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griffithlab / pVACtools

http://www.pvactools.org
BSD 3-Clause Clear License
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Support for custom epitope prediction algorithms #1103

Open boyangzhao opened 1 month ago

boyangzhao commented 1 month ago

Is there an option for pvactools to support custom epitope prediction algorithms that is not in the available list? And/or have an interface for how a custom prediction algorithm can be built so it is compatible with usage by pvactools?

susannasiebert commented 1 month ago

Unfortunately, we currently don't have step-by-step instructions on how to incorporate new algorithms into pVACtools but if you have a particular algorithm in mind, we're always happy to consider it. We've put together an issue to track various suggested prediction algorithms with some installation/implementation notes.

In terms of prediction algorithm implementation, pVACtools requires that all algorithms can be either called via the command line or an API. For command line algorithms, these are called via system calls to the tools executable. To make that more straightforward, we prefer that the algorithm does not require any special handling to point to executable as we don't want to clutter pVACtools with additional input parameters to point to the various tool executables (the one big exception here is standalone IEDB which supported a large number of prediction algorithms). Ideally the tools would be packaged and distributed on PyPI. For some tools (BigMHC and DeepImmuno), we have made forks of their respective GitHub repository to add a setup.py file so that their tools can be directly installed from GitHub using pip install. The prediction algorithm scripts are then available as command line entry points.