Crude initial packaging of neoantigen pipeline
Dear all,
I came across this paper here
https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-024-01388-3
and liked it.
The pipeline that generated those vaccines is Open Source and so I thought we should address packaging it in Debian and then see what happens. I admit that this is a bit of a multi-level experiment:
* Most obviously: It is something clinical. And I have dropped very clinical stuff in the past, like the "artificial pancreas" blood sugar management - even though very tempted.
* The paper just got out, any such pipeline would need to be adopted a) in further studies and b) by treatment guidelines and likely be certified in some way. That takes time. Maybe this package accelerates this process, although a Docker image is available. Please speak up if this is so, I think we all want to hear about it.
* I also hoped that we would learn about those who are using the package already and be made aware of additional packages that would be worthwhile to provide.
* I want to find bugs while packaging. I mean, in the past we emphasized that our infrastructure is good for hardening, so we should show it. The "varcode" package does not build with the versioneer.py provided, so I fixed that by removing it, and it still uses the imp package - but I do not mean any of these maintenance issues - I want the Open Source community and Debian in particular to identify a functional bug and thus hope to prove to the world that Open Source and Debian in particular has some merits in individualized/precision medicine.
I created so far
https://salsa.debian.org/med-team/python-varcode
https://salsa.debian.org/med-team/vaxrank
and have not created a repository for the main package yet, i.e. pVACtools, which is close to 2 GB in size. And there are too many build dependencies (https://github.com/orgs/openvax/repositories) yet missing to keep busy. So we have some time to think about what to do a bit more. This is somewhat timely with all the discussions about large data sets that come with our favorite AI chatbots, but - anyway - for later.
Best,
Steffen
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