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mskcc / neoantigen-pipeline

Pipeline for computing neoantigen qualities from DNA and RNA-Seq data
MIT License
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Create a container for NeoantigenEditing #1

Closed nikhil closed 6 months ago

nikhil commented 7 months ago

The suite of tools will need a container to run on nextflow.

Lets call the container NeoantigenEditing version 1.0.0 and push it to: https://hub.docker.com/u/mskcc

Have a look at this file for reference: https://github.com/mskcc/roslin-variant/blob/2.6.x/build/containers/picard/2.9/Dockerfile (ignore the COPY lines)

Dependencies are not listed, so you will need to inspect the code for them.

Example: you will need blastp as its run here: https://github.com/LukszaLab/NeoantigenEditing/blob/0126b82b1b4c0d44b6e3f5559c43e6022b8cdbd3/align_neoantigens_to_IEDB.py#L96

nikhil commented 6 months ago

Container is live here: https://hub.docker.com/r/mskcc/neoantigenediting