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: 2.18.7 -> 2.18.9 #42967

Merged
merged 1 commit into from Jul 6, 2018
Merged

Conversation

r-ryantm
Copy link
Contributor

@r-ryantm r-ryantm commented Jul 4, 2018

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.

This build is cached with Cachix. To use the cache follow these instructions:

One time setup in nixpkgs Git checkout:

cachix use r-ryantm
git remote add r-ryantm https://github.com/r-ryantm/nixpkgs.git

Test this build:

git fetch r-ryantm && git checkout 5ddbced87f793e986599f9c0bd64c571f6a79867 && nix-shell --pure -I nixpkgs=. -p picard-tools

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/ah3v1x61gmj9lan8a3qvy3824lqvjdgi-picard-tools-2.18.9/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 2.18.9 with grep in /nix/store/ah3v1x61gmj9lan8a3qvy3824lqvjdgi-picard-tools-2.18.9
- directory tree listing: https://gist.github.com/0972acdc51fe8a1cde470e4ab5e87993
- du listing: https://gist.github.com/6a66b6723ce4887cd108678369b87360
@GrahamcOfBorg
Copy link

Success on x86_64-darwin (full log)

Attempted: picard-tools

Partial log (click to expand)

building '/nix/store/95z6f052mijj7bzh3fj1yn5vnpbkp7cq-picard.jar.drv'...

trying https://github.com/broadinstitute/picard/releases/download/2.18.9/picard.jar
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   600    0   600    0     0   1149      0 --:--:-- --:--:-- --:--:--  1149
100 14.6M  100 14.6M    0     0  5050k      0  0:00:02  0:00:02 --:--:-- 6492k
building '/nix/store/m64v2dgp6x12phz9v0yqf1zmkzaj2c6i-picard-tools-2.18.9.drv'...
installing
/nix/store/kcvy6znsl7jhs6kk78vjvhw4i7w3lwhw-picard-tools-2.18.9

@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)

building '/nix/store/imw99gbrwlx9a02xmzy8yngshf7kdjs1-picard.jar.drv'...

trying https://github.com/broadinstitute/picard/releases/download/2.18.9/picard.jar
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   600    0   600    0     0   1167      0 --:--:-- --:--:-- --:--:--  1165
100 14.6M  100 14.6M    0     0  2766k      0  0:00:05  0:00:05 --:--:-- 3496k
building '/nix/store/ypymhrsysid1wqp5fns6cgiy4i0s7271-picard-tools-2.18.9.drv'...
installing
/nix/store/ah3v1x61gmj9lan8a3qvy3824lqvjdgi-picard-tools-2.18.9

@xeji xeji merged commit cb85999 into NixOS:master Jul 6, 2018
@r-ryantm r-ryantm deleted the auto-update/picard-tools branch July 6, 2018 19:38
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