Submitting patches

From GSA

We welcome patches from contributors internal to and external from the Broad Institute.

We have rigorous unit and integration tests to ensure to the best of our abilities that our software is free from regressions. The test data for our suite is unfortunately all on Broad mountpoints, so tests will run most easily on automount-ready Broad Linux servers. Tests can be run on personal workstations, but extensive work setting up mount points will be required.

To ensure that your patch is GATK-ready, please do the following:

• Run the unit tests to validate the GATK core ('ant test').
• Run the integration tests to validate the GATK core walkers ('ant integrationtest').
• If contributing to the GATK infrastructure, please supply unit tests for your changes.
• If contributing to analyses, please supply integration tests for your changes.

When you are confident in your patch, please submit a patch to gsahelp@broadinstitute.org. We will review your patch at our earliest opportunity and provide feedback.

Note to contributors external to the Broad Institute

Please note that our unit and integration tests require datasets that are only available within the Broad. If you do not have access to our data repository, please provide us with a patch and let us know.