Metadata-Version: 2.1
Name: ga4gh.vrs
Version: 0.6.2
Summary: "GA4GH Variation Representation Specification (VRS) reference implementation (https://github.com/ga4gh/vrs-python/)"
Home-page: https://github.com/ga4gh/vrs-python
Author: Reece Hart
Author-email: reecehart@gmail.com
License: UNKNOWN
Description: vrs-python
        !!!!!!!!!!
        
        
        |ci_rel| | |cov| | |pypi_rel|
        
        vrs-python provides Python language support for the [GA4GH Variation
        Representation Specification
        (VRS)](https://github.com/ga4gh/vr-spec).
        
        This repository contains several related components:
        
        * **ga4gh.vrs package** Python language support for the spec. 
        
        * **ga4gh.vrs.extras package** Python language support for additional
          functionality, including translating from and to other variant
          formats and a REST service to similar functionality.
          `ga4gh.vrs.extras` requires access to supporting data, as described
          below.
        
        * **Jupyter notebooks** Demonstrations of the functionality of
          `ga4gh.vrs` and `ga4gh.vrs.extras` in the form of easy-to-read
          notebooks.
        
        
        
        Installing ga4gh.vrs
        !!!!!!!!!!!!!!!!!!!!
        
        Installating with pip
        @@@@@@@@@@@@@@@@@@@@@
        
        ::
        
           $ pip install ga4gh.vrs[extras]
        
        The `[extras]` argument tells pip to install packages to fullfill the
        dependencies of the `ga4gh.vrs.extras` package.
        
        
        Installing for development
        @@@@@@@@@@@@@@@@@@@@@@@@@@
        
        The following instructions are for Ubuntu 18.04+ and MacOS.
        vrs-python is unlikely to work on Windows due to dependencies.
        
        ::
        
           $ git clone --recurse-submodules https://github.com/ga4gh/vrs-python.git
           $ cd vrs-python
           $ make devready
        
        (Python 3.5 and 3.6 should also work.)
        
        
        
        Installing Dependencies for ga4gh.vrs.extras
        !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
        
        The `ga4gh.vrs.extras` modules are not part of the VR spec per se.
        They are bundled with ga4gh.vrs for development and installation
        convenience.  These modules depend directly and indrectly on external
        data sources of sequences, transcripts, and genome-transcript
        alignments.  This section recommends one way to install the biocommons
        tools that provide these data.
        
        
        ::
        
           $ docker volume create --name=uta_vol
           $ docker volume create --name=seqrepo_vol
           $ docker-compose -f misc/stack/docker-compose.yml up
        
        This should start three containers:
        * [seqrepo](https://github.com/biocommons/seqrepo): a non-redundant archive of sequences
        * [seqrepo-rest-service](https://github.com/biocommons/seqrepo-rest-service): a REST service on seqrepo (localhost:5000)
        * [uta](https://github.com/biocommons/uta): a database of transcripts and alignments (localhost:5432)
        
        The seqrepo container will exit as soon as the data are downloaded.
        
        ::
        
           $ docker ps
           CONTAINER ID        IMAGE                                    //  NAMES
           86e872ab0c69        biocommons/seqrepo-rest-service:latest   //  stack_seqrepo-rest-service_1
           a40576b8cf1f        biocommons/uta:uta_20180821              //  stack_uta_1
        
        
        
        Running the Notebooks
        !!!!!!!!!!!!!!!!!!!!!
        
        Once installed as described above, type::
        
          $ source venv/3.7/bin/activate
          $ jupyter notebook --notebook-dir notebooks/
        
        
        The following jupyter extensions are recommended but not required::
        
          $ pip install jupyter_contrib_nbextensions
          $ jupyter contrib nbextension install --user
          $ jupyter nbextension enable toc2/main
          
        
        
        Security Note (from the GA4GH Security Team)
        !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
        
        A stand-alone security review has been performed on the specification
        itself.  This implementation is offered as-is, and without any
        security guarantees. It will need an independent security review
        before it can be considered ready for use in security-critical
        applications. If you integrate this code into your application it is
        AT YOUR OWN RISK AND RESPONSIBILITY to arrange for a security audit.
        
        
        .. |pypi_rel| image:: https://badge.fury.io/py/ga4gh.vrs.png
          :target: https://pypi.org/project/ga4gh.vrs
          :align: middle
        
        .. |ci_rel| image:: https://travis-ci.org/ga4gh/vrs-python.svg?branch=master
          :target: https://travis-ci.org/ga4gh/vrs-python
          :align: middle 
        
        .. |cov| image:: https://coveralls.io/repos/github/ga4gh/vrs-python/badge.svg?branch=
          :target: https://coveralls.io/github/ga4gh/vrs-python?branch=
        
Keywords: bioinformatics,ga4gh,genomics,hgvs,spdi,variation
Platform: any
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: >=3.6
Description-Content-Type: text/x-rst; charset=UTF-8
Provides-Extra: dev
Provides-Extra: extras
Provides-Extra: notebooks
