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{
lib,
buildPythonPackage,
fetchFromGitHub,
fetchpatch,
swig,
cython,
matplotlib,
numpy,
pandas,
pysam,
setuptools,
pytestCheckHook,
nix-update-script,
}:
buildPythonPackage rec {
pname = "htseq";
version = "2.0.4";
pyproject = true;
src = fetchFromGitHub {
owner = "htseq";
repo = "htseq";
rev = "release_${version}";
hash = "sha256-7ocrmuj9LOtPz9XbI5rKGcdE5JbFz/pZh00Nie65XxE=";
};
patches = [
# https://github.com/htseq/htseq/pull/84
(fetchpatch {
name = "replace-distutils-with-sysconfig.patch";
url = "https://github.com/htseq/htseq/commit/f0f1e464ee9aee56f0b44f905e7b3355b0bb8f29.patch";
hash = "sha256-yDYkXCPy+YFgnk1rnXwCB998aZwVd5nJeejZIgeEzAo=";
})
];
nativeBuildInputs = [ swig ];
build-system = [
cython
numpy
pysam
setuptools
];
dependencies = [
numpy
pysam
];
optional-dependencies = {
htseq-qa = [ matplotlib ];
};
pythonImportsCheck = [ "HTSeq" ];
nativeCheckInputs = [
pandas
pytestCheckHook
] ++ optional-dependencies.htseq-qa;
preCheck = ''
rm -r src HTSeq
export PATH=$out/bin:$PATH
'';
passthru.updateScript = nix-update-script {
extraArgs = [
"--version-regex"
"release_(.+)"
];
};
meta = with lib; {
homepage = "https://htseq.readthedocs.io/";
description = "A framework to work with high-throughput sequencing data";
maintainers = with maintainers; [ unode ];
};
}
|
