Command line interface client for VarFish Server.
Project description
VarFish CLI
Command line interface for VarFishServer.
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
From Source
$ 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
Changelog
0.5.1 (2023-02-09)
Bug Fixes
0.5.0 (2023-02-09)
Features
Documentation
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
Project details
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