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            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
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        "description": "sevenbridges-python\n===================\n\n[![Travis](https://travis-ci.org/sbg/sevenbridges-python.svg)](https://travis-ci.org/sbg/sevenbridges-python)\n[![PyPI version](https://badge.fury.io/py/sevenbridges-python.svg)](https://pypi.python.org/pypi/sevenbridges-python)\n[![Documentation](https://readthedocs.org/projects/sevenbridges-python/badge/?version=latest)](http://sevenbridges-python.readthedocs.org/en/latest/)\n[![Licence](https://img.shields.io/badge/licence-Apache-orange.svg)](https://github.com/sbg/sevenbridges-python/blob/develop/LICENCE)\n\n[CHANGESETS](https://github.com/sbg/sevenbridges-python/blob/develop/CHANGES.md)\n\nsevenbridges-python is a [Python](http://www.python.org/) library that\nprovides an interface for the [Seven Bridges Platform](https://www.sbgenomics.com/) the\n[Cancer Genomics Cloud](http://www.cancergenomicscloud.org/) and\n[Cavatica](http://www.cavatica.org) public APIs. It works with Python\nversions 2.6+ and supports Python 3.\n\nThe [Seven Bridges Platform](https://www.sbgenomics.com/) is a\ncloud-based environment for conducting bioinformatic analyses. It is a\ncentral hub for teams to store, analyze, and jointly interpret their\nbioinformatic data. The Platform co-locates analysis pipelines alongside\nthe largest genomic datasets to optimize processing, allocating storage\nand compute resources on demand.\n\nThe [The Cancer Genomics Cloud (CGC)](http://www.cancergenomicscloud.org/), powered by\n[Seven Bridges](https://www.sbgenomics.com/), is also a cloud-based computation\nenvironment. It was built as one of three pilot systems funded by the\n[National Cancer Institute](http://www.cancer.gov/) to explore the\nparadigm of colocalizing massive genomics datasets, like The\n[Cancer Genomics Atlas (TCGA)](http://cancergenome.nih.gov/), alongside secure\nand scalable computational resources to analyze them. The CGC makes more\nthan a petabyte of multi-dimensional data available immediately to\nauthorized researchers. You can add your own data to analyze alongside\nTCGA using predefined analytical workflows or your own tools.\n\n[Cavatica](http://www.cavatica.org/),\npowered by [Seven Bridges](https://www.sbgenomics.com/), is a data analysis and sharing\nplatform designed to accelerate discovery in a scalable, cloud-based\ncompute environment where data, results, and workflows are shared among\nthe world's research community. Cavatica is built in collaboration with\nthe Children Hospital of Philadelphia and it is focused on pediatric\ndata.\n\nDocumentation\n-------------\n\nThe latest documentation can be found on [readthedocs](http://sevenbridges-python.readthedocs.org/en/latest).\n\nInstallation\n------------\n\nThe easiest way to install sevenbridges-python is using pip. :\n\n    $ pip install sevenbridges-python\n\nGet the Code\n------------\n\nsevenbridges-python is actively developed on GitHub, where the code is\nalways available.\n\nThe easiest way to obtain the source is to clone the public repository :\n\n    $ git clone git://github.com/sbg/sevenbridges-python.git\n\nOnce you have a copy of the source, you can embed it in your Python\npackage, or install it into your site-packages by invoking: :\n\n    $ python setup.py install\n\nIf you are interested in reviewing this documentation locally, clone\nthis repository, position yourself in the docs directory and after\ninstalling `requirements.txt` (or `requirements2.txt` if using python 2), invoke:\n\n    $ make html\n\nRun Tests\n---------\n\nIn order to run tests clone this repository, position yourself in the\nroot of the cloned project and after installing `requirements.txt` (or\n`requirements2.txt` if using python 2), invoke:\n\n    $ pytest\n\nAuthentication and Configuration\n--------------------------------\n\nIn order to authenticate with the API, you should pass the following\nitems to sevenbridges-python:\n\n(a) Your authentication token\n(b) The API endpoint you will be interacting with. This is either the\n    endpoint for the Seven Bridges Platform or for the Seven Bridges\n    Cancer Genomics Cloud (CGC) or for CAVATICA.