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.
Installing this system involves these steps:
- Create, install, and activate a virtual environment.
- 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.
- If you are an end user, do "
pip install submit_cgap". Otherwise, do "make build". - Set up a
~/.cgap-keys.jsoncredentials file.
For detailed information about these installation steps, see Installing SubmitCGAP.
To run unit tests, do:
$ make test
Additional notes on testing these scripts for release can be found in Testing SubmitCGAP.
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.