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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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Patch #15

Closed maflister closed 2 years ago

maflister commented 2 years ago

Why is patch used in the pipeline? Would it not be easier for your team to provide a patched file with each release of the pipeline. It would remove a dependency that many users wouldn't normally have installed.

Thanks

riederd commented 2 years ago

Hi, thanks for your interest in nextNEOpi.

Patch is used to apply specific changes to NeoAg_immunogenicity_predicition_GBM.R which is, due to licence restrictions, not bundled or distributed with nextNEOpi. It is downloaded on runtime from GitHub.

However, we seem to have forgotten to add the patch program to the singularity image, which we will do for our next release.

Thanks