submit_cgap 4.2.0

Support for uploading file submissions to the Clinical Genomics Analysis Platform (CGAP).

A file submission tool for CGAP

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.

Testing

To run unit tests, do:

$ make test

Additional notes on testing these scripts for release can be found in Testing SubmitCGAP.

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.