nixpkgs/pkgs/applications/science/biology/strelka/default.nix
Artturin f9fdf2d402 treewide: move NIX_CFLAGS_COMPILE to the env attrset
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
2023-02-22 21:23:04 +02:00

44 lines
1.0 KiB
Nix

{lib, stdenv, fetchFromGitHub, cmake, zlib, python2}:
stdenv.mkDerivation rec {
pname = "strelka";
version = "2.9.10";
src = fetchFromGitHub {
owner = "Illumina";
repo = "strelka";
rev = "v${version}";
sha256 = "1nykbmim1124xh22nrhrsn8xgjb3s2y7akrdapn9sl1gdych4ppf";
};
nativeBuildInputs = [ cmake ];
buildInputs = [ zlib python2 ];
env.NIX_CFLAGS_COMPILE = toString [
"-Wno-error=maybe-uninitialized"
"-Wno-error=pessimizing-move"
];
preConfigure = ''
sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py
patchShebangs .
'';
postFixup = ''
pushd $out/lib/python/pyflow
sed -i 's|/bin/bash|${stdenv.shell}|' pyflowTaskWrapper.py
rm pyflowTaskWrapper.pyc
echo "import pyflowTaskWrapper" | python2
popd
'';
meta = with lib; {
description = "Germline and small variant caller";
license = licenses.gpl3;
homepage = "https://github.com/Illumina/strelka";
maintainers = with maintainers; [ jbedo ];
platforms = [ "x86_64-linux" ];
};
}