Consider integration of MixMHCPred2

griffithlab / pVACtools

http://www.pvactools.org

BSD 3-Clause Clear License

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Consider integration of MixMHCPred2 #1093

Open malachig opened 5 months ago

malachig commented 5 months ago

https://github.com/GfellerLab/MixMHC2pred

Based on the license we might need to request permission?

Implemented in C++.

susannasiebert commented 5 months ago

Related issue #240 and #1056

The main issue I see is that there are different executables for different operating systems but that should be pretty straightforward to determine in-code to use the correct one. We would need to require our users to include their applicable executable in their PATH, set it as an ENV variable, or make (yet another) command line option.

lukaas33 commented 4 weeks ago

Am I correct that currently the MHC2 alleles are not supported downstream by pvactools (pvacseq valid_alleles). If so, would supplying these alleles be possible at the moment?

susannasiebert commented 3 weeks ago

pVACtools support several class II binding affinity and elution algorithms but currently doesn't have any support for class II immunogenicity algorithms (see "MHC Class I and Class II predictions" section in our docs).