varfish-cli 0.3.4

Command line interface client for VarFish Server.

VarFish CLI

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

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

$ 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

Releasing

$ $EDITOR HISTORY.rst
$ git tag ...
$ rm -rf dist
$ python setup.py sdist
$ twine upload dist/*.tar.gz

History

v0.3.4

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

v0.3.3

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

v0.3.2

• Fixing structuring/unstructuring of genomic region

v0.3.1

• Allow disabling of verify_ssl in CLI

v0.3.0

• Adding implementation of REST API (#7).

v0.2.8

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

v0.2.7

• Fix reading of non-compressed genotypes TSV file.

v0.2.6

• Fixes to linting.

v0.2.5

• Switching build system to Github Actions

• Adding many tests

• Fixing verify_ssl for case list.

v0.2.4

• Added --no-verify-ssl.

v0.2.3

• Added state field to VariantSetImportInfo class.

• Added endpoint for updating variant set import info.

v0.2.2

• More MANIFEST.in fixes.

v0.2.1

• Fixing package (MANIFEST.in).

v0.2.0

• Adjusted to upstream REST API changes.

• Cases with all files can now be uploaded.

v0.1.0

• everything is new