==========
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/usage.html>`_.
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