nixpkgs/pkgs/applications/science/biology
aleksana 571c71e6f7 treewide: migrate packages to pkgs/by-name, take 1
We are migrating packages that meet below requirements:

1. using `callPackage`
2. called path is a directory
3. overriding set is empty (`{ }`)
4. not containing path expressions other than relative path (to
makenixpkgs-vet happy)
5. not referenced by nix files outside of the directory, other
than`pkgs/top-level/all-packages.nix`
6. not referencing nix files outside of the directory
7. not referencing `default.nix` (since it's changed to `package.nix`)
8. `outPath` doesn't change after migration

The tool is here: https://github.com/Aleksanaa/by-name-migrate.
2024-11-09 20:04:51 +08:00
..
ants treewide: replace stdenv.is with stdenv.hostPlatform.is 2024-09-25 00:04:37 +03:00
blast treewide: Fix indentation in strings 2024-10-22 21:36:42 +02:00
cd-hit
hh-suite hh-suite: fix build on GCC 13 2024-02-08 21:54:47 +00:00
iv treewide: replace stdenv.is with stdenv.hostPlatform.is 2024-09-25 00:04:37 +03:00
kallisto kallisto: 0.51.0 -> 0.51.1 2024-09-17 13:16:27 +00:00
minc-tools minc-tools: unstable-2020-07-25 -> 2.3.06-unstable-2023-08-12 2024-09-07 13:57:40 -04:00
mmseqs2 treewide: add meta.mainProgram to packages with a single binary 2024-03-19 03:14:51 +01:00
mrtrix treewide: replace stdenv.is with stdenv.hostPlatform.is 2024-09-25 00:04:37 +03:00
nest treewide: replace stdenv.is with stdenv.hostPlatform.is 2024-09-25 00:04:37 +03:00
obitools treewide: replace stdenv.is with stdenv.hostPlatform.is 2024-09-25 00:04:37 +03:00
samtools pkgs/applications: remove uneeded fetchpatch arguments 2024-05-21 03:12:20 +02:00
sumatools
trimmomatic treewide: Remove indefinite article from meta.description 2024-06-09 23:07:45 +02:00
truvari truvari: 4.1.0 -> 4.2.2 2024-07-04 21:38:05 +09:00