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Merge pull request #243407 from natsukium/paml/update

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paml: 4.9j -> 4.10.7
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Weijia Wang 2023-08-01 22:09:44 +02:00 committed by GitHub
commit 23332e13fe
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1 changed files with 22 additions and 13 deletions
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35
pkgs/applications/science/biology/paml/default.nix
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@ -1,23 +1,28 @@
{stdenv, fetchurl}:
{ lib
, stdenv
, fetchFromGitHub
}:
stdenv.mkDerivation rec {
version = "4.9j";
stdenv.mkDerivation (finalAttrs: {
pname = "paml";
src = fetchurl {
url = "http://abacus.gene.ucl.ac.uk/software/paml${version}.tgz";
sha256 = "0qflf3i27x6jwks3c6q560m1q8r043ja96syah145113iz5wdalp";
version = "4.10.7";
src = fetchFromGitHub {
owner = "abacus-gene";
repo = "paml";
rev = "refs/tags/${finalAttrs.version}";
hash = "sha256-P/oHaLxoQzjFuvmHyRdShHv1ayruy6O/I9w8aTyya2s=";
};
# Workaround build failure on -fno-common toolchains like upstream
# gcc-10. Otherwise build fails as:
# ld: /build/ccKomtcd.o:(.bss+0x4544): multiple definition of `SeqTypes';
# /build/ccx7EsgU.o:(.bss+0x2a0dfdc): first defined here
env.NIX_CFLAGS_COMPILE = "-fcommon";
env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.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
@ -28,12 +33,16 @@ stdenv.mkDerivation rec {
cp -v mcmctree $out/bin
cp -v pamp $out/bin
cp -v yn00 $out/bin
runHook postInstall
'';
meta = {
description = "Phylogenetic Analysis by Maximum Likelihood (PAML)";
longDescription = "PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.";
license = "non-commercial";
license = lib.licenses.gpl3Only;
homepage = "http://abacus.gene.ucl.ac.uk/software/paml.html";
changelog = "https://github.com/abacus-gene/paml/releases/tag/${finalAttrs.src.rev}";
platforms = lib.platforms.unix;
};
}
})