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angsd: pull patch pending upstream inclusion for parallel build fix

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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"
          |          ^~~~~~~~~~~
This commit is contained in:
Sergei Trofimovich 2023-08-20 08:50:53 +01:00
parent e7eb1f799c
commit f434e83d62
1 changed files with 23 additions and 1 deletions
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24
pkgs/applications/science/biology/angsd/default.nix
View File

@ -1,4 +1,14 @@
{ lib, stdenv, fetchFromGitHub, htslib, zlib, bzip2, xz, curl, openssl }:
{ lib
, stdenv
, fetchFromGitHub
, fetchpatch
, htslib
, zlib
, bzip2
, xz
, curl
, openssl
}:
stdenv.mkDerivation rec {
pname = "angsd";
@ -11,8 +21,20 @@ stdenv.mkDerivation rec {
rev = version;
};
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=";
})
];
buildInputs = [ htslib zlib bzip2 xz curl openssl ];
enableParallelBuilding = true;
makeFlags = [ "HTSSRC=systemwide" "prefix=$(out)" ];
meta = with lib; {