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{
lib,
buildPythonPackage,
fetchFromGitHub,
swig,
cython,
matplotlib,
numpy,
pandas,
pysam,
setuptools,
pytestCheckHook,
nix-update-script,
}:
buildPythonPackage rec {
pname = "htseq";
version = "2.0.9";
pyproject = true;
src = fetchFromGitHub {
owner = "htseq";
repo = "htseq";
rev = "release_${version}";
hash = "sha256-i83BY7/p98/pfYzebolNW/6yNwtb2R5ARCSG3rAq2/M=";
};
nativeBuildInputs = [ swig ];
build-system = [
cython
numpy
pysam
setuptools
];
dependencies = [
numpy
pysam
];
optional-dependencies = {
htseq-qa = [ matplotlib ];
};
pythonImportsCheck = [ "HTSeq" ];
nativeCheckInputs = [
pandas
pytestCheckHook
]
++ optional-dependencies.htseq-qa;
preCheck = ''
rm -r src HTSeq
export PATH=$out/bin:$PATH
'';
passthru.updateScript = nix-update-script {
extraArgs = [
"--version-regex"
"release_(.+)"
];
};
meta = {
homepage = "https://htseq.readthedocs.io/";
description = "Framework to work with high-throughput sequencing data";
maintainers = with lib.maintainers; [ unode ];
};
}
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