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{ lib
, fetchFromGitHub
, fetchpatch
, python3Packages
, zlib
, curl
, libdeflate
, bash
, coreutils
}:
python3Packages.buildPythonApplication rec {
pname = "flye";
version = "2.9.4";
pyproject = true;
src = fetchFromGitHub {
owner = "fenderglass";
repo = "flye";
rev = "refs/tags/${version}";
hash = "sha256-lwiY0VTEsLMMXt1VowsS3jj44v30Z766xNRwQtQKr10=";
};
patches = [
(fetchpatch {
# https://github.com/mikolmogorov/Flye/pull/691
name = "aarch64-fix.patch";
url = "https://github.com/mikolmogorov/Flye/commit/e4dcc3fdf0fa1430a974fcd7da31b03ea642df9b.patch";
hash = "sha256-Ny2daPt8eYOKnwZ6bdBoCcFWhe9eiIHF4vJU/occwU0=";
})
(fetchpatch {
# https://github.com/mikolmogorov/Flye/pull/711
name = "remove-distutils.patch";
url = "https://github.com/mikolmogorov/Flye/commit/fb34f1ccfdf569d186a4ce822ee18eced736636b.patch";
hash = "sha256-52bnZ8XyP0HsY2OpNYMU3xJgotNVdQc/O2w3XIReUdQ=";
})
(fetchpatch {
# https://github.com/mikolmogorov/Flye/pull/670
name = "remove-find_module.patch";
url = "https://github.com/mikolmogorov/Flye/commit/441b1c6eb0f60b7c4fb1a40d659c7dabb7ad41b6.patch";
hash = "sha256-RytFIN1STK33/nvXpck6woQcwV/e1fmA8AgmptiIiDU=";
})
];
postPatch = ''
substituteInPlace flye/polishing/alignment.py \
--replace-fail "/bin/bash" "${lib.getExe bash}"
'';
build-system = [ python3Packages.setuptools ];
propagatedBuildInputs = [ coreutils ];
buildInputs = [
zlib
curl
libdeflate
];
pythonImportsCheck = [ "flye" ];
nativeCheckInputs = [ python3Packages.pytestCheckHook ];
preCheck = ''
export PATH=$out/bin:$PATH
'';
meta = with lib; {
description = "De novo assembler for single molecule sequencing reads using repeat graphs";
homepage = "https://github.com/fenderglass/Flye";
license = licenses.bsd3;
mainProgram = "flye";
maintainers = with maintainers; [ assistant ];
};
}
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