[Bioc-devel] How can I maintain a stable list of source urls

[Neumann, Steffen]

Hi,

this sounds very much like the bioconda approach,
they have self-archived / mirrored the packages, 
which is not ideal. 

The Bio.tools people also ran into that issue earlier, 
and as mentioned in [1] is now fixed on the bioconductor side
with stable download links. 

Yours, 
Steffen

[1] https://github.com/bio-tools/biotoolsRegistry/issues/425#issuecomment-557270484 


On Tue, 2020-03-31 at 12:27 -0700, Tim Sears wrote:
> Hi
> I am working to make bioconductor packages available through the nix
> package manager (https://nixos.org/). Currently nixpkgs points to a
> source
> url on one of the bioconductor mirrors. nixpkgs tracks the url and a
> sha256
> hash of the unpacked source link. Unfortunately the links themselves
> often
> disappear as the packages get updated either due to a version number
> change
> or changes inside the repo that affect the hash output. This breaks
> corresponding nix package. This happens even for stable bioconductor
> versions like 3.10. nixpkgs aims for reproducible builds, which means
> when
> things change, the url should reflect the change too and the contents
> behich old urls should be preserved long enough to manage
> the  change. Do
> you have any suggestions short of rebuilding a bioconductor mirror
> with
> immutable urls?
> 
> Thanks,
> TIm
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- 

Current bits of interest:


* PSI Spring Meeting Online, 23.-25.03.2020, 
  http://www.psidev.info/hupo-psi-meeting-2020

* Annual symposium of German Society for Metabolomics e.V. (DGMet)
  in Berlin 4.-5th November. https://www.mdc-berlin.de/dgmet-2020


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