\n\nYou can find your authentication token on the respective pages:\n\n- <https://igor.sbgenomics.com/developer> for the Seven Bridges Platform\n- <https://cgc.sbgenomics.com/developer> for the CGC\n- <https://cavatica.sbgenomics.com/developer> for Cavatica\n\nThe API endpoints for each environment are:\n\n- <https://api.sbgenomics.com/v2> for the Seven Bridges Platform\n- <https://cgc-api.sbgenomics.com/v2> for the CGC.\n- <https://cavatica-api.sbgenomics.com/v2> for CAVATICA\n\nFor more information about the API, including details of the available\nparameters for each API call, you should check the API documentation\nbefore using this library:\n\n- <http://docs.sevenbridges.com/docs/the-api> for the Seven Bridges Platform.\n- <http://docs.cancergenomicscloud.org/docs/the-cgc-api> for the CGC.\n- <http://docs.cavatica.org/docs/the-api> for CAVATICA\n\nInitialize configuration using the configuration file\n-----------------------------------------------------\n\nOnce you obtain your authentication token you can pass it to the Config\nobject. You can instantiate your API object by passing the appropriate\nconfiguration. There are three ways you can pass configure the library:\n\n1.  Pass parameters `url` and `token` explicitly when initializing the\n    config object.\n2.  Put the API endpoint and token in the environment variables\n    `API_URL` and `AUTH_TOKEN` respectively.\n3.  Use the configuration file `$HOME/.sevenbridges/credentials` with\n    defined parameters.\n\n### Explicit initialization\n\n```python\nimport sevenbridges as sbg\napi = sbg.Api(url='https://api.sbgenomics.com/v2', token='<TOKEN_HERE>')\n```\n\n### Initialization via environment variables\n\n```python\nimport sevenbridges as sbg\n\nimport os\n\n# Usually these would be set in the shell beforehand\nos.environ['SB_API_ENDPOINT'] = 'https://api.sbgenomics.com/v2'\nos.environ['SB_AUTH_TOKEN'] = '<TOKEN_HERE>'\n\napi = sbg.Api()\n```\n\n### Initialization via config file\n\n```python\nimport sevenbridges as sbg\nconfig = sbg.Config(profile='cgc')\napi = sbg.Api(config=config)\n```\n\n### Notes on config file format\n\nThe `$HOME/.sevenbridges/credentials` file has a simple .ini file\nformat, for example:\n\n    [default]\n    api_endpoint = https://api.sbgenomics.com/v2\n    auth_token = <TOKEN_HERE>\n\n    [cgc]\n    api_endpoint = https://cgc-api.sbgenomics.com/v2\n    auth_token = <TOKEN_HERE>\n\n    [cavatica]\n    api_endpoint = https://cavatica-api.sbgenomics.com/v2\n    auth_token = <TOKEN_HERE>\n\n#### Initializing the sevenbridges-python library\n\nThe API object represents the central resource for querying, saving and\nperforming all other actions on your resources. Once you have\ninstantiated the configuration class, pass it to the API class\nconstructor.\n\n```python\nimport sevenbridges as sbg\napi_config = sbg.Config()  # Or any other choice of initialization method\napi = sbg.Api(config=api_config)\n```\n\nExamples\n--------\n\nThe following code illustrates the way the library should be used. For\nmore detailed examples consult the documentation, hosted on readthedocs.\n\n```python\nimport sevenbridges as sbg\n\napi_config = sbg.Config()  # Or any other choice of initialization method\napi = sbg.Api(config=api_config)\n\n# Get current user\nuser = api.users.me()\n\n# Query your projects\nprojects = api.projects.query(limit=100)\n\n# Fetch project files\nproject = projects[0]\nfiles = project.get_files()\n```\n\nContributing\n------------\n\nContributions, bug reports and issues are very welcome.\n\nYou can make your own contributions by forking the develop branch of\nthis repository, making your changes, and issuing pull request on the\ndevelop branch. Contributors should read the [Seven Bridges Notice to Contributors](CONTRIBUTORS_NOTICE.md) and sign the [Seven Bridges Contributor Agreement](https://secure.na1.echosign.com/public/esignWidget?wid=CBFCIBAA3AAABLblqZhAqt_9rHEqy2MggS0uWRmKHUN2HYi8DWNjkgg5N68iKAhRFTy7k2AOEpRHMMorxc_0*)\nbefore submitting a pull request.\n\nCopyright\n---------\n\nCopyright (c) 2016-2018 Seven Bridges Genomics, Inc. All rights\nreserved.\n\nThis project is open-source via the [Apache 2.0 License](http://www.apache.org/licenses/LICENSE-2.0).",
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