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