github.com/bihealth/varfish-cli/issues/26)) ([#32](https://www.github.com/bihealth/varfish-cli/issues/32)) ([73703bd](https://www.github.com/bihealth/varfish-cli/commit/73703bd73796b066de689954caa19a5767f97d76))\n\n\n### Documentation\n\n* fixing CI status badge ([#34](https://www.github.com/bihealth/varfish-cli/issues/34)) ([9967bbd](https://www.github.com/bihealth/varfish-cli/commit/9967bbd7a706d8338c188468a67a8bbebdb7a330))\n\n## 0.4.0\n\n- Adding support for varannos REST API (#24).\n\n## 0.3.5\n\n- Allowing to upload per-case gene annotation file (#20).\n- Adding client endpoint for retrieving case from API (#18).\n\n## 0.3.4\n\n- Adding support for latest varfish-annotator output for svs (#16).\n\n## 0.3.3\n\n- Case importer distinguished smallvar and SV DB info files (#13).\n\n## 0.3.2\n\n- Fixing structuring/unstructuring of genomic region\n\n## 0.3.1\n\n- Allow disabling of `verify_ssl` in CLI\n\n## 0.3.0\n\n- Adding implementation of REST API (#7).\n\n## 0.2.8\n\n- Adding support to specify genome build on import (defaulting to GRCh37).\n\n## 0.2.7\n\n- Fix reading of non-compressed genotypes TSV file.\n\n## 0.2.6\n\n- Fixes to linting.\n\n## 0.2.5\n\n- Switching build system to Github Actions\n- Adding many tests\n- Fixing `verify_ssl` for case list.\n\n## 0.2.4\n\n- Added `--no-verify-ssl`.\n\n## 0.2.3\n\n- Added state field to `VariantSetImportInfo` class.\n- Added endpoint for updating variant set import info.\n\n## 0.2.2\n\n- More `MANIFEST.in` fixes.\n\n## 0.2.1\n\n- Fixing package (`MANIFEST.in`).\n\n## 0.2.0\n\n- Adjusted to upstream REST API changes.\n- Cases with all files can now be uploaded.\n\n## 0.1.0\n\n- everything is new\n",
    "bugtrack_url": null,
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Manuel Holtgrewe
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