vep: init at 110

[apraga]

This software has required significant work to package and need other PR to be merge beforehand : #185691 #186459 #186464 and the infamous #186462.
The package has been formatted with nixpkgs-fmt. I was not able to run tests but this software has been used for hundred of runs in research setting.

Description of changes

New packages for Variant Effect Predictor.

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
  • sandbox = relaxed
  • sandbox = true
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• 24.05 Release Notes (or backporting 23.05 and 23.11 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
• Fits CONTRIBUTING.md.

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[nixos-discourse]

This pull request has been mentioned on NixOS Discourse. There might be relevant details there:

https://discourse.nixos.org/t/prs-ready-for-review/3032/3701

[apraga]

Thanks for your review. Your changes have been incorporated. I've also switched to using the release version (with fetchzip as it's not available with fetchfromgithub) instead of git commits. Code have been formatted with nixfmt-rfc-style. The changes are in a separated commit for readability.

[apraga]

Oops, somehow I forgot to clean references to pkgs. Thanks !

[apraga]

@rhendric If you have time to take another look at this PR, that would be great. Thanks !

[apraga]

@rhendric Okay, this should be better, thanks !

[apraga]

@rhendric If you have some time to look at it, it would be great :)

[apraga]

@rhendric When testing the package, the binaries are not installed. Not sure how it worked before (we used it in production) but this has been fixed. If you have any comment about the wrapping, please tell me.
Edit: tested with vep -i homo_sapiens_GRCh38.vcf --cache . --merged

[apraga]

@rhendric I've merged the commits and rebase against master. Do you think we can (finally) put this PR to rest ? :)