Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

picard-tools: 2.18.11 -> 2.18.12 #46211

Merged
merged 1 commit into from Sep 10, 2018

Conversation

r-ryantm
Copy link
Contributor

@r-ryantm r-ryantm commented Sep 6, 2018

Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from picard-tools.

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

Checks done (click to expand)
Instructions to test this update (click to expand)

One-time optional setup to skip building using Cachix:

  1. Install cachix from https://cachix.org/
  2. Use r-ryantm's cache:
    cachix use r-ryantm
    

Test this update by entering a nix shell, seeing what is inside the
result, and if applicable, running some binaries:

nix-shell --pure -I nixpkgs=https://github.com/r-ryantm/nixpkgs/archive/f72cba212cef160eb82a9f3c7cbf0e983f7af9d0.tar.gz -p picard-tools
ls -la /nix/store/kr7f99imsnn1vzfaiq336ws0bdq9dqv5-picard-tools-2.18.12

cc @jbedo for testing.

Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
picard-tools
@GrahamcOfBorg
Copy link

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
Copy link

Success on x86_64-linux (full log)

Attempted: picard-tools

Partial log (click to expand)

                                 Dload  Upload   Total   Spent    Left  Speed
100   600    0   600    0     0   3947      0 --:--:-- --:--:-- --:--:--  3947
100 14.7M  100 14.7M    0     0  21.7M      0 --:--:-- --:--:-- --:--:-- 34.8M
copying path '/nix/store/6i2l9mbszlds0p36wgips3d0p6rmnwb6-polkit-0.115' from 'https://cache.nixos.org'...
copying path '/nix/store/488aya5f34bry24dx185k595ygrxbdnb-gconf-3.2.6' from 'https://cache.nixos.org'...
copying path '/nix/store/sw6l31gjkw31kc2gqc49dn98hzdiqmci-gnome-vfs-2.24.4' from 'https://cache.nixos.org'...
copying path '/nix/store/91wwfym087fcrg2iscd5bz3qq1zgz1k8-openjdk-8u181b13-jre' from 'https://cache.nixos.org'...
building '/nix/store/1cy6lc3n42lh5v3qn48xdhnn8vfckfg8-picard-tools-2.18.12.drv'...
installing
/nix/store/kr7f99imsnn1vzfaiq336ws0bdq9dqv5-picard-tools-2.18.12

@GrahamcOfBorg
Copy link

Success on x86_64-darwin (full log)

Attempted: picard-tools

Partial log (click to expand)


trying https://github.com/broadinstitute/picard/releases/download/2.18.12/picard.jar
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   600    0   600    0     0   1158      0 --:--:-- --:--:-- --:--:--  1156
100 14.7M  100 14.7M    0     0  5293k      0  0:00:02  0:00:02 --:--:-- 8945k
copying path '/nix/store/hn4b0kmqmx08i953lkgd3507y4q5sbrx-zulu1.8.0_121-8.20.0.5' from 'https://cache.nixos.org'...
building '/nix/store/big6q3ihmvvd1s4f9572ppkjmb1qzq02-picard-tools-2.18.12.drv'...
installing
/nix/store/jqk38jnwq5yakcm76xlwnw9qgkya0c9w-picard-tools-2.18.12

@matthewbauer matthewbauer merged commit 05d379f into NixOS:master Sep 10, 2018
@r-ryantm r-ryantm deleted the auto-update/picard-tools branch September 11, 2018 01:36
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

3 participants