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{stdenv, fetchFromGitHub, cmake, zlib, python2}:
stdenv.mkDerivation rec {
pname = "strelka";
version = "2.9.10";
src = fetchFromGitHub {
owner = "Illumina";
repo = "strelka";
rev = "v${version}";
sha256 = "1nykbmim1124xh22nrhrsn8xgjb3s2y7akrdapn9sl1gdych4ppf";
};
nativeBuildInputs = [ cmake ];
buildInputs = [ zlib python2 ];
preConfigure = ''
sed -i 's|/usr/bin/env python|${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 stdenv.lib; {
description = "Germline and small variant caller";
license = licenses.gpl3;
homepage = https://github.com/Illumina/strelka;
maintainers = with maintainers; [ jbedo ];
platforms = [ "x86_64-linux" ];
broken = true;
};
}
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