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f9fdf2d402
with structuredAttrs lists will be bash arrays which cannot be exported which will be a issue with some patches and some wrappers like cc-wrapper this makes it clearer that NIX_CFLAGS_COMPILE must be a string as lists in env cause a eval failure
40 lines
1.6 KiB
Nix
40 lines
1.6 KiB
Nix
{stdenv, fetchurl}:
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stdenv.mkDerivation rec {
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version = "4.9j";
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pname = "paml";
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src = fetchurl {
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url = "http://abacus.gene.ucl.ac.uk/software/paml${version}.tgz";
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sha256 = "0qflf3i27x6jwks3c6q560m1q8r043ja96syah145113iz5wdalp";
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};
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# Workaround build failure on -fno-common toolchains like upstream
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# gcc-10. Otherwise build fails as:
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# ld: /build/ccKomtcd.o:(.bss+0x4544): multiple definition of `SeqTypes';
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# /build/ccx7EsgU.o:(.bss+0x2a0dfdc): first defined here
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env.NIX_CFLAGS_COMPILE = "-fcommon";
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preBuild = ''
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cd ./src/
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'';
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installPhase = ''
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mkdir -pv $out/bin
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cp -v codeml $out/bin
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cp -v baseml $out/bin
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cp -v basemlg $out/bin
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cp -v chi2 $out/bin
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cp -v codeml $out/bin
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cp -v evolver $out/bin
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cp -v mcmctree $out/bin
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cp -v pamp $out/bin
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cp -v yn00 $out/bin
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'';
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meta = {
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description = "Phylogenetic Analysis by Maximum Likelihood (PAML)";
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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.";
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license = "non-commercial";
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homepage = "http://abacus.gene.ucl.ac.uk/software/paml.html";
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};
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}
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