mirror of
https://github.com/NixOS/nixpkgs.git
synced 2024-12-13 17:23:08 +00:00
571c71e6f7
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.
49 lines
1.6 KiB
Nix
49 lines
1.6 KiB
Nix
{ lib
|
|
, stdenv
|
|
, fetchFromGitHub
|
|
}:
|
|
|
|
stdenv.mkDerivation (finalAttrs: {
|
|
pname = "paml";
|
|
version = "4.10.7";
|
|
|
|
src = fetchFromGitHub {
|
|
owner = "abacus-gene";
|
|
repo = "paml";
|
|
rev = "refs/tags/${finalAttrs.version}";
|
|
hash = "sha256-P/oHaLxoQzjFuvmHyRdShHv1ayruy6O/I9w8aTyya2s=";
|
|
};
|
|
|
|
env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.hostPlatform.isDarwin "-D_POSIX_C_SOURCE";
|
|
|
|
preBuild = ''
|
|
cd ./src/
|
|
'';
|
|
|
|
installPhase = ''
|
|
runHook preInstall
|
|
|
|
mkdir -pv $out/bin
|
|
cp -v codeml $out/bin
|
|
cp -v baseml $out/bin
|
|
cp -v basemlg $out/bin
|
|
cp -v chi2 $out/bin
|
|
cp -v codeml $out/bin
|
|
cp -v evolver $out/bin
|
|
cp -v mcmctree $out/bin
|
|
cp -v pamp $out/bin
|
|
cp -v yn00 $out/bin
|
|
|
|
runHook postInstall
|
|
'';
|
|
|
|
meta = {
|
|
description = "Phylogenetic Analysis by Maximum Likelihood (PAML)";
|
|
longDescription = "PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.";
|
|
license = lib.licenses.gpl3Only;
|
|
homepage = "http://abacus.gene.ucl.ac.uk/software/paml.html";
|
|
changelog = "https://github.com/abacus-gene/paml/releases/tag/${lib.removePrefix "refs/tags/" finalAttrs.src.rev}";
|
|
platforms = lib.platforms.unix;
|
|
};
|
|
})
|