varfish-cli 0.5.0

Command line interface client for VarFish Server.

VarFish CLI

Command line interface for VarFishServer.

Getting Started

• VarFish Homepage
• Manual
  • Installation Instructions
• Docker Compose Installer

VarFish Repositories

• varfish-server -- The VarFish Server is the web frontend used by the end users / data analysts.
• 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 -- The VarFish Command Line Interface allows to import data through the VarFish REST API.
• varfish-db-downloader -- The VarFish DB Downloader is a command line tool for downloading the background database.
• 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

$ git clone [e-mail]: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.

$ 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 (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