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delly: 0.8.2 -> 0.8.5 #99128

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merged 1 commit into from Oct 16, 2020
Merged

delly: 0.8.2 -> 0.8.5 #99128

merged 1 commit into from Oct 16, 2020

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@jbedo
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@jbedo jbedo commented Sep 29, 2020

Motivation for this change

New release of delly.

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • Built on platform(s)
    • 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"
  • 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)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.
@jbedo
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@jbedo jbedo commented Sep 29, 2020

@scalavision
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@scalavision scalavision commented Sep 30, 2020

I run through a whole genome bam file, it resulted in 30k+ lines of vcf file. I will benchmark against gold standard tomorrow, I think however, that this can be merged after the license has been updated. Thanks a lot for providing this update!

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@scalavision scalavision left a comment

Seems the license has changed from gpl3 to bsd2, @jbedo , could you update this as well?

dellytools/delly@06f0b0c#diff-04c6e90faac2675aa89e2176d2eec7d8R12

@jbedo
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@jbedo jbedo commented Sep 30, 2020

Oops, completely missed the license change!

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@scalavision scalavision left a comment

Hm... I think it is actually BSD3 isn't it, not mit? If you can change to bsd3 it would be nice :-)

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@jbedo jbedo commented Oct 1, 2020

Hm... I think it is actually BSD3 isn't it, not mit? If you can change to bsd3 it would be nice :-)

Not sure how I got that wrong, I meant to write bsd3.

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@scalavision scalavision left a comment

Nice! Thanks :-)

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@scalavision scalavision commented Oct 16, 2020

@ryantm could you have a look at this one? As far as I can tell everything is ok. I have also tested running the tool locally.

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@ryantm ryantm commented Oct 16, 2020

Result of nixpkgs-review pr 99128 1

1 package built:
- delly

@ryantm ryantm merged commit f9728ad into NixOS:master Oct 16, 2020
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tests tests
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action
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delly, delly.passthru.tests on aarch64-linux No attempt
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Evaluation Performance Report Evaluator Performance Report
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delly, delly.passthru.tests on x86_64-linux Success
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grahamcofborg-eval ^.^!
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grahamcofborg-eval-check-maintainers matching changed paths to changed attrs...
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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="d8d8f93"; rev="d8d8f9390a623f88c548aa8dd9b2c3c50e817d57"; } ./pkgs/t
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grahamcofborg-eval-lib-tests nix-build --arg pkgs import ./. {} ./lib/tests/release.nix
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@ofborg[bot]
grahamcofborg-eval-nixos nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="d8d8f93"; rev="d8d8f9390a623f88c548aa8dd9b2c3c50e817d57"; } ./nixos/
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@ofborg[bot]
grahamcofborg-eval-nixos-manual nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="d8d8f93"; rev="d8d8f9390a623f88c548aa8dd9b2c3c50e817d57"; } ./nixos/
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@ofborg[bot]
grahamcofborg-eval-nixos-options nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="d8d8f93"; rev="d8d8f9390a623f88c548aa8dd9b2c3c50e817d57"; } ./nixos/
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@ofborg[bot]
grahamcofborg-eval-nixpkgs-manual nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="d8d8f93"; rev="d8d8f9390a623f88c548aa8dd9b2c3c50e817d57"; } ./pkgs/t
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@ofborg[bot]
grahamcofborg-eval-nixpkgs-tarball nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="d8d8f93"; rev="d8d8f9390a623f88c548aa8dd9b2c3c50e817d57"; } ./pkgs/t
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grahamcofborg-eval-nixpkgs-unstable-jobset nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="d8d8f93"; rev="d8d8f9390a623f88c548aa8dd9b2c3c50e817d57"; } ./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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3 participants