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kent: init at 394 #81550

Merged
merged 1 commit into from Oct 2, 2020
Merged

kent: init at 394 #81550

merged 1 commit into from Oct 2, 2020

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@scalavision
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@scalavision scalavision commented Mar 2, 2020

Motivation for this change

Kent utilities are a very versatile and fast suite of bioinformatic tools that has been available for a long time. It has some very nice tools to optimize for visualization of big data.

Things done

I have put the mit license, however some of these tools are not allowed to be used outside non-profit organizations. My understanding of nixpkgs is that it is completely non-profit.

For lib, inc and utils the MIT wording has been used:

The licenses where there are exceptions from the mit license says this:

License hereby is granted for personal, academic and non-profit purposes

Should I choose something else than mit?

It is possible to build the utility suite without these libraries, but I am also working on adding ensembl-vep, where these libraries are required. Since there also are commercial binaries in nixpkgs, I don't think this should be a problem, but I am not a lawyer ..

I really hope these tools can be added to nixpkgs.

  • [ x] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • Built on platform(s)
    • [x ] NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
  • [ x] Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • [x ] Ensured that relevant documentation is up to date
  • [x ] Fits CONTRIBUTING.md.
@puzzlewolf
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@puzzlewolf puzzlewolf commented Mar 29, 2020

Hey, the discussion here: #31210 should help with the licensing issue. Also this situation seems to be comparable: #77519.

It seems to me that, unfortunately, the restriction made by
License hereby is granted for personal, academic and non-profit purposes actually makes those parts unfree. However, I'd really like someone more knowledgeable to weigh in here.

@scalavision
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@scalavision scalavision commented Mar 31, 2020

Thank for the pointers @puzzlewolf !!

I'll look into them during the weekend. I think unfree could be an option as well :-)

@GregorySchwartz
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@GregorySchwartz GregorySchwartz commented Aug 31, 2020

This code works for me in Arch linux and Ubuntu.

@ryantm
ryantm approved these changes Sep 24, 2020
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@ryantm ryantm commented Sep 24, 2020

Result of nixpkgs-review pr 81550 1

1 package built:
- kent
@scalavision scalavision force-pushed the scalavision:add-kent-utils-to-bioinf branch 2 times, most recently from bee7a47 to 9b3c167 Oct 1, 2020
@scalavision scalavision force-pushed the scalavision:add-kent-utils-to-bioinf branch from 9b3c167 to a6f124f Oct 1, 2020
@scalavision
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@scalavision scalavision commented Oct 1, 2020

not able to see what it failed on, was it a timeout?

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@ryantm ryantm commented Oct 1, 2020

@scalavision
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@scalavision scalavision commented Oct 2, 2020

@ryantm is everything ok with this PR? I see there is one changes requested, but I am not able to find out what it is. I guess it is the change of license, and that this disappeared when I force pushed. I messed up a bit with the history, so had to fix it.

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@ryantm ryantm commented Oct 2, 2020

@scalavision I probably just didn't re-approve it. Checking now!

@ryantm
ryantm approved these changes Oct 2, 2020
@ryantm ryantm merged commit 6aadae6 into NixOS:master Oct 2, 2020
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grahamcofborg-eval ^.^!
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grahamcofborg-eval-check-meta config.nix: checkMeta = true
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grahamcofborg-eval-darwin nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="a6f124f"; rev="a6f124f57b0fc216f5c4f2f8ff141fc292da5a40"; } ./pkgs/t
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grahamcofborg-eval-lib-tests nix-build --arg pkgs import ./. {} ./lib/tests/release.nix
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grahamcofborg-eval-nixos nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="a6f124f"; rev="a6f124f57b0fc216f5c4f2f8ff141fc292da5a40"; } ./nixos/
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grahamcofborg-eval-nixos-manual nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="a6f124f"; rev="a6f124f57b0fc216f5c4f2f8ff141fc292da5a40"; } ./nixos/
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grahamcofborg-eval-nixos-options nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="a6f124f"; rev="a6f124f57b0fc216f5c4f2f8ff141fc292da5a40"; } ./nixos/
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grahamcofborg-eval-nixpkgs-manual nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="a6f124f"; rev="a6f124f57b0fc216f5c4f2f8ff141fc292da5a40"; } ./pkgs/t
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grahamcofborg-eval-nixpkgs-tarball nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="a6f124f"; rev="a6f124f57b0fc216f5c4f2f8ff141fc292da5a40"; } ./pkgs/t
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grahamcofborg-eval-nixpkgs-unstable-jobset nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="a6f124f"; rev="a6f124f57b0fc216f5c4f2f8ff141fc292da5a40"; } ./pkgs/t
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grahamcofborg-eval-package-list nix-env -qa --json --file .
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grahamcofborg-eval-package-list-no-aliases nix-env -qa --json --file . --arg config { allowAliases = false; }
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@GregorySchwartz
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@GregorySchwartz GregorySchwartz commented Nov 6, 2020

kent is missing an entry in all packages so I get an error with pkgs.kent as the attribute is not found.

@ryantm ryantm mentioned this pull request Nov 6, 2020
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@ryantm ryantm commented Nov 6, 2020

@GregorySchwartz Oops. Fixed in #103036

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