Metadata-Version: 2.1
Name: aacrgenie
Version: 14.1.0
Summary: AACR Project GENIE ETL
Home-page: https://github.com/Sage-Bionetworks/Genie
Author: Thomas Yu
Author-email: thomas.yu@sagebionetworks.org
License: MIT
Project-URL: Bug Tracker, https://github.com/Sage-Bionetworks/Genie/issues
Project-URL: Source Code, https://github.com/Sage-Bionetworks/Genie
Platform: any
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering
Requires-Python: <3.10,>=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: synapseclient (>=2.5.1)
Requires-Dist: pandas (>=1.0)
Requires-Dist: httplib2 (>=0.11.3)
Requires-Dist: pycryptodome (>=3.12.0)
Requires-Dist: PyYAML (>=5.1)
Requires-Dist: chardet (>=3.0.4)

![genie banner](https://raw.githubusercontent.com/Sage-Bionetworks/Genie/master/genie_banner.png)

# AACR Project GENIE

[![PyPi](https://img.shields.io/pypi/v/aacrgenie.svg?style=for-the-badge&label=PyPi&logo=PyPi)](https://pypi.org/project/aacrgenie)
[![Docker Automated](https://img.shields.io/docker/automated/sagebionetworks/genie.svg?style=for-the-badge&logo=docker)](https://hub.docker.com/r/sagebionetworks/genie)
[![GitHub CI](https://img.shields.io/github/workflow/status/Sage-Bionetworks/Genie/build.svg?&style=for-the-badge&logo=github)](https://github.com/nlpsandbox/nlpsandbox-client)


## Introduction

This repository documents code used to gather, QC, standardize, and analyze data uploaded by institutes participating in AACR's Project GENIE (Genomics, Evidence, Neoplasia, Information, Exchange). 

## Dependencies

These are tools or packages you will need, to be able to reproduce these results:
- Python 3.7 or higher
- `pip install -r requirements.txt`
- [bedtools](https://bedtools.readthedocs.io/en/latest/content/installation.html)

## File Validator

```
pip install aacrgenie
genie -v
```

This will install all the necessary components for you to run the validator locally on all of your files, including the Synapse client.  Please view the help to see how to run to validator.

```
genie validate -h
genie validate data_clinical_supp_SAGE.txt SAGE
```

## Contributing

Please view [contributing guide](CONTRIBUTING.md) to learn how to contribute to the GENIE package.


