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}:buildPythonPackage (finalAttrs: { pname = "cnvkit"; version = "0.9.13"; pyproject = true;
src = fetchFromGitHub { owner = "etal"; repo = "cnvkit"; tag = "v${finalAttrs.version}"; hash = "sha256-6W0rJUeHO7m3zacgkL3WzyFVmdet1zJAGyafsQv1AXE="; };
patches = [ # test: update a call to --smooth-bootstrap[=int, now] (fetchpatch { url = "https://github.com/etal/cnvkit/commit/c5c7c06b7fb873ed7ae44593c11a91d45f433e54.patch"; hash = "sha256-H9Nr4JL7bc9CQ/BmXkOAwjbr/ykvbnjyyWrVSrVH9kg="; }) ];
pythonRelaxDeps = [ # https://github.com/etal/cnvkit/issues/815 "pomegranate" # https://github.com/etal/cnvkit/pull/1048 "pyparsing" ];
nativeBuildInputs = [ makeWrapper ];
buildInputs = [ R ];
postPatch = let rscript = lib.getExe' R "Rscript"; in # Patch shebang lines in R scripts '' substituteInPlace cnvlib/segmentation/flasso.py \ --replace-fail "#!/usr/bin/env Rscript" "#!${rscript}"
substituteInPlace cnvlib/segmentation/cbs.py \ --replace-fail "#!/usr/bin/env Rscript" "#!${rscript}"
substituteInPlace cnvlib/segmentation/__init__.py \ --replace-fail 'rscript_path: str = "Rscript"' 'rscript_path="${rscript}"'
substituteInPlace cnvlib/commands.py \ --replace-fail 'default="Rscript"' 'default="${rscript}"'
'';
dependencies = [ biopython matplotlib numpy pandas pomegranate pyfaidx pyparsing pysam reportlab rPackages.DNAcopy scikit-learn scipy ];
# Make sure R can find the DNAcopy package postInstall = '' wrapProgram $out/bin/cnvkit.py \ --set R_LIBS_SITE "${rPackages.DNAcopy}/library" \ --set MPLCONFIGDIR "/tmp/matplotlib-config" '';
installCheckPhase = '' runHook preInstallCheck
${python.executable} -m pytest --deselect=test/test_commands.py::CommandTests::test_batch \ --deselect=test/test_commands.py::CommandTests::test_segment_hmm
cd test # Set matplotlib config directory for the tests export MPLCONFIGDIR="/tmp/matplotlib-config" export HOME="/tmp" mkdir -p "$MPLCONFIGDIR"
# Use the installed binary - it's already wrapped with R_LIBS_SITE make cnvkit="$out/bin/cnvkit.py" || { echo "Make tests failed" exit 1 }
runHook postInstallCheck '';
doInstallCheck = true;
pythonImportsCheck = [ "cnvlib" ];
nativeCheckInputs = [ pytestCheckHook R ];
meta = { homepage = "https://cnvkit.readthedocs.io"; description = "Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data"; changelog = "https://github.com/etal/cnvkit/releases/tag/${finalAttrs.src.tag}"; license = lib.licenses.asl20; maintainers = [ lib.maintainers.jbedo ]; };})