57 lines
1,021 B
Nix
57 lines
1,021 B
Nix
{ lib
|
|
, fetchPypi
|
|
, rPackages
|
|
, rWrapper
|
|
, buildPythonPackage
|
|
, biopython
|
|
, numpy
|
|
, scipy
|
|
, scikitlearn
|
|
, pandas
|
|
, matplotlib
|
|
, reportlab
|
|
, pysam
|
|
, future
|
|
, pillow
|
|
, pomegranate
|
|
, pyfaidx
|
|
}:
|
|
|
|
buildPythonPackage rec {
|
|
pname = "CNVkit";
|
|
version = "0.9.7";
|
|
|
|
src = fetchPypi {
|
|
inherit pname version;
|
|
sha256 = "d68adc0121e17c61a3aa28c0a9ba6526510a5a0df0f0a6eb1818bab71b7e927a";
|
|
};
|
|
|
|
propagatedBuildInputs = [
|
|
biopython
|
|
numpy
|
|
scipy
|
|
scikitlearn
|
|
pandas
|
|
matplotlib
|
|
reportlab
|
|
pyfaidx
|
|
pysam
|
|
future
|
|
pillow
|
|
pomegranate
|
|
];
|
|
|
|
postPatch = ''
|
|
substituteInPlace setup.py \
|
|
--replace "pandas >= 0.20.1, < 0.25.0" "pandas"
|
|
'';
|
|
|
|
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";
|
|
license = licenses.asl20;
|
|
maintainers = [ maintainers.jbedo ];
|
|
};
|
|
}
|