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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
parent 0b6ee2c783 d2c506948b
commit 23332e13fe
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GPG key ID: 4AEE18F83AFDEB23
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 { stdenv.mkDerivation (finalAttrs: {
version = "4.9j";
pname = "paml"; pname = "paml";
src = fetchurl { version = "4.10.7";
url = "http://abacus.gene.ucl.ac.uk/software/paml${version}.tgz";
sha256 = "0qflf3i27x6jwks3c6q560m1q8r043ja96syah145113iz5wdalp"; src = fetchFromGitHub {
owner = "abacus-gene";
repo = "paml";
rev = "refs/tags/${finalAttrs.version}";
hash = "sha256-P/oHaLxoQzjFuvmHyRdShHv1ayruy6O/I9w8aTyya2s=";
}; };
# Workaround build failure on -fno-common toolchains like upstream env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.isDarwin "-D_POSIX_C_SOURCE";
# 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";
preBuild = '' preBuild = ''
cd ./src/ cd ./src/
''; '';
installPhase = '' installPhase = ''
runHook preInstall
mkdir -pv $out/bin mkdir -pv $out/bin
cp -v codeml $out/bin cp -v codeml $out/bin
cp -v baseml $out/bin cp -v baseml $out/bin
@ -28,12 +33,16 @@ stdenv.mkDerivation rec {
cp -v mcmctree $out/bin cp -v mcmctree $out/bin
cp -v pamp $out/bin cp -v pamp $out/bin
cp -v yn00 $out/bin cp -v yn00 $out/bin
runHook postInstall
''; '';
meta = { meta = {
description = "Phylogenetic Analysis by Maximum Likelihood (PAML)"; description = "Phylogenetic Analysis by Maximum Likelihood (PAML)";
longDescription = "PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc."; longDescription = "PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.";
license = "non-commercial"; license = lib.licenses.gpl3Only;
homepage = "http://abacus.gene.ucl.ac.uk/software/paml.html"; homepage = "http://abacus.gene.ucl.ac.uk/software/paml.html";
changelog = "https://github.com/abacus-gene/paml/releases/tag/${finalAttrs.src.rev}";
platforms = lib.platforms.unix;
}; };
} })