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
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
v0.4.0
Adding support for varannos REST API (#24).
v0.3.5
Allowing to upload per-case gene annotation file (#20).
Adding client endpoint for retrieving case from API (#18).
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
Project details
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