tjh.dev
nixpkgs mirror (for testing)
github.com/NixOS/nixpkgs
nix
1{
2 lib,
3 stdenv,
4 fetchFromGitHub,
5}:
6
7stdenv.mkDerivation (finalAttrs: {
8 pname = "paml";
9 version = "4.10.7";
10
11 src = fetchFromGitHub {
12 owner = "abacus-gene";
13 repo = "paml";
14 tag = finalAttrs.version;
15 hash = "sha256-P/oHaLxoQzjFuvmHyRdShHv1ayruy6O/I9w8aTyya2s=";
16 };
17
18 env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.hostPlatform.isDarwin "-D_POSIX_C_SOURCE";
19
20 preBuild = ''
21 cd ./src/
22 '';
23
24 installPhase = ''
25 runHook preInstall
26
27 mkdir -pv $out/bin
28 cp -v codeml $out/bin
29 cp -v baseml $out/bin
30 cp -v basemlg $out/bin
31 cp -v chi2 $out/bin
32 cp -v codeml $out/bin
33 cp -v evolver $out/bin
34 cp -v mcmctree $out/bin
35 cp -v pamp $out/bin
36 cp -v yn00 $out/bin
37
38 runHook postInstall
39 '';
40
41 meta = {
42 description = "Phylogenetic Analysis by Maximum Likelihood (PAML)";
43 longDescription = "PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.";
44 license = lib.licenses.gpl3Only;
45 homepage = "http://abacus.gene.ucl.ac.uk/software/paml.html";
46 changelog = "https://github.com/abacus-gene/paml/releases/tag/${finalAttrs.version}";
47 platforms = lib.platforms.unix;
48 };
49})