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nixpkgs/pkgs/by-name/an/angsd/package.nix

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angsd: pull patch pending upstream inclusion for parallel build fix Without the change rapallel builds fail occasionally as: $ make --shuffle -j ... g++ -c -O3 -D__STDC_FORMAT_MACROS argStruct.cpp g++ -c -O3 -D__STDC_FORMAT_MACROS ancestral_likes.cpp gcc -c -O3 -D__STDC_FORMAT_MACROS fet.c g++ -c -O3 -D__STDC_FORMAT_MACROS abcGL.cpp g++ -c -O3 -D__STDC_FORMAT_MACROS pop1_read.cpp g++ -c -O3 -D__STDC_FORMAT_MACROS angsd.cpp g++ -c -O3 -D__STDC_FORMAT_MACROS abcHWE_F.cpp gcc -c -O3 -D__STDC_FORMAT_MACROS kprobaln.c g++ -c -O3 -D__STDC_FORMAT_MACROS mpileup.cpp argStruct.cpp:3:10: fatal error: version.h: No such file or directory 3 | #include "version.h" | ^~~~~~~~~~~ compilation terminated. angsd.cpp:11:10: fatal error: version.h: No such file or directory 11 | #include "version.h" | ^~~~~~~~~~~
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{ lib
, stdenv
, fetchFromGitHub
, fetchpatch
, htslib
, zlib
, bzip2
, xz
, curl
, openssl
}:
angsd: init at 0.937
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stdenv.mkDerivation rec {
pname = "angsd";
angsd: 0.938 -> 0.940
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version = "0.940";
angsd: init at 0.937
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src = fetchFromGitHub {
owner = "ANGSD";
repo = "angsd";
angsd: 0.938 -> 0.940
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sha256 = "sha256-Ppxgy54pAnqJUzNX5c12NHjKTQyEEcPSpCEEVOyZ/LA=";
pkgs/applications: replace "${version}" with version
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rev = version;
angsd: init at 0.937
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};
angsd: pull patch pending upstream inclusion for parallel build fix Without the change rapallel builds fail occasionally as: $ make --shuffle -j ... g++ -c -O3 -D__STDC_FORMAT_MACROS argStruct.cpp g++ -c -O3 -D__STDC_FORMAT_MACROS ancestral_likes.cpp gcc -c -O3 -D__STDC_FORMAT_MACROS fet.c g++ -c -O3 -D__STDC_FORMAT_MACROS abcGL.cpp g++ -c -O3 -D__STDC_FORMAT_MACROS pop1_read.cpp g++ -c -O3 -D__STDC_FORMAT_MACROS angsd.cpp g++ -c -O3 -D__STDC_FORMAT_MACROS abcHWE_F.cpp gcc -c -O3 -D__STDC_FORMAT_MACROS kprobaln.c g++ -c -O3 -D__STDC_FORMAT_MACROS mpileup.cpp argStruct.cpp:3:10: fatal error: version.h: No such file or directory 3 | #include "version.h" | ^~~~~~~~~~~ compilation terminated. angsd.cpp:11:10: fatal error: version.h: No such file or directory 11 | #include "version.h" | ^~~~~~~~~~~
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patches = [
# Pull pending inclusion upstream patch for parallel buil fixes:
# https://github.com/ANGSD/angsd/pull/590
(fetchpatch {
name = "parallel-make.patch";
url = "https://github.com/ANGSD/angsd/commit/89fd1d898078016df390e07e25b8a3eeadcedf43.patch";
hash = "sha256-KQgUfr3v8xc+opAm4qcSV2eaupztv4gzJJHyzJBCxqA=";
})
];
angsd: init at 0.937
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buildInputs = [ htslib zlib bzip2 xz curl openssl ];
angsd: pull patch pending upstream inclusion for parallel build fix Without the change rapallel builds fail occasionally as: $ make --shuffle -j ... g++ -c -O3 -D__STDC_FORMAT_MACROS argStruct.cpp g++ -c -O3 -D__STDC_FORMAT_MACROS ancestral_likes.cpp gcc -c -O3 -D__STDC_FORMAT_MACROS fet.c g++ -c -O3 -D__STDC_FORMAT_MACROS abcGL.cpp g++ -c -O3 -D__STDC_FORMAT_MACROS pop1_read.cpp g++ -c -O3 -D__STDC_FORMAT_MACROS angsd.cpp g++ -c -O3 -D__STDC_FORMAT_MACROS abcHWE_F.cpp gcc -c -O3 -D__STDC_FORMAT_MACROS kprobaln.c g++ -c -O3 -D__STDC_FORMAT_MACROS mpileup.cpp argStruct.cpp:3:10: fatal error: version.h: No such file or directory 3 | #include "version.h" | ^~~~~~~~~~~ compilation terminated. angsd.cpp:11:10: fatal error: version.h: No such file or directory 11 | #include "version.h" | ^~~~~~~~~~~
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enableParallelBuilding = true;
angsd: init at 0.937
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makeFlags = [ "HTSSRC=systemwide" "prefix=$(out)" ];
meta = with lib; {
description = "Program for analysing NGS data";
homepage = "http://www.popgen.dk/angsd";
maintainers = [ maintainers.bzizou ];
license = licenses.gpl2;
};
}
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