picard-tools: 2.18.5 -> 2.18.7

[r-ryantm]

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/siklhy9pl9xl9cq3nlqhln038554h72g-picard-tools-2.18.7/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 2.18.7 with grep in /nix/store/siklhy9pl9xl9cq3nlqhln038554h72g-picard-tools-2.18.7
• directory tree listing: https://gist.github.com/a49ed5f2ff312ce6180174183901e38f
• du listing: https://gist.github.com/243f4d89d2100ef27d332e3562d5f173

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.

Experimental: this build is cached with Cachix. To use the cache follow these experimental 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 34624ffeead4c7e304b43954e154df908401866b && nix-shell --pure -I nixpkgs=. -p picard-tools

[GrahamcOfBorg]

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]

Success on x86_64-darwin (full log)

Attempted: picard-tools

Partial log (click to expand)

building '/nix/store/7i067f90l6hy6mcj1v8622ga0i04sw0k-picard.jar.drv'...

trying https://github.com/broadinstitute/picard/releases/download/2.18.7/picard.jar
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   600    0   600    0     0   1219      0 --:--:-- --:--:-- --:--:--  1217
100 14.6M  100 14.6M    0     0  3137k      0  0:00:04  0:00:04 --:--:-- 4557k
building '/nix/store/nzjnsgczn1lnxv444a27s9nxnm0vh06n-picard-tools-2.18.7.drv'...
installing
/nix/store/9zy3fsm9xfkiyd05cwf1yfvpkwj508f5-picard-tools-2.18.7

[GrahamcOfBorg]

Success on x86_64-linux (full log)

Attempted: picard-tools

Partial log (click to expand)

building '/nix/store/gwsyp6iymyz21klba81bsj789fpz54qn-picard.jar.drv'...

trying https://github.com/broadinstitute/picard/releases/download/2.18.7/picard.jar
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   600    0   600    0     0   1312      0 --:--:-- --:--:-- --:--:--  1310
100 14.6M  100 14.6M    0     0  4690k      0  0:00:03  0:00:03 --:--:-- 7583k
building '/nix/store/k5jmr5c8c9r8xg7sjcvxdiqshqp6c2rj-picard-tools-2.18.7.drv'...
installing
/nix/store/siklhy9pl9xl9cq3nlqhln038554h72g-picard-tools-2.18.7