Metadata-Version: 1.1
Name: varfish_cli
Version: 0.3.4
Summary: Command line interface client for VarFish Server.
Home-page: https://github.com/bihealth/varfish-cli
Author: Manuel Holtgrewe
Author-email: manuel.holtgrewe@bihealth.de
License: MIT license
Description: .. image:: https://github.com/bihealth/varfish-cli/workflows/CI/badge.svg
            :target: https://github.com/bihealth/varfish-cli/actions
            :alt: Continuous Integration Status
        .. image:: https://app.codacy.com/project/badge/Grade/83ee38265942489193d6ce8a547eb9f9
            :target: https://www.codacy.com/gh/bihealth/varfish-cli/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=bihealth/varfish-cli&amp;utm_campaign=Badge_Grade
        .. image:: https://app.codacy.com/project/badge/Coverage/83ee38265942489193d6ce8a547eb9f9
            :target: https://www.codacy.com/gh/bihealth/varfish-cli/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=bihealth/varfish-cli&amp;utm_campaign=Badge_Coverage
        .. image:: https://img.shields.io/badge/License-MIT-green.svg
            :alt: MIT License
            :target: https://opensource.org/licenses/MIT
        
        ===========
        VarFish CLI
        ===========
        
        Command line interface for [VarFishServer](https://github.com/bihealth/varfish-server)
        
        ---------------
        Getting Started
        ---------------
        
        - `VarFish Homepage <https://www.cubi.bihealth.org/software/varfish/>`__
        - `Manual <https://varfish-server.readthedocs.io/en/latest/>`__
            - `Installation Instructions <https://varfish-server.readthedocs.io/en/latest/admin_install.html>`__.
        - `Docker Compose Installer <https://github.com/bihealth/varfish-docker-compose#run-varfish-server-using-docker-compose>`__.
        
        --------------------
        VarFish Repositories
        --------------------
        
        `varfish-server <https://github.com/bihealth/varfish-server>`__
            The VarFish Server is the web frontend used by the end users / data analysts.
        `varfish-annotator <https://github.com/bihealth/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 <https://github.com/bihealth/varfish-cli>`__
            The VarFish Command Line Interface allows to import data through the VarFish REST API.
        `varfish-db-downloader <https://github.com/bihealth/varfish-db-downloader>`__
            The VarFish DB Downloader is a command line tool for downloading the background database.
        `varfish-docker-compose <https://github.com/bihealth/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
        ------------
        
        .. code-block:: bash
        
            $ 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.
        
        .. code-block:: bash
            
            $ 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
        ---------
        
        .. code-block:: bash
        
            $ $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
        
Keywords: varfish_cli
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
