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        "author": "Jesse Brennan",
        "author_email": "brennan@ucsc.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "# newt-transformer\n[![Build Status](https://travis-ci.org/DataBiosphere/newt-transformer.svg?branch=master)](https://travis-ci.org/DataBiosphere/newt-transformer)\n\nMetadata transformer to convert from gen3 to something readable by \ncgp-dss-data-loader\n\n## Common Setup\n\n1. **(optional)**  We recommend using a Python 3\n   [virtual environment](https://docs.python.org/3/tutorial/venv.html).\n\n1. Run:\n\n   `pip3 install newt-transformer`\n\n## Setup for Development\n1. Clone the repo:\n\n   `git clone https://github.com/jessebrennan/newt-transformer.git`\n\n1. Go to the root directory of the cloned project:\n\n   `cd newt-transformer`\n\n1. Run (ideally in a new [virtual environment](https://docs.python.org/3/tutorial/venv.html)):\n\n   `make develop`\n\n## Running Tests\n1. make sure you followed Setup for Development\n\n1. Run:\n\n   `make test`\n\n## Transforming data from sheepdog-exporter\n1. The first step is to extract the Gen3 data you want using the\n[sheepdog exporter](https://github.com/david4096/sheepdog-exporter). The TopMed public data extracted\nfrom sheepdog is available [on the release page](https://github.com/david4096/sheepdog-exporter/releases/tag/0.3.1)\nunder Assets. Assuming you use this data, you will now have a file called `topmed-public.json`\n\n1. Make sure you are running the virtual environment you set up in the **Setup** instructions.\n\n1. Now we need to transform the data. From the root of the project run:\n\n   `newt new /path/to/topmed-public.json --output-json transformed-topmed-public.json`\n\n   This will generate a transformed output file called `transformed-topmed-public.json`.\n\n   The `new` argument specifies that we want the most recent version of the transformer output format.\n   It can be replaced with a `gen3` argument, but this older format will soon be deprecated.\n\n1. Likely you want to upload this data to the DSS. Instructions for this can be found  at\n   [the DSS data loader repo](https://github.com/DataBiosphere/cgp-dss-data-loader).\n\n## Transformer Architecture\n![see github for details](diagrams/newt-architecture.svg)",
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        "keywords": "genomics,metadata,NIHDataCommons",
        "license": "Apache License 2.0",
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