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picard-tools: 2.18.4 -> 2.18.5 #41104

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merged 1 commit into from May 26, 2018
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r-ryantm
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Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/picard-tools/versions.

These checks were done:

meta.description for picard-tools is: '"Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF."'.

cc @jbedo for testing.

Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/picard-tools/versions.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/y7q0bsph0zldfjkz4ci3f41ba5va810w-picard-tools-2.18.5/bin/picard had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.18.5 with grep in /nix/store/y7q0bsph0zldfjkz4ci3f41ba5va810w-picard-tools-2.18.5
- directory tree listing: https://gist.github.com/1938ad634fa882d94e8d28fd1625547c
- du listing: https://gist.github.com/4b51e89646327900f6ef6f2242f5d0bd
@GrahamcOfBorg
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No attempt on aarch64-linux (full log)

The following builds were skipped because they don't evaluate on aarch64-linux: picard-tools

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnfree = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnfree = true; }
to ~/.config/nixpkgs/config.nix.


@GrahamcOfBorg
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Success on x86_64-darwin (full log)

Attempted: picard-tools

Partial log (click to expand)

building '/nix/store/biw2kzsk07w4gx651l9jy9xsjk625gx5-picard.jar.drv'...

trying https://github.com/broadinstitute/picard/releases/download/2.18.5/picard.jar
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   600    0   600    0     0   3045      0 --:--:-- --:--:-- --:--:--  3045
100 14.6M  100 14.6M    0     0  5806k      0  0:00:02  0:00:02 --:--:-- 8515k
building '/nix/store/63jwim6z51c2fzaj4ywvinl8y62cgsdk-picard-tools-2.18.5.drv'...
installing
/nix/store/rrmnanz0kmy9c1sps8d41sz4li0i006n-picard-tools-2.18.5

@GrahamcOfBorg
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Success on x86_64-linux (full log)

Attempted: picard-tools

Partial log (click to expand)


trying https://github.com/broadinstitute/picard/releases/download/2.18.5/picard.jar
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   600    0   600    0     0   1119      0 --:--:-- --:--:-- --:--:--  1117
copying path '/nix/store/l3gpzxr7aa6a49gkzywnw8ldq7cnf80k-openjdk-8u172b11-jre' from 'https://cache.nixos.org'...
100 14.6M  100 14.6M    0     0  1509k      0  0:00:09  0:00:09 --:--:-- 1479k
building '/nix/store/whnaql1gryl6al349ikv0nnjs1bxs7wl-picard-tools-2.18.5.drv'...
installing
/nix/store/y7q0bsph0zldfjkz4ci3f41ba5va810w-picard-tools-2.18.5

@grahamc grahamc merged commit 44c428f into NixOS:master May 26, 2018
@r-ryantm r-ryantm deleted the auto-update/picard-tools branch May 26, 2018 22:26
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3 participants