Metadata-Version: 2.1
Name: varfish-cli
Version: 0.5.0
Summary: Command line interface client for VarFish Server.
Home-page: https://github.com/bihealth/varfish-cli
Author: Manuel Holtgrewe
Author-email: manuel.holtgrewe@bihealth.de
License: MIT license
Keywords: varfish_cli
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: AUTHORS.rst

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# VarFish CLI

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

## Getting Started

- [VarFish Homepage](https://www.cubi.bihealth.org/software/varfish/)
- [Manual](https://varfish-server.readthedocs.io/en/latest/)
    - [Installation Instructions](https://varfish-server.readthedocs.io/en/latest/admin_install.html)
- [Docker Compose Installer](https://github.com/bihealth/varfish-docker-compose#run-varfish-server-using-docker-compose)

## VarFish Repositories

- [varfish-server](https://github.com/bihealth/varfish-server) --
  The VarFish Server is the web frontend used by the end users / data analysts.
- [varfish-annotator](https://github.com/bihealth/varfish-annotator) --
  The VarFish Annotator is a command line utility used for annotating VCF files and converting them to files that can be imported into VarFish Server.
- [varfish-cli](https://github.com/bihealth/varfish-cli) --
  The VarFish Command Line Interface allows to import data through the VarFish REST API.
- [varfish-db-downloader](https://github.com/bihealth/varfish-db-downloader) --
  The VarFish DB Downloader is a command line tool for downloading the background database.
- [varfish-docker-compose](https://github.com/bihealth/varfish-docker-compose) --
  Quickly get started running a VarFish server by using Docker Compose.
  We provide a prebuilt data set with some already imported data.

## Installation

### From Source

```bash
$ git clone git@github.com:bihealth/varfish-cli.git
$ cd varfish-cli
$ conda create -n varfish-cli python=3.7
$ conda activate varfish-cli
$ pip install -e .
$ 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
```

### Using pip


`varfish-cli` is also available as a pip-Package.
Preferably install into a separate venv.

```bash
$ pip install varfish-cli
$ 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
```


# Changelog

## [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
