[Bioc-devel] How can I maintain a stable list of source urls
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]]
_______________________________________________ Bioc-devel at r-project.org mailing list 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 --- IPB Halle Bioinformatics and Scientific Data Dr. Steffen Neumann http://www.IPB-Halle.DE *** Working from Home, available by Mail, Phone, Video Calls *** Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409