Command line interface client for VarFish Server.
Project description
VarFish Command Line Interface
Command line interface for bihealth/varfish-server.
[!NOTE] This repository focuses on the command line interface program
varfish-cli
. If you are new to VarFish, you may want to start at the repository bihealth/varfish-server.
- User Manual: varfish-cli user manual
Installation
You can install varfish-cli
from bioconda:
To create a new conda environment named varfish-cli
with the package:
mamba create -y -n varfish-cli -c bioconda varfish-cli
conda activate varfish-cli
varfish-cli --help
To get help with individual sub commands:
varfish-cli importer
# OR
varfish-cli importer --help
You will also need to create a configuration file in your home folder with the server address:
$ 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
Developer Information
Development Setup
Preqrequisites:
- Python >=3.10
Clone the repository:
git clone git@github.com:bihealth/varfish-cli.git
cd varfish-cli-ng
Now, create a virtualenv and install the software and its development requirements:
virtualenv venv
source venv/bin/activate
pip install -r requirements/develop.txt
pip install -e .
Finally, create the configuration file:
$ 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
GitHub Project Management with Terraform
export GITHUB_OWNER=bihealth
export GITHUB_TOKEN=ghp_<thetoken>
cd utils/terraform
terraform init
terraform import github_repository.varfish-cli varfish-cli
terraform validate
terraform fmt
terraform plan
terraform apply
Changelog
0.6.2 (2024-01-23)
Bug Fixes
- properly assign version in release-please (#91) (3037f7a)
- version for release-please in CI (#89) (2aedb64)
Documentation
0.6.1 (2024-01-23)
Continuous Integration
0.6.0 (2024-01-23)
Features
- add "projects project-list" command (#50) (057abd5)
- conversion from DRAGEN QC to legacy varfish format (#85) (#86) (043dbc3)
- migrate argparse code to typer (#48) (#61) (d1c86d4)
- migration from attrs to pydantic (#49) (#65) (2c9e402)
Documentation
- installation instructions in manual (#69) (0afb87c)
- updating README, adding terraform docs (#68) (f6dd1bf)
0.5.3 (2023-07-17)
Features
Bug Fixes
0.5.2 (2023-07-17)
Bug Fixes
0.5.2 (2023-06-12)
Bug Fixes
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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