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        "description": "# bdbag\n[![Build Status](https://travis-ci.org/fair-research/bdbag.svg)](https://travis-ci.org/fair-research/bdbag)\n[![Coverage Status](https://img.shields.io/coveralls/github/fair-research/bdbag/master.svg)](https://coveralls.io/github/fair-research/bdbag?branch=master)\n[![PyPi Version](https://img.shields.io/pypi/v/bdbag.svg)](https://pypi.python.org/pypi/bdbag)\n[![PyPi Wheel](https://img.shields.io/pypi/wheel/bdbag.svg)](https://pypi.python.org/pypi/bdbag)\n[![Python Versions](https://img.shields.io/pypi/pyversions/bdbag.svg)](https://pypi.python.org/pypi/bdbag)\n[![License](https://img.shields.io/pypi/l/bdbag.svg)](http://www.apache.org/licenses/LICENSE-2.0)\n\n## Big Data Bag Utilities\n\nThe `bdbag` utilities are a collection of software programs for working with\n[BagIt](https://datatracker.ietf.org/doc/draft-kunze-bagit/) packages that conform to the BDBag and Bagit/RO profiles.\n\nThe `bdbag` [profiles](https://github.com/fair-research/bdbag/tree/master/profiles) specify the use of the fetch.txt file, require serialization, and specify what manifests must be provided with a *bdbag*.\n\nThese utilities combine various other components such as the\n[Bagit-Python](https://github.com/LibraryOfCongress/bagit-python) bag creation utility and the\n[Bagit-Profiles-Validator](https://github.com/ruebot/bagit-profiles)\nutility into a single, easy to use software package.\n\nEnhanced bag support includes:\n\n* Update-in-place functionality for existing bags.\n* Automatic archiving and extraction of bags using ZIP, TAR, and TGZ formats.\n* Automatic generation of remote file manifest entries and fetch.txt via configuration file.\n* Automatic file retrieval based on the contents of a bag's fetch.txt file with multiple protocol support.\n* Built-in profile validation.\n* Built-in support for creation of bags with [Bagit/RO profile](https://github.com/ResearchObject/bagit-ro) compatibility.\n\nAn experimental Graphical User Interface (GUI) for `bdbag` can be found [here](https://github.com/fair-research/bdbag_gui).\n\n#### Technical Papers\n\n[\"I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets\"](https://zenodo.org/record/820878) explains the motivation for BDBags and the related Minid construct, provides details on design and implementation, and gives examples of use. \n\n[\"Reproducible big data science: A case study in continuous FAIRness\"](https://www.biorxiv.org/content/early/2018/02/27/268755) presents a data analysis use case in which BDBags and Minids are used to capture a transcription factor binding site analysis.\n\n### Dependencies\n\n* [Python 2.7](https://www.python.org/downloads/release/python-27/) is the minimum Python version required.\n* The code and dependencies are also compatible with Python 3, versions 3.4 through 3.7.\n\n### Installation\nThe latest `bdbag` release is available on PyPi and can be installed using `pip`:\n\n```sh\npip install bdbag\n```\n\nNote that the above command will install `bdbag` with only the minimal dependencies required to run.\nIf you wish to install `bdbag` with the extra fetch transport handler support provided by `boto` (for AWS S3)\nand `globus` (for Globus Transfer) packages, use the following command:\n```sh\npip install bdbag[boto,globus]\n```\n\n### Installation from Source\nYou can use `pip` to install `bdbag` directly from GitHub:\n\n```sh\nsudo pip install git+https://github.com/fair-research/bdbag\n```\nor:\n```sh\npip install --user git+https://github.com/fair-research/bdbag\n```\n\nYou can also [download](https://github.com/fair-research/bdbag/archive/master.zip) the current `bdbag` source code from GitHub or\nalternatively clone the source from GitHub if you have *git* installed:\n\n```sh\ngit clone https://github.com/fair-research/bdbag\n```\nFrom the root of the `bdbag` source code directory execute the following command:\n```sh\nsudo pip install .\n```\nor:\n```sh\npip install --user .\n```\nNote that if you want to install the extra dependencies from a local source directory you would use the following command:\n```sh\npip install .[boto,globus]\n```\n\n### Testing\nThe unit tests can be run by invoking the following command from the root of the `bdbag` source code directory:\n```sh\npython setup.py test\n```\n\n### Usage\n\nThis software can be used from the command-line environment by running the `bdbag` script.  For detailed usage\ninstructions, see the [CLI Guide](./doc/cli.md).\n\n### Configuration\n\nSome components of the `bdbag` software can be configured via JSON-formatted configuration files.\nSee the [Configuration Guide](./doc/config.md) for further details.\n\n### Application Programming Interface\n\nIt is also possible to use `bdbag` from within other Python programs via an API.\nSee the [API Guide](./doc/api.md) for further details.\n\n### Utilities\n\nA CLI utility module is provided for various ancillary tasks commonly involved with authoring **bdbags**.\nSee the [Utility Guide](./doc/utils.md) for further details.\n\n### Change Log\n\nThe change log is located [here](CHANGELOG.md).\n\n\n",
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