Metadata-Version: 2.1
Name: newt-transformer
Version: 0.1.6
Summary: Amphibious new data transformer to prepare various sources for CGP DSS Data Loader
Home-page: https://github.com/DataBiosphere/newt-transformer
Author: Jesse Brennan
Author-email: brennan@ucsc.edu
License: Apache License 2.0
Description: # newt-transformer
        [![Build Status](https://travis-ci.org/DataBiosphere/newt-transformer.svg?branch=master)](https://travis-ci.org/DataBiosphere/newt-transformer)
        
        Metadata transformer to convert from gen3 to something readable by 
        cgp-dss-data-loader
        
        ## Common Setup
        
        1. **(optional)**  We recommend using a Python 3
           [virtual environment](https://docs.python.org/3/tutorial/venv.html).
        
        1. Run:
        
           `pip3 install newt-transformer`
        
        ## Setup for Development
        1. Clone the repo:
        
           `git clone https://github.com/jessebrennan/newt-transformer.git`
        
        1. Go to the root directory of the cloned project:
        
           `cd newt-transformer`
        
        1. Run (ideally in a new [virtual environment](https://docs.python.org/3/tutorial/venv.html)):
        
           `make develop`
        
        ## Running Tests
        1. make sure you followed Setup for Development
        
        1. Run:
        
           `make test`
        
        ## Transforming data from sheepdog-exporter
        1. The first step is to extract the Gen3 data you want using the
        [sheepdog exporter](https://github.com/david4096/sheepdog-exporter). The TopMed public data extracted
        from sheepdog is available [on the release page](https://github.com/david4096/sheepdog-exporter/releases/tag/0.3.1)
        under Assets. Assuming you use this data, you will now have a file called `topmed-public.json`
        
        1. Make sure you are running the virtual environment you set up in the **Setup** instructions.
        
        1. Now we need to transform the data. From the root of the project run:
        
           `newt new /path/to/topmed-public.json --output-json transformed-topmed-public.json`
        
           This will generate a transformed output file called `transformed-topmed-public.json`.
        
           The `new` argument specifies that we want the most recent version of the transformer output format.
           It can be replaced with a `gen3` argument, but this older format will soon be deprecated.
        
        1. Likely you want to upload this data to the DSS. Instructions for this can be found  at
           [the DSS data loader repo](https://github.com/DataBiosphere/cgp-dss-data-loader).
        
        ## Transformer Architecture
        ![see github for details](diagrams/newt-architecture.svg)
        
Keywords: genomics,metadata,NIHDataCommons
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
