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delly: init at 0.8.1 #70871

Merged
merged 2 commits into from
Oct 11, 2019
Merged

delly: init at 0.8.1 #70871

merged 2 commits into from
Oct 11, 2019
+42 −0

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scalavision
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Motivation for this change
Things done
  • [ x] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
  • 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 nix-review --run "nix-review wip"
  • [ x] Tested execution of all binary files (usually in ./result/bin/)
  • [ x] 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.
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@scalavision
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Delly is a very much used tool used to find structural variants within dna sequenced, short read data. It would be very nice to have it in nixpkgs.

@ofborg ofborg bot added 8.has: package (new) This PR adds a new package 11.by: package-maintainer This PR was created by the maintainer of the package it changes 10.rebuild-darwin: 0 This PR does not cause any packages to rebuild on Darwin 10.rebuild-linux: 1-10 labels Oct 9, 2019
markuskowa
markuskowa requested changes Oct 9, 2019
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@mmahut mmahut changed the title Add delly to biology pkgs delly: init at 0.8.1 Oct 10, 2019
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mmahut commented Oct 10, 2019

After fixing the issues above, please squash your commits too.

@scalavision scalavision force-pushed the add-delly-to-biology-pkgs branch from 7386c29 to 5cf9aeb Compare October 10, 2019 12:04
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Thanks for all the nice feedback! I've removed buildPhase, only using prePhase. Also I've cleaned up the installPhase, which seems to work.

Anyone knows why the checkMeta validation doesn't work? It says something about scylla-db. I don't think I have anything related to that.

@scalavision scalavision mentioned this pull request Oct 10, 2019
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@veprbl
fixup
898c2c8 
prePhase is not a thing
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veprbl commented Oct 10, 2019

Eval should be fixed by c0d5833

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veprbl commented Oct 10, 2019

@GrahamcOfBorg build delly

@veprbl veprbl merged commit 3d86097 into NixOS:master Oct 11, 2019
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8.has: package (new) This PR adds a new package 10.rebuild-darwin: 0 This PR does not cause any packages to rebuild on Darwin 10.rebuild-linux: 1-10 11.by: package-maintainer This PR was created by the maintainer of the package it changes
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