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{ lib
, fetchFromGitHub
, fetchpatch
, rPackages
, rWrapper
, buildPythonPackage
, biopython
, numpy
, scipy
, scikitlearn
, pandas
, matplotlib
, reportlab
, pysam
, future
, pillow
, pomegranate
, pyfaidx
, python
, R
}:
buildPythonPackage rec {
pname = "CNVkit";
version = "0.9.7";
src = fetchFromGitHub {
owner = "etal";
repo = "cnvkit";
rev = "v${version}";
sha256 = "022zplgqil5l76vri647cyjx427vnbg5r2gw6lw712d2janvdjm7";
};
patches = [
# Fix: AttributeError: module 'pandas.io.common' has no attribute 'EmptyDataError'
(fetchpatch {
url = "https://github.com/etal/cnvkit/commit/392adfffedfa0415e635b72c5027835b0a8d7ab5.patch";
sha256 = "0s0gwyy0hybmhc3jij2v9l44b6lkcmclii8bkwsazzj2kc24m2rh";
})
];
propagatedBuildInputs = [
biopython
numpy
scipy
scikitlearn
pandas
matplotlib
reportlab
pyfaidx
pysam
future
pillow
pomegranate
rPackages.DNAcopy
];
postPatch = ''
substituteInPlace setup.py \
--replace "pandas >= 0.20.1, < 0.25.0" "pandas"
'';
checkInputs = [ 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
'';
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";
license = licenses.asl20;
maintainers = [ maintainers.jbedo ];
};
}
|
