Command line interface client for VarFish Server.
Project description
VarFish CLI
Command line interface for [VarFishServer](https://github.com/bihealth/varfish-server)
Getting Started
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 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
Releasing
$ $EDITOR HISTORY.rst
$ git tag ...
$ rm -rf dist
$ python setup.py sdist
$ twine dist/*.tar.gz
History
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
Project details
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