Metadata-Version: 2.1
Name: submit-cgap
Version: 1.4.1
Summary: Support for uploading file submissions to the Clinical Genomics Analysis Platform (CGAP).
Home-page: https://github.com/dbmi-bgm/SubmitCGAP
License: MIT
Keywords: submit-cgap
Author: 4DN-DCIC Team
Author-email: support@4dnucleome.org
Requires-Python: >=3.6.1,<3.10
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Database :: Database Engines/Servers
Requires-Dist: awscli (>=1.18.174)
Requires-Dist: boto3 (>=1.16.14,<2)
Requires-Dist: dcicutils (>=3.9.0)
Requires-Dist: requests (>=2.24.0,<3)
Project-URL: Repository, https://github.com/dbmi-bgm/SubmitCGAP.git
Description-Content-Type: text/x-rst

==========
SubmitCGAP
==========


A file submission tool for CGAP
===============================

.. image:: https://travis-ci.org/dbmi-bgm/SubmitCGAP.svg
   :target: https://travis-ci.org/dbmi-bgm/SubmitCGAP
   :alt: Build Status

.. image:: https://coveralls.io/repos/github/dbmi-bgm/SubmitCGAP/badge.svg
   :target: https://coveralls.io/github/dbmi-bgm/SubmitCGAP
   :alt: Coverage

.. image:: https://readthedocs.org/projects/submitcgap/badge/?version=latest
   :target: https://submitcgap.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status

Description
===========

This is a tool for uploading certain kinds of files to CGAP.

Current support is for submission of new cases, family histories, and gene lists.


Installation
============

Installing this system involves these steps:

1. Create, install, and activate a virtual environment.
2. *Only if you are a developer*, install poetry and select the source repository.
   Others will not have a source repository to select,
   so should skip this step.
3. If you are an end user, do "``pip install submit_cgap``".
   Otherwise, do "``make build``".
4. Set up a ``~/.cgap-keys.json`` credentials file.

For detailed information about these installation steps, see
`Installing SubmitCGAP <https://submitcgap.readthedocs.io/en/latest/installation.html>`_.


Testing
=======

To run unit tests, do::

   $ make test

Additional notes on testing these scripts for release can be found in
`Testing SubmitCGAP <TESTING.rst>`__.


Getting Started
===============

Once you have finished installing this library into your virtual environment,
you should have access to the ``submit-metadata-bundle`` and the ``submit-genelist``
commands. For more information about how to format files for submission and how to
use these commands, see `Getting Started <https://submitcgap.readthedocs.io/en/latest/getting_started.html>`_.

