2019-06-19 04:26:26 +01:00
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{ lib
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, fetchPypi
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, rPackages
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, rWrapper
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, buildPythonPackage
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, biopython
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, numpy
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, scipy
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2020-07-07 17:34:48 +01:00
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, scikitlearn
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2019-06-19 04:26:26 +01:00
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, pandas
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, matplotlib
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, reportlab
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, pysam
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, future
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, pillow
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, pomegranate
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, pyfaidx
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}:
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buildPythonPackage rec {
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pname = "CNVkit";
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2020-06-05 18:44:33 +01:00
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version = "0.9.7";
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2019-06-19 04:26:26 +01:00
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src = fetchPypi {
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inherit pname version;
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2020-06-05 18:44:33 +01:00
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sha256 = "d68adc0121e17c61a3aa28c0a9ba6526510a5a0df0f0a6eb1818bab71b7e927a";
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2019-06-19 04:26:26 +01:00
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};
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propagatedBuildInputs = [
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biopython
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numpy
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scipy
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2020-07-07 17:34:48 +01:00
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scikitlearn
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2019-06-19 04:26:26 +01:00
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pandas
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matplotlib
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reportlab
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pyfaidx
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pysam
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future
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pillow
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pomegranate
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];
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2019-09-29 05:27:04 +01:00
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postPatch = ''
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substituteInPlace setup.py \
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--replace "pandas >= 0.20.1, < 0.25.0" "pandas"
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'';
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2020-07-07 17:34:48 +01:00
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pythonImportsCheck = [ "cnvlib" ];
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2019-06-19 04:26:26 +01:00
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meta = with lib; {
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homepage = "https://cnvkit.readthedocs.io";
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description = "A Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data";
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license = licenses.asl20;
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maintainers = [ maintainers.jbedo ];
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};
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}
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