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What happens if I push all of nixpkgs
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1.8 kB · 91 lines
Nix
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# dependencies R, biopython, matplotlib, numpy, pandas, pomegranate, pyfaidx, pysam, rPackages, reportlab, scikit-learn, scipy,
# tests pytestCheckHook,}:
buildPythonPackage rec { pname = "cnvkit"; version = "0.9.12"; pyproject = true;
src = fetchFromGitHub { owner = "etal"; repo = "cnvkit"; tag = "v${version}"; hash = "sha256-ZdE3EUNZpEXRHTRKwVhuj3BWQWczpdFbg4pVr0+AHiQ="; };
patches = [ (fetchpatch { name = "fix-numpy2-compat"; url = "https://github.com/etal/cnvkit/commit/5cb6aeaf40ea5572063cf9914c456c307b7ddf7a.patch"; hash = "sha256-VwGAMGKuX2Kx9xL9GX/PB94/7LkT0dSLbWIfVO8F9NI="; }) ];
pythonRelaxDeps = [ # https://github.com/etal/cnvkit/issues/815 "pomegranate" ];
# Numpy 2 compatibility postPatch = '' substituteInPlace skgenome/intersect.py \ --replace-fail "np.string_" "np.bytes_" '';
dependencies = [ biopython matplotlib numpy pandas pomegranate pyfaidx pysam rPackages.DNAcopy reportlab scikit-learn scipy ];
pythonImportsCheck = [ "cnvlib" ];
nativeCheckInputs = [ pytestCheckHook R ];
disabledTests = [ # AttributeError: module 'pomegranate' has no attribute 'NormalDistribution' # https://github.com/etal/cnvkit/issues/815 "test_batch" "test_segment_hmm" ];
meta = { homepage = "https://cnvkit.readthedocs.io"; description = "Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data"; changelog = "https://github.com/etal/cnvkit/releases/tag/v${version}"; license = lib.licenses.asl20; maintainers = [ lib.maintainers.jbedo ]; };}