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