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{ lib
, fetchFromGitHub
, fetchpatch
, rPackages
, buildPythonPackage
, biopython
, numpy
, scipy
, scikit-learn
, pandas
, matplotlib
, reportlab
, pysam
, future
, pillow
, pomegranate
, pyfaidx
, python
, pythonOlder
, R
}:
buildPythonPackage rec {
pname = "cnvkit";
version = "0.9.11";
format = "setuptools";
disabled = pythonOlder "3.7";
src = fetchFromGitHub {
owner = "etal";
repo = "cnvkit";
rev = "refs/tags/v${version}";
hash = "sha256-tlR1LsR+M1nkzk3CgrkkNcSGP3juv25GXddWDDWJ5ao=";
};
postPatch = ''
# see https://github.com/etal/cnvkit/issues/589
substituteInPlace setup.py \
--replace 'joblib < 1.0' 'joblib'
# see https://github.com/etal/cnvkit/issues/680
substituteInPlace test/test_io.py \
--replace 'test_read_vcf' 'dont_test_read_vcf'
'';
propagatedBuildInputs = [
biopython
numpy
scipy
scikit-learn
pandas
matplotlib
reportlab
pyfaidx
pysam
future
pillow
pomegranate
rPackages.DNAcopy
];
nativeCheckInputs = [ R ];
checkPhase = ''
pushd test/
${python.interpreter} test_io.py
${python.interpreter} test_genome.py
${python.interpreter} test_cnvlib.py
${python.interpreter} test_commands.py
${python.interpreter} test_r.py
popd # test/
'';
pythonImportsCheck = [
"cnvlib"
];
meta = with lib; {
homepage = "https://cnvkit.readthedocs.io";
description = "A Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data";
changelog = "https://github.com/etal/cnvkit/releases/tag/v${version}";
license = licenses.asl20;
maintainers = [ maintainers.jbedo ];
};
}
|
