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tiddit: init 3.6.1 #312995

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tiddit: init 3.6.1 #312995

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apraga
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@apraga apraga commented May 19, 2024

Genomic tool to call structural variations.

Description of changes

New package : a CLI tool written in python. It depends on 2 other executables, not packaged as a separate derivation.

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:
  • 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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apraga commented May 20, 2024

Thanks for your review (and fast too). I've updated the PR accordingly. Please tell me if something is missing.

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apraga commented Jun 29, 2024

@fabaff This PR should be ready to merge and your comment should have been addressed. If you could look at it, it would be nice :)

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apraga commented Oct 26, 2024

@fabaff Hi, I've rebased the change against master, removed useless arguments and applied nixfmt. Does that looks good to you ? Thanks

@Aleksanaa
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Please check ofborg build failure below. If you don't have the device and there's no clue to fix them upstream (issues/prs), please mark these platforms as broken.

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this is a clang vs gcc issue. can use clang on linux like:

nix-build -E 'with import ./.{}; fermi2.override { stdenv = clangStdenv; }'

pkgs/by-name/fe/fermi2/package.nix Show resolved Hide resolved
mainProgram = "fermi2";
license = licenses.mit;
maintainers = with maintainers; [ apraga ];
platforms = platforms.unix;
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I think this is only supported by x86-64 so that needs to be specified.

Suggested change
platforms = platforms.unix;
platforms = lib.intersectLists lib.platforms.x86_64 lib.platforms.unix;

pkgs/by-name/ro/ropebwt2/package.nix Show resolved Hide resolved
Genomic tool to call structural variations.

This packages requires 2 executables,packaging fermi2, bwt2, that are
packaged in the same derivation and added to the path later on.
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nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 312995


x86_64-darwin

✅ 4 packages built:
  • fermi2
  • ropebwt2
  • tiddit
  • tiddit.dist

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 312995


x86_64-linux

✅ 4 packages built:
  • fermi2
  • ropebwt2
  • tiddit
  • tiddit.dist

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5 participants